Eubacterium

FEBS Lett, 1988 Apr 25, 231(2), 284 - 90
Is the 9 kDa thylakoid membrane phosphoprotein functionally and structurally analogous to the 'H' subunit of bacterial reaction centres?
Packham NK.
Although the amino acid sequence of the 9 kDa (phospho)protein of chloroplasts has been determined, the function of this thylakoid membrane protein in photosynthetic electron transport and the reason for its physiological control remains unclear . In this paper, I briefly review the evidence which indicates that the phosphorylation of the 9 kDa protein results in a partial inhibition of photosynthetic oxygen evolution by increasing the stability of the semiquinone bound to QA the primary, plastoquinone-binding site of photosystem II (PS II) . I propose that in its dephosphorylated state, the 9 kDa thylakoid membrane protein may serve PS II to ensure efficient photochemical charge separation by aiding the transfer of reducing equivalents out of the reaction centre to the attendant plastoquinone pool . This function is analogous to that proposed for the H-subunit of the reaction centre of photosynthetic eubacteria . Whether these two proteins have evolved from a common ancestral reaction centre protein is discussed in the light of a comparison of their amino acid sequences and predicted secondary structures.

Nucleic Acids Res, 1988 Apr 25, 16(8), 3511 - 24
In vitro incorporation of eubacterial, archaebacterial and eukaryotic 5S rRNAs into large ribosomal subunits of Bacillus stearothermophilus; Hartmann RK et al.; Bacillus stearothermophilus large ribosomal subunits were reconstituted in the presence of 5S rRNAs from different origins and tested for their biological activities . The results obtained have shown that eubacterial and archaebacterial 5S rRNAs can easily substitute for B . stearothermophilus 5S rRNA in the reconstitution, while eukaryotic 5S rRNAs yield ribosomal subunits with reduced biological activities . From our results we propose an interaction between nucleotides 42-47 of 5S rRNA and nucleotides 2603-2608 of 23S rRNA during the assembly of the 50S ribosomal subunit . Other experiments with eukaryotic 5.8S rRNAs reveal, if at all, a very low incorporation of these RNA species into the reconstituted ribosomes.

J Bacteriol, 1988 Apr, 170(4), 1752 - 8
Isolation of flagella from the archaebacterium Methanococcus voltae by phase separation with Triton X-114; Kalmokoff ML et al.; The flagella of Methanococcus voltae were isolated by using three procedures . Initially, cells were sheared to release the filaments, which were purified by differential centrifugation and banding in KBr gradients . Flagella were also prepared by solubilization of cells with 1% (vol/vol) Triton X-100 and purified as described above . Both of these techniques resulted in variable recovery and poor yield of flagellar filaments . Purification of intact flagella (filament, hook, and basal body) was achieved by using phase transition separation with Triton X-114 . Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified flagella revealed two major proteins, with molecular weights of 33,000 and 31,000 . This result indicates the likely presence of two flagellins . The filament had a diameter of 13 nm . The basal structure consisted of a small knob, while a slight thickening of the filament immediately adjacent to this area was the only evidence of a hook region . Flagella from three other Methanococcus species were isolated by this technique and found to have the same ultrastructure as flagella from M . voltae . Isolation of flagella from three eubacteria and another methanogen (Methanospirillum hungatei {M . hungatii}) by the phase separation technique indicated that the detergent treatment did not affect the structure of basal bodies . Intact ring structures and well-differentiated hook regions were apparent in each of these flagellar preparations.

Can J Microbiol, 1988 Apr, 34(4), 552 - 6
Phylogenetic relationships vs . phenotypic diversity: how to achieve a phylogenetic classification system of the eubacteria; Stackebrandt E; To establish a hierarchic classification system, ranks cannot be defined by the exclusive and inflexible application of phylogenetic parameters . Because both stability and practicality are prerequisites for a successful system, decisions about the delineation of genera must be made by combining phylogenetic coherency with unifying phenotypic properties of taxonomic value consistent with the needs of a hierarchic system . The phylogenetic depth (age) of a genus has no influence on the decision as long as the members of the genus can be reliably identified as such . The description of those higher taxa that are not easily definable today because of the lack of common phenotypic properties must be postponed until new insights are available . In the end this approach will be both phylogenetic and practical, thus avoiding the use of two classification systems.

Can J Microbiol, 1988 Apr, 34(4), 427 - 35
The domains of slow bacterial growth; Chesbro W; Commonly used culture systems, e.g., batch culture and the chemostat, work poorly for defining the behavior of slowly growing bacteria, i.e., cultures with mass doubling times, tD, longer than 10-12 h . This has slowed the process of understanding how bacteria behave at the longer tD's that embrace most of their existence . Culture systems are identified that give useful access to these longer doubling times . When these slow-growth systems are used with nutrient-limited populations, it is found that cellular concentrations of guanosine 5'-diphosphate 3'-diphosphate, the main effector of the stringent response, commence rising above basal levels at tD's longer than 12 h until, at a tD of 60-70 h, the level is reached that causes the interdiction of protein and ribosome synthesis characteristic of the response . The abrupt onset of the stringent response in eubacteria at a particular tD, corresponding to a specific rate of nutrient uptake, makes oft-used growth equations that do not account for this onset, e.g., those of Monod or Pirt, poor descriptors of slow growth . A serious imbalance between lateral and transverse wall formation rates which, unless corrected, would lead to abnormal cell division can be inferred to develop at tD's longer than 10-12 h . The necessary correction may be supplied by the effects of increased levels of guanosine 5'-diphosphate 3'-diphosphate on transverse wall synthesis.

Appl Environ Microbiol, 1988 Mar, 54(3), 734 - 40
Analysis of drug resistance in the archaebacterium Methanococcus voltae with respect to potential use in genetic engineering; Possot O et al.; The sensitivity of the methanogenic archaebacterium Methanococcus voltae to 12 inhibitors was tested in liquid medium . Four compounds appeared to be inhibitors of growth . Their MICs were as follows: pseudomonic acid, 0.1 micrograms/ml (0.19 microM); puromycin, 2 micrograms/ml (3.6 microM); methionine sulfoximine, 30 micrograms/ml (170 microM); and fusidic acid, 100 micrograms/ml (170 microM) . On solid medium, the MICs were similar and the frequency of spontaneous resistance was found to be 5 X 10(-5) (methionine sulfoximine), 10(-7) (pseudomonic acid), and less than 10(-7) (puromycin and fusidic acid) . Pseudomonic acid was found to inhibit isoleucyl-tRNA synthetase activity as measured by the in vitro aminoacylation of M . voltae tRNA with L-{U-14C}isoleucine . Fusidic acid and puromycin were shown to inhibit poly(U)-dependent polyphenylalanine synthesis in S30 extracts . Acetylpuromycin was inhibitory at much higher concentrations both in vivo and in vitro for M . voltae . Thus, the pac gene of Streptomyces alboniger, which is responsible for acetylation of puromycin and which conferred resistance to puromycin when introduced in eubacteria and eucaryotes, is a potential selective marker in gene transfer experiments with M . voltae . The latter was recently shown to be transformable . The same would be true for the cat gene of Tn9, which encodes resistance to fusidic acid in eubacteria in addition to resistance to chloramphenicol.

FEBS Lett, 1988 Feb 15, 228(2), 317 - 20
Asparaginyl-rhamnose: a novel type of protein-carbohydrate linkage in a eubacterial surface-layer glycoprotein; Messner P et al.; The subunits of the crystalline surface layer of Bacillus stearothermophilus, strain NRS 2004/3a contain carbohydrates covalently linked to protein . Hydrolysis of a glycopeptide obtained by pronase digestion of the glycoprotein and analysis of the fragments revealed that rhamnose is N-glycosidically linked to the amide nitrogen of an asparaginyl residue.

Eur J Biochem, 1988 Feb 1, 171(3), 655 - 9
Biosynthesis of vitamin B-12 in anaerobic bacteria . Experiments with Eubacterium limosum on the origin of the amide groups of the corrin ring and of N-3 of the 5,6-dimethylbenzimidazole part; Vogt JR et al.; The pathway of vitamin B-12 biosynthesis in anaerobic bacteria differs in several respects from the pathway found in aerobic or aerotolerant microorganisms . The aim of this investigation was to elucidate the formation of the 5,6-dimethylbenzimidazole part and the amide groups of vitamin B-12 in anaerobic bacteria . {15N}Ammonium chloride or L-{amido-15N}glutamine or a mixture of {15N}ammonium sulfate and {15N}glycine was added to fermentations with Eubacterium limosum . The vitamin B-12 isolated from these fermentations was methylated and degraded to cobinamide and 1,5,6-trimethylbenzimidazole . The amide groups of cobinamide were hydrolyzed and the amide nitrogen of the side chains a, b, c, d, e and g trapped as benzamide . The 15N incorporation was determined by mass spectroscopy . Thus in the experiment with {15N}ammonium chloride the benzamide and the 1,5,6-trimethylbenzimidazole contained 9.6% 15N, whereas in the experiment with L-{amido-15N}glutamine 37.5% of the molecules were 15N labeled . The 1H-NMR spectrum of 1,5,6-trimethylbenzimidazole revealed that the 15N from the ammonium salts and from glutamine was incorporated into N-3 of the 5,6-dimethylbenzimidazole moiety of vitamin B-12 . With a mixture of {15N}ammonium sulfate and {15N}glycine both nitrogens of 5,6-dimethylbenzimidazole became 15N-labeled . These experiments demonstrate that in E . limosum the amide nitrogen of glutamine is not only the precursor of the six amide groups of the corrin ring, but also of N-3 of the 5,6-dimethylbenzimidazole moiety of vitamin B-12.

J Bacteriol, 1988 Feb, 170(2), 995 - 7
Distribution of 10-formyltetrahydrofolate synthetase in eubacteria; Whitehead TR et al.; The distribution of 10-formyltetrahydrofolate synthetase, which activates formate for use as a one-carbon donor in a variety of biosynthetic reactions, was determined for a variety of eubacteria . Organisms from several genera were found to lack detectable synthetase activity; however, all organisms tested were found to contain 5,10-methylenetetrahydrofolate dehydrogenase activity.

Biol Chem Hoppe Seyler, 1988 Feb, 369(2), 109 - 13
Purification and properties of an archaebacterial enzyme: citrate synthase from Sulfolobus solfataricus; Lohlein-Werhahn G et al.; Citrate synthase from the thermoacidophilic archaebacterium Sulfolobus solfataricus was purified to homogeneity . The synthase is a dimer composed of subunits of Mr approximately equal to 40,000 . The Km values of acetyl-CoA and oxalacetate are 7 microM and 20 microM, respectively . NADH (Ki = 3.5mM) and ATP (Ki = 0.36mM) are competitive inhibitors vs acetyl-CoA . The dimeric structure and the inhibition by nucleotides (ATP greater than NADH) correlate the archaebacterial enzyme to synthases from eukaryotes and Gram-positive eubacteria.

Biophys Chem, 1988 Feb, 29(1-2), 39 - 49
Bacterial surface proteins . Some structural, functional and evolutionary aspects; Baumeister W et al.; The structure of several eubacterial and archaebacterial surface (glyco)proteins as determined by three-dimensional electron microscopy is described . Particular emphasis is placed on surface proteins which interact with membranes . Some structure-function relationships deduced from the structural information, such as shape maintenance and molecular recognition phenomena, are discussed.

J Bacteriol, 1988 Feb, 170(2), 946 - 53
Coumarin and quinolone action in archaebacteria: evidence for the presence of a DNA gyrase-like enzyme; Sioud M et al.; The action of novobiocin and coumermycin (two coumarins which interact with the gyrB subunit of eubacterial DNA gyrase) and ciprofloxacin (a fluoroquinolone which interacts with the gyrA subunit of DNA gyrase) was tested on several archaebacteria, including five methanogens, two halobacteria, and a thermoacidophile . Most strains were sensitive to doses of coumarins (0.02 to 10 micrograms/ml) which specifically inhibit DNA gyrase in eubacteria . Ciprofloxacin inhibited growth of the haloalkaliphilic strain Natronobacterium gregoryi and of the methanogen Methanosarcina barkeri . In addition, ciprofloxacin partly relieved the sensitivity to coumarins (and vice versa) . Novobiocin inhibited DNA replication in Halobacterium halobium rapidly and specifically . Topological analysis has shown that the 1.7-kilobase plasmid from Halobacterium sp . strain GRB is negatively supercoiled; this plasmid was relaxed after novobiocin treatment . These results support the existence in archaebacteria of a coumarin and quinolone target related to eubacterial DNA gyrase.

Microbiologia, 1988 Feb, 4(1), 5 - 27
Archaebacteria: their phylogenetic relationship with the eubacterial and eukaryotic kingdoms; Sanz JL et al.; In microbiology the discovery of archaebacteria ten years ago has wrought a profound change in the concepts of physiology, taxonomy, ecology, biochemistry, molecular biology, genetics and phylogeny . This review offers a concise summary of the state of the art in this field with special reference to taxonomy and ecology as well as to the different methodologies used to study the phylogeny of this unusual group of microorganisms that question many well established biological concepts.

J Bacteriol, 1988 Feb, 170(2), 720 - 6
Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells; Giovannoni SJ et al.; Examination of collections of 16S rRNA sequences revealed sequence domains that were unique to (and invariant within) the three primary lines of cellular descent: the archaebacteria, the eubacteria, and the eucaryotes . Oligodeoxynucleotides complementary to these conserved sequence domains were synthesized and used as hybridization probes . Each of the radiolabeled probes specifically hybridized to nylon membrane-bound 16S rRNA from the targeted kingdom . A probe complementary to a universally conserved sequence in 16S rRNAs was used as a positive control, while its complement provided a negative control for nonspecific binding . The abilities of the probes to bind specifically to whole, fixed cells representing a broad array of phylogenetic diversity were tested in whole-cell dot blot assays . Again, all of the probes specifically bound the targeted groups . By microautoradiography, the method was extended to permit phylogenetic identification of single cells microscopically.

J Bacteriol, 1988 Feb, 170(2), 611 - 6
Molecular cloning of a gene encoding a 45,000-dalton polypeptide associated with bile acid 7-dehydroxylation in Eubacterium sp . strain VPI 12708; White WB et al.; Eubacterium sp . strain VPI 12708 is an intestinal anaerobic bacterium which possesses an inducible bile acid 7-dehydroxylation activity . Two cholic acid-induced polypeptides with apparent molecular weights of 27,000 and 45,000, respectively, coeluted with bile acid 7-dehydroxylation activity upon anaerobic high-performance gel filtration chromatography of crude cellular protein extracts . The 45,000-dalton polypeptide was purified to greater than 95% homogeneity by high-performance liquid chromatography gel filtration and high-performance liquid-DEAE chromatography . The first 28 amino acid residues of the N terminus of this polypeptide were determined by gas-phase sequencing, and a corresponding mixed oligonucleotide (20-mer) was synthesized . Southern blot analysis of EcoRI total digests of chromosomal DNA showed a 2.6-kilobase fragment which hybridized to the 32P-labeled 20-mer . This fragment was enriched for by size fractionation of an EcoRI total digest of genomic DNA and ligated into bacteriophage lambda gt11 . Recombinant phage containing the putative gene encoding the 45,000-dalton polypeptide were detected with the 32P-labeled 20-mer by plaque hybridization techniques . The insert was 2.6 kilobases in length and may contain the entire coding sequence for the 45,000-dalton polypeptide . The 2.6-kilobase insert was subcloned into pUC8 and transformed into Escherichia coli DH5 alpha . However, the 45,000-dalton polypeptide was not detected in cell extracts of this organism when specific antibody was used . Preliminary nucleic acid sequence data correlated exactly with the amino acid sequence . A cholic acid-induced mRNA species of greater than 6 kilobases in size was identified by Northern (RNA) blot analysis of total RNA, suggesting that the gene coding for this polypeptide is part of a larger operon.

Nucleic Acids Res, 1988 Jan 11, 16(1), 1 - 19
Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters; Reiter WD et al.; The 5'-termini were precisely mapped for five constitutive and one UV-inducible transcript from the Sulfolobus virus-like particle SSV1 . The comparison of the DNA sequences around these transcriptional initiation sites revealed the presence of two conserved sequence elements: a trinucleotide sequence close to the initiation site itself and an AT-rich hexanucleotide sequence centered about 26 nucleotides upstream of it . Similar DNA sequences were found upstream of the transcriptional start sites for the ribosomal RNA genes in Sulfolobus and upstream of transcriptional start sites in other archaebacteria, allowing the derivation of a general consensus sequence for archaebacterial promoters . This consensus sequence is unlike that found in eubacteria but it resembles promoters recognized by eukaryotic RNA polymerase II.

J Periodontol, 1988 Jan, 59(1), 32 - 9
A comparison of the reactivity of Eubacterium species with localized and serum immunoglobulins from rapidly progressive and adult periodontitis patients; Martin SA et al.; Immunoglobulins in sera and in supernatant fluids of explant cultures of diseased gingival tissues from 20 rapidly progressive and 20 adult periodontitis sites were tested by an ELISA assay for reactivity with typed strains of Eubacterium alactolyticum, E . brachy, E . limosum and E . nodatum . Immunoglobulins present in tissue culture fluids from both rapidly progressive and adult periodontitis samples reactive with E . brachy and E . nodatum were significantly greater (P less than 0.05) than those reactive with E . alactolyticum or E . limosum . The titers to E . brachy in tissue culture fluids from adult periodontitis were significantly greater (P less than 0.05) than those from rapidly progressive periodontitis; there was no difference in titers to the other three species . The only significant difference in serum titers was that sera from patients with rapidly progressive periodontitis had significantly greater reactivity to E . alactolyticum than did sera from adult periodontitis patients . These data indicate that immunoglobulins in the sera of rapidly progressive and adult periodontitis patients do not necessarily reflect the reactivity of localized immunoglobulins present in the diseased gingival tissue explant culture fluids from these patients.

Prog Clin Biol Res, 1988, 274, 557 - 76
Evolution of the P450 gene superfamily; Nebert DW et al.; A P450 gene nomenclature system has recently been proposed on the basis of divergent evolution of distinct families and subfamilies among eukaryotes and prokaryotes . At present, eleven gene families have been described, eight of which exist in all mammals . The current number of P450 genes in each species is believed to reflect, at least in part, selective advantages as animals and plants have struggled for coexistence during the last 1 billion years . It is likely that P450 genes will also be found in archaebacteria, as well as most or all eubacteria and eukaryotes . Using Wu-Kabat analysis, we propose regions of the P450 protein involved in membrane attachment, flavoprotein-binding, heme-binding, and substrate specificity . The invariant amino acid sequence (F**G***C*G in the heme-binding region) is unique to the fifty P450 proteins characterized to date and is not found in any of the more than 5,430 other proteins presently in the database . The regulatory trans-acting protein factors and their associated upstream cis-acting DNA elements of the orthologous mouse, rat and human P450A1 gene are complex but appear to be highly conserved during the 80 million years since the mammalian radiation.

Drugs, 1988, 35 Suppl 2, 45 - 50
The synergistic effect of cefotaxime and desacetylcefotaxime against clinical isolates of anaerobic bacteria; Devlin HR et al.; The synergistic interaction of cefotaxime and desacetylcefotaxime against 187 clinically significant anaerobic organisms was investigated . Fusobacterium nucleatum, Actinomyces odontolyticus, propionibacteria, lactobacilli, peptostreptococci, Streptococcus intermedius and Veillonella were sensitive to cefotaxime . Both Eubacterium lentum and Streptococcus morbillorum were resistant . The susceptibility of the clostridia varied from 0.125 to greater than 256 mg/L; only 20% of species demonstrated synergy between cefotaxime and desacetylcefotaxime . The minimum inhibitory concentration (MIC) of cefotaxime against members of the genus Bacteroides ranged from 0.0625 to greater than 256 mg/L . The MIC50 of cefotaxime to Bacteroides fragilis and B . vulgatus was lowered from 6 and 4 mg/L, respectively, to 2 and 1 mg/L, respectively, when 4 mg/L desacetylcefotaxime was added to the medium . Full or partial synergy was demonstrated by 50.7% of the Bacteroides species tested . While cefotaxime and desacetylcefotaxime act synergistically against many members of the genus Bacteroides, the MIC of at least 10% of strains is not affected by this combination.

Nucleic Acids Res, 1988, 16 Suppl, r1 - 70
Compilation of 5S rRNA and 5S rRNA gene sequences; Wolters J et al.; The BERLIN RNA DATABANK as of December 31, 1987, contains a total of 509 sequences of 5S rRNAs or their genes, which is an increase of 45% over the last (1986) compilation (1) . It covers sequences from 38 archaebacteria, 184 eubacteria, 14 plastids, 4 mitochondria, 258 eukaryotes and 11 eukaryotic pseudogenes . The BERLIN RNA DATABANK uses the format of the EMBL Nucleotide Sequence Data Library complemented by a Sequence Alignment (SA) field including secondary structure information as presented in this publication . The BERLIN RNA DATABANK is available on 360 or 1200 kb diskettes.

Orig Life Evol Biosph, 1988, 18(1-2), 41 - 57
New prospects for deducing the evolutionary history of metabolic pathways in prokaryotes: aromatic biosynthesis as a case-in-point; Ahmad S et al.; Metabolic pathways of prokaryotes are more biochemically diverse than is generally recognized . Distinctive biochemical features are shared by phylogenetic clusters . The hierarchical levels of character-state clustering depends upon evolutionary events which fortuitously became fixed in the genome of a common ancestor . Prokaryotes can now be ordered on a phylogenetic tree . This allows the evolutionary steps that underlie the construction and regulation of appropriately complex biochemical pathways to be traced in an evolutionary progression of prokaryote types that house these pathways . Essentially the approach is to deduce ancestral character states at ever deeper phylogenetic levels, utilizing logical principles of maximum parsimony . The current perspective on the evolution of the biochemical pathway for biosynthesis of aromatic amino acids is developed as a case-in-point model for analyses that should be feasible with many major metabolic systems . Phenylalanine biosynthesis probably arose prior to the addition of branches leading to tyrosine and tryptophan . An evolutionary scenario is developed that begins with non-enzymatic reactions which may have operated in primitive systems, followed by the evolution of an enzymatic system that pre-dated the divergence of major lineages of modern eubacteria (Gram-positive bacteria, Gram-negative purple bacteria, and cyanobacteria).

Mol Microbiol, 1988 Jan, 2(1), 81 - 7
The three-dimensional structures of S-layers of two novel Eubacterium species isolated from inflammatory human processes; Sjogren A et al.; The three-dimensional structures of the crystalline surface layers of two species of Eubacteria have been determined by electron microscopy and computerized image processing . The S-layer of Eubacterium sp . ES4C has tetragonal symmetry, with a unit cell spacing of 10.6 nm and a thickness of 9.5 nm, while that of Eubacterium sp . AHN 990 has hexagonal symmetry a = b = 15.7 nm and a thickness of 13 nm . The resolutions in the reconstructions were 2.5 nm and 1.8 nm, respectively . The reconstruction of the S-layer of strain ES4C reveals a distinct domain structure: a major tetramer, arms connecting adjacent unit cells, and a minor tetramer . The S-layer of strain AHN 990, on the other hand, has a rather complex arrangement, centred around the six-fold axis.

Biosystems, 1988, 21(3-4), 177 - 87
Ribosomal RNA and the major lines of evolution: a perspective; Ragan MA; Does the "universal tree" based on small-subunit ribosomal RNA sequences show the phylogenetic relationship of all modern organisms? The answer is "yes" only if all these rRNAs are orthologous . Herein I argue that the major rRNA lineages (e.g . eubacterial, one or more archaebacterial and eukaryotic nucleocytoplasmic) probably arose from a divergent population of rRNAs in the progenote, antedating the universal common ancestral organism . Thus the major lineages of rRNA are probably not orthologous, but paralogous . The extrapolated date for the origin of the common ancestral small-subunit rRNA (3.6-4.7 x 10(9) years ago) is consistent with major rRNA lineages being paralogous . This perspective on the early evolution of genes and organisms rationalizes the presence of unexpected ribosomal characters in microsporidia, and bears on xenogenous and endogenous theories of the origin of the organelles in eukaryotes.

Mol Biol Rep, 1988, 13(2), 103 - 15
Signals determining translational start-site recognition in eukaryotes and their role in prediction of genetic reading frames; Louis BG et al.; A special methionyl-tRNA (RNAi) is universally required to initiate translation . The conversation of this reactant throughout evolution, as well as its unusual decoding properties, suggested an alternate mechanism for tRNA-mRNA interactions at initiation . We have reported that the sequence of bases neighboring the start codons of many eubacterial genes are complementary not only to the 16S rRNA 3' end and to the anticodon of tRNAi, but, also, have the potential to base-pair the D, T or extended anticodon loops of this tRNAi . The coding properties of tRNAi and mutations that affect translation suggest that these signals may function . This hypothesis explains the observation that unusual triplets can start prokaryotic and mitochondrial genes and predicts the occurrence of other reading frames . Furthermore, it suggests a unifying model of chain initiation based on RNA-RNA contacts and displacements . Here we examine the start domain of 290 eukaryotic genes for their ability to base-pair the tRNAi loops and the 18S rRNA . We observe that both methionine start, and methionine coding regions have the potential to pair with the 18S rRNA, but that the nucleotide distribution about start codons strongly favoured such pairings over that near internal AUGs . The 5' extended anticodon of tRNAi is methylated, and was not represented in the mRNA with high frequency . However, the tetramer AUGg did occur with high frequency in the start domain . A modification of the tRNAi T loop also decreases its base-pairing potential . Interestingly, complementarity to the T loop did not occur with high frequency in the start sites . The early coding region, 10 to 34 nucleotides 3' to the initiator AUG, is complementary to the tRNAi D loop in many cases, while no such affinity is found near internal AUGs . The nucleotides around initiator AUGs were heavily biassed toward the sequence gccaccAUGgcg . No such tendency was noted around internal AUGs . Although the role of this sequence bias is unclear, the sequence gccaccAUGg has been shown by Kozak to promote initiation . Another distinguishing feature was a C-rich tract 7 to 34 nucleotides 5' to the initiator AUGs . Ability to pair with more than eight bases of the start consensus sequence, matching of 6 or 7 nucleotides to the D loop on the 3' side, an C-richness on the 5' side were used as criteria for distinguishing start AUGs.(ABSTRACT TRUNCATED AT 400 WORDS)

J Mol Evol, 1988, 27(4), 365 - 76
On the early evolution of RNA polymerase; Lazcano A et al.; The lines of evidence suggesting that RNA preceded double-stranded DNA as an informational macromolecule are briefly reviewed . RNA polymerase is hypothesized to have been one of the earliest proteins to appear . It is argued that an important vestige of the original enzyme is found in the contemporary eubacterial beta' subunit of DNA-dependent RNA polymerase and its homologues among the archaebacterial and eukaryotic enzymes . The evidence that supports a catalytic role in replicase activity of this polypeptide is reviewed . It is suggested that several characteristics of the Escherichia coli transcriptional apparatus are relatively recent evolutionary developments . The phylogenetic importance of the eubacterial beta' subunit from RNA polymerase and its homologues is emphasized, because it allows the study of the evolutionary relationships of the major cellular lines (eubacteria, archaebacteria, and eukaryotes) as well as of some viral lineages.

J Mol Evol, 1988, 27(2), 121 - 5
A unique type of eubacterial 5S rRNA in members of the order Planctomycetales; Bomar D et al.; Analysis of the 5S ribosomal RNA from members of the eubacterial order Planctomycetales, i.e., Planctomyces, Pirella, Gemmata, and Isosphaera, reveals several unexpected features . Firstly, the primary structures are significantly shorter than those of the majority of eubacteria and vary in length between 109 and 111 nucleotides . Secondly, the lack of an insertion at position 66 is a feature not encountered before in prokaryotic 5S rRNAs . Thirdly, as compared to the proposed eubacterial "minimal" 5S rRNA structure (Erdmann and Wolters 1986) the secondary structure contains numerous base-pair transversions . The isolated position of the planctomycetes as an individual eubacterial division and the phylogenetic position of its genera are in accord with the results obtained from 16S rRNA cataloguing.

Jpn J Cancer Res, 1988 Jan, 79(1), 117 - 24
Antitumor activity and its properties of Eubacterium lentum; Morinaga S et al.; In the present study, some basic effects of Eubacterium lentum (TYH-11), isolated from normal intestinal flora, upon the immune system and various experimental tumor cell lines were investigated . E . lentum showed no direct cytotoxicity against Ehrlich ascites tumor, while Serratia marcescens (TY-142) did show direct cytotoxicity . E . lentum presented striking antitumor activity which differed according to the injection route and time . This strain showed antitumor activity against 11 experimental tumor cell lines including Ehrlich ascites tumor, Meth-A, etc., but not against EL4 or Lewis lung carcinoma . The antitumor activity in this strain was recognized to lie in the cell wall and granular fractions . The effect of this strain on the immune system was studied by using plaque formation and the footpad reaction . When mice received 5 injections of E . lentum, the plaque number increased to treble the control level . Spleen weight was also increased following administration of E . lentum . In normal and tumor-bearing mice immunized with SRBC alone, the footpad reaction was increased significantly to the control level by administration of E . lentum.

Biofactors, 1988 Jan, 1(1), 27 - 9
The nutrient factor queuine: biosynthesis, occurrence in transfer RNA and function; Kersten H; Queuine, 7-(( (4,5-cis-dihydroxy-2-cyclopenten-1-yl)-amino}-methyl)-7-deazagu ani ne is synthesized de novo only in eubacteria and is preseent in place of guanine 34 in specific tRNAs containing anticodones GUN where N is one of the four canonical nucleotides . The biosynthetic pathway starting with GTP shares common steps with that of pteridines and riboflavin, and involves iron ions and a 'vitamin B12' coenzyme . Lower and higher eukaryotes are supplied with queuine by nutrition or the intestinal flora . The modification of tRNA with queuine is tissue specific and depends on the metabolic state of cells and tissues . Starvation for queuine and/or Q-deficiency in tRNA causes a few specific changes in the pattern of protein synthesis involving lactate dehydrogenases and cytochromes.

Eur J Biochem, 1987 Dec 30, 170(1-2), 149 - 57
Semi-preparative HPLC purification of ribosomal proteins from Bacillus stearothermophilus and sequence determination of the highly conserved protein S19; Hirano H et al.; Several proteins from the Bacillus stearothermophilus 30S ribosomal subunit which could not be isolated by conventional open-column chromatography were purified by high-performance liquid chromatography using a semi-preparative reverse-phase C4 column . Protein S19 was purified by this technique and the complete amino acid sequence determined . Protein S19 was fragmented and the peptides isolated in picomole quantities were sequenced by an improved manual 4-N,N-dimethylaminoazobenzene-4'-isothiocyanate (DABITC) technique; the presence of five consecutive C-terminal lysines in the S19 sequence was confirmed by gas-phase sequencing and fast-atom-bombardment (FAB) mass spectrometry . Protein S19 is composed of 91 amino acid residues which correspond to a molecular mass of 10,428 Da . 71% of the B . stearothermophilus S19 sequence was found to be identical with the corresponding ribosomal protein from Escherichia coli {Yaguchi and Wittmann (1978), FEBS Lett . 88, 227} and both sequences can be aligned without gaps . Among the known 26 amino acid sequences of the B . stearothermophilus and E . coli ribosome such a high degree of conservation has only been observed for a few proteins, all of which are known to be involved in the protein biosynthesis process . Although a clear function has not yet been assigned to protein S19, its high sequence conservation in these two eubacteria clearly indicates an important role of this protein for the function of the ribosome.

J Biol Chem, 1987 Dec 5, 262(34), 16585 - 9
Eukaryotic initiation factor 4D, the hypusine-containing protein, is conserved among eukaryotes; Gordon ED et al.; When mammalian cells are grown in medium containing {3H}spermidine, a single major tritiated protein identical to eukaryotic initiation factor 4D becomes labeled . This protein contains 1 residue/molecule of tritiated hypusine (N epsilon-(4-amino-2-hydroxybutyl)lysine), a rare amino acid which has been found in no other protein . In order to investigate the conservation of this protein, we examined two nonmammalian eukaryotes, the yeast Saccharomyces cerevisiae and the insect Drosophila melanogaster, and the eubacterial prokaryote Escherichia coli for the presence of the hypusine-containing protein . When the eukaryotic cells were grown in the presence of {3H}spermidine, electrophoretic analysis revealed a single labeled protein . In each case, the apparent molecular weight was near 18,000 and the relative pI was approximately 5.2, similar to the hypusine-containing protein of mammals . Amino acid analysis confirmed the presence of tritiated hypusine in each case, and silver staining of two-dimensional polyacrylamide gels demonstrated that, in yeast and fruit flies as in mammals, the protein is relatively abundant . In the eubacterium E . coli, one tritiated protein was predominant, but its molecular weight was 24,000 and we found no evidence that it contained tritiated hypusine . We found no evidence for the existence of the hypusine-containing protein in the archaebacterium Methanococcus voltae . These data suggest that the hypusine-containing protein is conserved among eukaryotes.

J Bacteriol, 1987 Dec, 169(12), 5745 - 54
alpha-Amylase gene of Streptomyces limosus: nucleotide sequence, expression motifs, and amino acid sequence homology to mammalian and invertebrate alpha-amylases; Long CM et al.; The nucleotide sequence of the coding and regulatory regions of the alpha-amylase gene (aml) of Streptomyces limosus was determined . High-resolution S1 mapping was used to locate the 5' end of the transcript and demonstrated that the gene is transcribed from a unique promoter . The predicted amino acid sequence has considerable identity to mammalian and invertebrate alpha-amylases, but not to those of plant, fungal, or eubacterial origin . Consistent with this is the susceptibility of the enzyme to an inhibitor of mammalian alpha-amylases . The amino-terminal sequence of the extracellular enzyme was determined, revealing the presence of a typical signal peptide preceding the mature form of the alpha-amylase.

FEBS Lett, 1987 Nov 16, 224(1), 65 - 70
Primary structures of three highly acidic ribosomal proteins S6, S12 and S15 from the archaebacterium Halobacterium marismortui; Kimura J et al.; The amino acid sequences of three extremely acidic ribosomal proteins, S6, S12, and S15, from Halobacterium marismortui have been determined . The sequences were obtained by the sequence analysis of peptides derived by enzymatic digestion with trypsin . Stapylococcus aureus protease and chymotrypsin, as well as by cleavage with dilute HCl . The proteins, S6, S12 and S15, consist of 116, 147 and 102 amino acid residues, and have molecular masses of 12,251, 16,440 and 11,747 Da, respectively . Comparison of the amino acid sequences of these proteins with ribosomal protein sequences of other organisms revealed that halobacterial protein S12 has homology with the eukaryotic protein S16A from Saccharomyces cerevisiae, while S15 is significantly related to the Xenopus laevis S19 protein . No homology was found between these halobacterial proteins and any eubacterial ribosomal proteins.

J Bacteriol, 1987 Nov, 169(11), 4950 - 61
Spiroplasma virus 4: nucleotide sequence of the viral DNA, regulatory signals, and proposed genome organization; Renaudin J et al.; The replicative form (RF) of spiroplasma virus 4 (SpV4) has been cloned in Escherichia coli, and the cloned RF has been shown to be infectious by transfection (M . C . Pascarel-Devilder, J . Renaudin, and J.-M . Bove, Virology 151:390-393, 1986) . The cloned SpV4 RF was randomly subcloned and was fully sequenced by the dideoxy chain termination technique, using the M13 cloning and sequencing system . The nucleotide sequence of the SpV4 genome contains 4,421 nucleotides with a G+C content of 32 mol% . The triplet TGA is not a termination codon but, as in Mycoplasma capricolum (F . Yamao, A . Muto, Y . Kawauchi, M . Iwami, S . Iwagani, Y . Azumi, and S . Osawa, Proc . Natl . Acad . Sci . USA 82:2306-2309, 1985), probably codes for tryptophan . With these assumptions, nine open reading frames (ORFs) were identified . All nine are characterized by an ATG or GTG initiation codon, one or several termination codons, and a Shine-Dalgarno sequence upstream of the initiation codon . The nine ORFs are distributed in all three reading frames . One of the ORFs (ORF1) corresponds to the 60,000-dalton capsid protein gene . Analysis of codon usage showed that T- and A-terminated codons are preferably used, reflecting the low G+C content (32 mol%) of the SpV4 genome . The viral DNA contains two G+C-rich inverted repeat sequences . One could be involved in transcription termination and the other in initiation of cDNA strand synthesis . The SpV4 genome was found to contain at least three promoterlike sequences quasi-identical to those of eubacteria . These results fully support the bacterial origin of spiroplasmas.

J Bacteriol, 1987 Oct, 169(10), 4486 - 92
Sulfometuron methyl-sensitive and -resistant acetolactate synthases of the archaebacteria Methanococcus spp; Xing RY et al.; The herbicide sulfometuron methyl (SM) inhibited growth of some methanococci . Of 28 strains tested, the growth of 7 was completely inhibited by 0.55 mM SM . Growth of an additional 14 strains was partially inhibited, and the growth of 7 strains was unaffected by this concentration of SM . In some cases, the branched-chain amino acids protected growth . Growth inhibition was correlated with the Ki for SM of acetolactate synthase (ALS) . For the enzymes from bacteria representative of the sensitive, partially resistant, and resistant methanococci (Methanococcus aeolicus, Methanococcus maripaludis, and Methanococcus voltae, respectively), the Ki for SM was 0.0012, 0.34, and greater than 1.0 mM, respectively . Inhibition was uncompetitive with respect to pyruvate . Based on these observations, ALS appeared to be the major if not the sole site of action of SM in the methanococci . The sensitivity of the ALS from these three methanococci to feedback inhibition by branched-chain amino acids was also quite different . Although all three were sensitive to feedback inhibition by valine, the Ki varied 20-fold, from 0.01 to 0.22 mM . Moreover, only the ALS from M . maripaludis was sensitive to inhibition by leucine, and the Ki was 1.8 mM . The Ki for isoleucine for the ALS from both M . maripaludis and M . voltae was about 0.1 mM . The ALS from M . aeolicus was not inhibited by isoleucine . In other respects, the ALSs from the methanococci were very similar . After dialysis, thiamine pyrophosphate but not FAD and Mg2+ was required for maximal activity, and they were all rapidly inactivated by oxygen . Although the methanococcal ALSs exhibited diverse properties, the range of catalytic and regulatory properties closely resembled those of the eubacterial enzymes.

Appl Environ Microbiol, 1987 Oct, 53(10), 2363 - 7
Effects of potassium ion concentrations on the antimicrobial activities of ionophores against ruminal anaerobes; Dawson KA et al.; The antimicrobial activities of monensin and lasalocid against representative strains of ruminal bacteria were evaluated in medium containing three different concentrations of potassium (1.3, 7.9, or 23.3 mM) . The growth of Eubacterium ruminantium was inhibited by low concentrations of ionophores (less than or equal to 0.16 mg/liter), while the strain of Streptococcus bovis tested was resistant to high concentrations of ionophores (40 mg/liter) at all potassium concentrations tested . The MICs of the ionophores for strains of Bacteroides succinogenes, Butyrivibrio fibrisolvens, Ruminococcus albus, and Ruminococcus flavefaciens and for one strain of Bacteroides ruminicola increased with increasing potassium concentrations in the medium . High concentrations of ionophores (40 mg/liter) decreased the maximum cell yields or increased the lag times or both in cultures of one strain of Bacteroides ruminicola and two strains of Selenomonas ruminantium but did not completely inhibit the growth of these organisms . Increased potassium concentrations in the medium (from 7.9 to 23.3 mM) decreased the lag times or increased the cell yields or both when these three strains were grown in ionophore-containing medium, while the activities of lasalocid and monensin against these organisms were enhanced in the medium containing low potassium concentrations (1.3 mM) . The data from this study suggest that extracellular potassium concentrations may influence the antimicrobial activities of ionophores in the rumen.

Nucleic Acids Res, 1987 Sep 25, 15(18), 7593 - 603
Structure and evolution of the 4.5-5S ribosomal RNA intergenic region from Glycine max (soya bean); Nazar RN et al.; The nucleotide sequence for the 4.5-5S ribosomal DNA region from the chloroplastids of soya beans was determined as the basis of further comparative studies on the structure and evolution of this intergenic region . Comparisons with other plant sequences as well as equivalent sequences in eubacteria suggest that the longer internal transcribed spacer regions of plants have evolved, at least in part, by DNA sequence duplications and that the presence of the 4.5S rRNA in chloroplast may result from the accidental acquisition of a RNA maturation site during the evolution of longer internal transcribed spacer regions . Estimates of the secondary structures also indicate only a very limited retention of structural features and suggest that the primary role of the intergenic sequences may be to bring processed sites into close proximity.

Nucleic Acids Res, 1987 Sep 11, 15(17), 7081 - 90
Characterization of the small RNA of the bacteriophage phi 29 DNA packaging machine; Guo PX et al.; The prohead connector of the bacteriophage luminal diameter 29 DNA packaging machine was reconstructed with the small RNA that regulates DNA packaging in vitro . The complete sequence of the 120 nucleotide RNA proved its origination from the promoter PE1(A1) of the left early region of phi 29 DNA, the end packaged first during assembly . The prohead RNA was clearly distinct from eubacterial 5S rRNA in sequence and composition.

J Pediatr Gastroenterol Nutr, 1987 Sep-Oct, 6(5), 686 - 96
Duodenal bile acids among children: keto derivatives and aerobic small bowel bacterial overgrowth; Kocoshis SA et al.; Duodenal bile acids, identified by gas-liquid chromatography (GLC) and gas chromatography-mass spectrometry (GC-MS), were correlated with quantitative aerobic and anaerobic duodenal culture in 26 children with enteropathies . Four patients whose duodenal fluid contained either greater than or equal to 10(6) gram-negative aerobes or greater than or equal to 10(6) aerobic lactobacilli per milliliter had a significantly greater molar percentage of keto-bile acids (32.3 +/- 8.4%) than did 19 controls (0.72 +/- 1.50%) chosen because duodenal fluid contained less than or equal to 10(4) bacteria per milliliter or three other patients with greater than or equal to 10(6) anaerobes (6.1 +/- 4.6%) . As expected, free bile acids were seen in greater quantities (10.75 +/- 3.25%) among the patients with anaerobic overgrowth or aerobic Lactobacillus overgrowth than among the controls (1.6 +/- 1.0%) or the other three aerobic overgrowth patients (2.2 +/- 1.4%) . Incubation of glycocholate or glycochenodeoxycholate for 60 h with Eubacterium tortuosum from one patient or Escherichia coli from another produced the types of bile acids found in the duodenum of those patients . Successful antibacterial therapy improved gastrointestinal function and normalized duodenal bile acids not only among patients with anaerobic overgrowth but also among those with pure aerobic overgrowth . These data suggest that pure aerobic bacterial overgrowth syndrome occurs in children, and that altered duodenal bile acid composition may play a pathophysiologic role in this disorder.

Biochem Cell Biol, 1987 Sep, 65(9), 776 - 82
DNA-dependent RNA polymerase from Pseudomonas aeruginosa; Allan B et al.; DNA-dependent RNA polymerase was purified from Pseudomonas aeruginosa . The subunit structure was typical of other eubacterial RNA polymerases in having beta' (157,000), beta (148,000), sigma (87,000), and alpha 2 (45,000) subunits as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis . The enzyme was dependent on Mg2+, displaying optimal activity at 10 mM MgCl2 . Ca2+ and Zn2+ could not replace MgCl2 in the assay system, while Mn2+, produced partial activity . KCl at concentrations greater than 10 mM inhibited enzyme activity . Optimal enzyme activity was observed at pH 8.5-9.0 . The RNA polymerase was stable in 50% (w/v) glycerol at 4 degrees C for more than 3 months . Enzyme activity was inhibited in vitro by heparin, streptolydigin, streptovaracin, actinomycin D, and rifampicin.

Eur J Biochem, 1987 Sep 1, 167(2), 211 - 9
The plasma membrane ATPase of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius . Purification and immunological relationships to F1-ATPases; Lubben M et al.; The plasma-membrane-associated ATPase of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius characterized in a previous work {M . Lubben & G . Schafer (1987) Eur . J . Biochem . 164, 533-540} has been solubilized . It can be easily removed from the membrane by mild treatment with zwitterionic detergents, therefore it appears to be a peripheral membrane protein analogous to the soluble F1-ATPase of eubacteria and eukaryotes . Further purification has been achieved by subsequent gel permeation and ion-exchange chromatography . The final purity is greater than 70% as judged by staining intensities after SDS/polyacrylamide gel electrophoresis . The ATPase consists of two major polypeptides of 65 kDa (alpha) and 51 kDa (beta) in comparable quantities; a minor band (20 kDa) is assumed to be a contaminant or a constitutive part of the enzyme, possibly copurified in substoichiometric amount . The native molecular mass of the solubilized ATPase determined by gel permeation is 430 kDa . Considering the precision of these methods, it remains open whether a 3:3 stoichiometry reflects the contribution of alpha and beta subunits to the quaternary structure, in analogy to known F1-ATPases . The catalytic properties resemble those of the membrane-bound state . There are two pH optima at 5.3 and 8.0 in the absence and only one optimum at 6.5 in the presence of the activating anion sulfite . Activity is strictly dependent on the divalent cations Mg2+ or Mn2+ . ATP and dATP are hydrolyzed with highest rates; also other purine and pyrimidine nucleotides are cleaved significantly, but not ADP, pyrophosphate and p-nitrophenyl phosphate . The ATPase is insensitive to azide or vanadate but is inhibited by relatively low concentrations of nitrate . Polyclonal antisera have been raised against the beta subunit of the Sulfolobus ATPase . Cross-reactivities with cellular or membrane extracts of a number of archaebacteria, eubacteria and chloroplasts have been analyzed by means of Western blotting and immunodecoration . A strong cross-reactivity with other genera of the Sulfolobales is observed, also with Methanobacterium, Methanosarcina, Methanolobus and Halobacterium . Even membranes of the eubacterium Escherichia coli and of eukaryotic chloroplast react with the antibodies . With one exception, in all cases the molecular mass of the cross-reacting polypeptide falls in the range of 51-56 kDa . Only in Halobacterium halobium, bands at 66 and 68 kDa have been detected . In order to identify the cross-reacting polypeptides, the purified F1-ATPases of E . coli, chloroplasts and beef heart mitochondria have been tested.(ABSTRACT TRUNCATED AT 400 WORDS)

Mol Biol Evol, 1987 Sep, 4(5), 445 - 72
Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences; Hori H et al.; A phylogenetic tree of most of the major groups of organisms has been constructed from the 352 5S ribosomal RNA sequences now available . The tree suggests that there are several major groups of eubacteria that diverged during the early stages of their evolution . Metabacteria (= archaebacteria) and eukaryotes separated after the emergence of eubacteria . Among eukaryotes, red algae emerged first; and, later, thraustochytrids (a Proctista group), ascomycetes (yeast), green plants (green algae and land plants), "yellow algae" (brown algae, diatoms, and chrysophyte algae), basidiomycetes (mushrooms and rusts), slime- and water molds, various protozoans, and animals emerged, approximately in that order . Three major types of photosynthetic eukaryotes--i.e., red algae (= Chlorophyll a group), green plants (Chl . a + b group) and yellow algae (Chl . a + c)--are remotely related to one another . Other photosynthetic unicellular protozoans--such as Cyanophora (Chl . a), Euglenophyta (Chl . a + b), Cryptophyta (Chl . a + c), and Dinophyta (Chl . a + c)--seem to have separated shortly after the emergence of the yellow algae.

J Clin Microbiol, 1987 Aug, 25(8), 1540 - 5
Characteristics and sites of infection of Eubacterium nodatum, Eubacterium timidum, Eubacterium brachy, and other asaccharolytic eubacteria; Hill GB et al.; Three new species, Eubacterium nodatum, Eubacterium timidum, and Eubacterium brachy, were described, primarily from subgingival samples taken from patients with moderate and severe adult periodontitis . Except for the isolation of E . brachy from a pleuropulmonary infection, these species have not been reported from other infected body sites . We report on the isolation of these species and an undescribed group (D-6) of asaccharolytic eubacteria also found in periodontal disease from numerous different sites of infection, mostly the head and neck . A similarity in cellular morphological properties of E . nodatum and Actinomyces sp . was noted previously . Additional similarities, particularly to Actinomyces israelii, that we found are the formation of molar tooth colonies and the isolation from cases of lumpy jaw and from the genital tract of women in association with the use of an intrauterine contraceptive device . E . timidum and E . brachy did not occur more often from any particular site outside of the head, neck, and respiratory tract . The group D-6 strains came from a variety of sites in the trunk and pelvis . These species are all obligately anaerobic, asaccharolytic, and generally nonreactive, and they grow poorly and slowly on media commonly used to isolate anaerobic bacteria . L-Lysine (0.5%) markedly stimulated the growth of E . nodatum and, to a lesser extent, another acetate- and butyrate-producing group, Eubacterium sp . group D-6, but we did not find comparable stimulants for the other species . We found the production of phenyl acetate to be a helpful marker in the identification of E . timidum and Eubacterium sp . group D-6 . Although the isolation and identification of most of these species remain somewhat difficult, the evidence from dental infections and the present report suggests that these species are potential pathogens that are likely to be overlooked in infected clinical material without special attention to more prolonged incubation and use of enriched isolation media.

Biol Chem Hoppe Seyler, 1987 Aug, 368(8), 921 - 5
The N-terminal sequence of ribosomal protein L10 from the archaebacterium Halobacterium marismortui and its relationship to eubacterial protein L6 and other ribosomal proteins; Dijk J et al.; The amino-terminal sequence of ribosomal protein L10 from Halobacterium marismortui has been determined up to residue 54, using both a liquid- and a gas-phase sequenator . The two sequences are in good agreement . The protein is clearly homologous to protein HcuL10 from the related strain Halobacterium cutirubrum . Furthermore, a weaker but distinct homology to ribosomal protein L6 from Escherichia coli and Bacillus stearothermophilus can be detected . In addition to 7 identical amino acids in the first 36 residues in all four sequences a number of conservative replacements occurs, of mainly hydrophobic amino acids . In this common region the pattern of conserved amino acids suggests the presence of a beta-alpha fold as it occurs in ribosomal proteins L12 and L30 . Furthermore, several potential cases of homology to other ribosomal components of the three ur-kingdoms have been found.

FEBS Lett, 1987 Jul 27, 219(2), 269 - 73
A putative internal promoter in the 16 S/23 S intergenic spacer of the rRNA operon of archaebacteria and eubacteria; Mankin AS et al.; The existence of the internal promoter Pi in the 16 S/23 S intergenic spacers of the rRNA operons of an eubacterium Escherichia coli and archaebacterium Halobacterium halobium is proposed . The possible functional significance of these promoters is discussed.

Science, 1987 Jul 24, 237(4813), 409 - 11
Linear plasmids of the bacterium Borrelia burgdorferi have covalently closed ends; Barbour AG et al.; The genetics of spirochetes, a division of eubacteria, has been little studied . Double-stranded linear plasmids were found in Borrelia burgdorferi, the agent of Lyme disease . A 49-kilobase linear plasmid contained the ospA and ospB genes, which encode the major outer membrane proteins of strain B31 . Molecules of the 49-kilobase plasmid rapidly reannealed after alkaline denaturation; rapid renaturation was prevented if the 49-kilobase plasmids were first treated with S1 nuclease . When denatured plasmid molecules were examined directly, single-stranded circles of approximately 100-kilobase circumference were seen . These studies provide direct visual evidence that the linear plasmids have covalently closed ends . This form of DNA occurs in some animal viruses, but it has not heretofore been described in prokaryotic organisms.

Eur J Biochem, 1987 Jul 15, 166(2), 325 - 32
The in vivo stability, maturation and aminoacylation of anticodon-substituted Escherichia coli initiator methionine tRNAs; Grosjean H et al.; We have constructed eight anticodon-modified Escherichia coli initiator methionine (fMet) tRNAs by insertion of synthetic ribotrinucleotides between two fragments ('half molecules') derived from the initiator tRNA . The trinucleotides, namely CAU (the normal anticodon), CAA, CAC, CAG, GAA, GAC, GAG and GAU, were joined to the 5' and 3' tRNA fragments with T4 RNA ligase . The strategy of reconstruction permitted the insertion of radioactive 32P label between nucleotides 36 and 37 . tRNAs were microinjected into the cytoplasm of Xenopus laevis oocytes, and the following properties were evaluated: the stability of these eubacterial tRNA variants in the eukaryotic oocytes; the enzymatic modification of the adenosine at position 37 (3' adjacent to the anticodon) and aminoacylation of the chimeric tRNAs by endogenous oocyte aminoacyl-tRNA synthetases . In contrast to other variants, the two RNAs having CAU and GAU anticodons were stable and underwent quantitative modification at A-37 . These results show that the enzyme responsible for the modification of A-37 to N-{N-(9-beta-D-ribofuranosylpurine-6-yl)carbamoyl}threonine (t6A) is present in the cytoplasm of oocytes and is very sensitive to the anticodon environment of the tRNA . Also, these same GAU and CAU anticodon-containing tRNAs are fully aminoacylated with the heterologous oocyte aminoacyl-tRNA synthetases in vivo . During the course of this work we developed a generally applicable assay for the aminoacylation of femtomole amounts of labelled tRNAs.

FEBS Lett, 1987 Jun 15, 217(2), 191 - 6
Variable base pairing in a helix of eubacterial 5 S ribosomal RNA points to the existence of a conformational switch; Van den Eynde H et al.; A survey of 160 published sequences of eubacterial 5 S rRNAs shows that there exists structural variability in one of the helices of the generally accepted secondary structure model . Four structural variants are found, which differ with respect to the position and the number of bulges present . Most eubacterial 5 S RNAs fit into at least two of these conformations . A reaction scheme connecting the four observed conformations by changes in the base pairing scheme is proposed . Each of the known 5 S RNA sequences fits into conformations interconvertible by the proposed reactions.

Isr J Med Sci, 1987 Jun, 23(6), 676 - 7
Spiroplasmas: gene structure and expression; Renaudin J et al.; Upon sequencing of the SpV4 genome, eight putative open reading frames (ORFs) including that for the 65-kilodalton (kDa) capsid protein were detected . They involve all three reading frames . Three promoter sequences were found, as well as a transcription terminator and the initiation site for complementary strand synthesis . Ribosome binding sites and regulatory sequences are closely related to those of Eubacteria . Codon usage analysis showed that A and T terminated codons are preferably used . UAA is the major termination codon . Upon cloning of the full-size SpV4 replicative form, the capsid protein gene could not be expressed in Escherichia coli, whereas the spiralin gene cloned in the same bacterium is expressed . These results suggest that in spiroplasmas, as in Mycoplasma capricolum, UGA is not a termination codon, but very probably codes for tryptophan . Spiralin contains no tryptophan . Hence, its gene contains no UGA codons and can thus be expressed in E . coli . On the other hand, the gene for capsid protein has nine UGA codons and cannot be fully expressed in the bacterium . Our results fully support the bacterial origin of spiroplasmas.

J Bacteriol, 1987 Jun, 169(6), 2702 - 7
Cell wall and lipid composition of Isosphaera pallida, a budding eubacterium from hot springs; Giovannoni SJ et al.; Isosphaera pallida is an unusual gliding, budding eubacterium recently isolated from North American hot springs . Electron micrographs of ultrathin sections revealed a cell wall atypical of eubacteria: two electrondense layers separated by an electron-transparent layer, with no evident peptidoglycan layer . Growth was not inhibited by penicillin . Cell walls were isolated from sheared cells by velocity sedimentation . The rigid-layer fraction, prepared from cell walls by treatment with boiling 10% sodium dodecyl sulfate, was hydrolyzed and chemically analyzed for muramic acid . This essential component of peptidoglycan was absent . Amino acid analysis demonstrated a proteinaceous wall structure . Pitlike surface structures seen in negatively stained whole cells and thin sections were correlated with periodically spaced perforations of the rigid sacculus . An analysis of the lipid composition of I . pallida revealed typical ester-linked lipids with unbranched fatty acids, in contrast to the isoprenyl ether-linked lipids of archaebacteria, which also have proteinaceous cell walls . Capnoids, unusual sulfonolipids which are present in gliding bacteria of the Cytophaga-Flexibacter group, were absent.

Appl Environ Microbiol, 1987 Jun, 53(6), 1273 - 6
Quin's oval and other microbiota in the rumens of molasses-fed sheep; Vicini JL et al.; Two rumen-cannulated wether sheep were fed a diet containing 1 kg of a liquid-molasses mixture, 80 g of soybean oil meal, and 100 g of chopped wheat straw once a day . In 6 weeks and thereafter, the microbiota adapted such that Quin's oval, a very large bacterium, was present in huge numbers (11.3 X 10(10) and 1.3 X 10(10) ml-1 after 73 days) . Direct microscopic counts were also done on small bacteria, moderate-sized Selenomonas spp., and small Entodinium spp., which were the only protozoa seen . After the necessary dilution of rumen contents to make the microbial cells visible, Quin's ovals were seen to be much smaller in sheep 1 than in sheep 2 . Most-probable-number estimates indicated that Methanobrevibacter spp . were present at 10(7) ml-1, Methanosarcina spp . were present at 10(3) ml-1, and Eubacterium limosum-like bacteria were present at 10(5) to 10(6) ml-1 . In the adapted sheep, the dry portion of the diet was rapidly consumed, but the molasses mixture was consumed over a 9- to 10-h period . Volatile fatty acids in the rumen were present in very low amounts just prior to feeding and were much higher during the consumption of the diet, with about a 1:1 molar ratio of propionate to acetate between 1 and 9 h after feeding . Data were obtained on hourly feed consumption, levels of volatile fatty acids, and pH.(ABSTRACT TRUNCATED AT 250 WORDS)

Microbiologia, 1987 Jun, 3(2), 71 - 89
Phototrophic bacteria (an incoherent group of prokaryotes) . A taxonomic versus phylogenetic survey; Truper HG; In spite of their apparently consistent classical systematic scheme the phototropic bacteria are, as 16S-rRNA oligonucleotide cataloguing and sequencing have shown, deeply split into phylogenetic divisions of very little relationships between one another . Phototrophy as a mode of energy metabolism occurs in the phylogenetic divisions of a) "Gram-positive eubacteria", b) "Cyanobacteria/Chloroplasts", c) "Green Sulfur Bacteria", d) "Chloroflexus and related taxa", and e) "Purple Bacteria and related taxa", i.e . in five of the nine phylogenetic divisions of eubacteria . The arising disagreements are discussed and an attempt is made towards a stepwise reconciliation of taxonomy with phylogeny . The strong and the weak points in the taxonomy of phototrophic eubacteria are pointed out within the existing families . Emphasis is given to areas where taxonomic studies are urgently needed.

Eur J Biochem, 1987 May 15, 165(1), 171 - 5
Mode of inhibition of the DNA polymerase of Methanococcus vannielii by aphidicolin; Zabel HP et al.; The mode of action of aphidicolin on DNA synthesis catalysed by the DNA polymerase of Methanococcus vannielii is competitive for dCTP, noncompetitive for dATP, dGTP and dTTP and uncompetitive for activated DNA . The kinetic data are accounted for by a mechanism in which dCTP and aphidicolin compete for the dCTP-specific binding site on the DNA polymerase . The dissociation constant for the aphidicolin--DNA-polymerase complex is 0.04-0.07 microM . Similar modes of inhibition of DNA synthesis exist for DNA polymerase alpha of higher eucaryotes but not for eubacteria or viruses and suggests a close functional relationship between the DNA polymerase of eucaryotes and of the archaebacterium M . vannielii.

Eur J Biochem, 1987 May 4, 164(3), 533 - 40
A plasma-membrane associated ATPase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius; Lubben M et al.; Thermoacidophilic archaebacteria have gained much interest because of their phylogenetic distance to eubacteria and eukaryotes and also because of their unique living conditions . Investigation of the energy-converting system therefore offers a key for understanding the evolutionary position and environmental adaptation of these unusual bacteria . A plasma-membrane-associated adenosine triphosphatase with specific activities of 0.3-0.6 mumol min-1 (mg protein)-1 has been detected in the thermoacidophilic archaebacterium Sulfolobus acidocaldarius (DSM 639) . The enzyme exhibits two optima at pH 5.5 and 8.0, sulfite activation leads to only one optimum at pH 6.25 . In the presence of the divalent cations Mg2+ or Mn2+ it hydrolyzes ATP with highest reactivity and also other purine and pyrimidine nucleotides, but not ADP and pyrophosphate . A specific stimulation by monovalent cations is not observed . The ATPase activity is not inhibited by N,N'-dicyclohexylcarbodiimide, azide or vanadate, but it is by the vascular ATPase inhibitor nitrate with an {I}50 of 8 mM . Linear Arrhenius plots up to 75 degrees C reflect pronounced adaptation to the hot environment of the archaebacterium . The solubilized ATPase as localized by activity staining in non-denaturating gels and further analyzed by sodium dodecyl sulfate electrophoresis is composed of two major polypeptides of 65 and 51 kDa reminiscent of the alpha and beta subunits of eubacterial and eukaryotic F0F1-ATPases . The ATPase is suggested as a probable candidate for a reversibly acting ATP synthase responsible for oxidative phosphorylation found in Sulfolobus acidocaldarius.

J Bacteriol, 1987 May, 169(5), 1886 - 90
Metabolism of gallate and phloroglucinol in Eubacterium oxidoreducens via 3-hydroxy-5-oxohexanoate; Krumholz LR et al.; The pathway for the anaerobic catabolism of gallic acid by Eubacterium oxidoreducans was studied by using both in vivo and cell-free systems . Cells grown with gallate and crotonate, but with no formate or H2, excreted pyrogallol and phloroglucinol into the medium . Gallate was decarboxylated by crude cell extracts, with pyrogallol as the only detectable product . Whole cells converted pyrogallol to phloroglucinol . A phloroglucinol reductase catalyzed the conversion of phloroglucinol to dihydrophloroglucinol when NADPH was used as the source of electrons . Both formate dehydrogenase (EC 1.2.1.43) and hydrogenase (EC 1.18.99.1) were present in cell extracts of gallate-formate-grown cells . These two enzymes were both NADP linked . Since either H2 or formate is required for cell growth with gallate or phloroglucinol, these results suggest that the oxidation of the reduced substrate may be indirectly linked to the reduction of phloroglucinol . A dihydrophloroglucinol hydrolase was present, which hydrolyzed dihydrophloroglucinol to 3-hydroxy-5-oxohexanoate . This six-carbon ring cleavage product then presumably can be broken down by a series of reactions similar to beta-oxidation . These reactions cleaved the six-carbon acid to 3-hydroxybutyryl-coenzyme A yielding acetate and butyrate as end products . A number of key enzymes involved in beta-oxidation and substrate-level phosphorylation were demonstrated in cell extracts.

Isr J Med Sci, 1987 May, 23(5), 357 - 60
Organization and structure of tRNA genes in Spiroplasma melliferum; Rogers MJ et al.; To investigate the organization of tRNA genes in the honeybee pathogen, Spiroplasma melliferum (previously referred to as Spiroplasma sp . BC3), total labeled tRNA from S . melliferum was used as a hybridization probe to an EcoRI digest of the genomic DNA . The results show two, or possibly three, strongly hybridizing bands . Comparing the pattern obtained to that of Bacillus subtilis DNA suggests either that the S . melliferum tRNA genes are more extensively clustered or, more likely, that the S . melliferum genome does not encode a full complement of tRNA genes, as has been suggested for other Mollicutes . We screened a library of EcoRI fragments of S . melliferum DNA cloned in pBR322 with total radioactive tRNA as a probe and selected one of the tRNA gene clusters . Subsequent sequence analysis of a portion of the clone showed 10 tRNA genes probably comprising a single operon . Comparison of sequence with a tRNA gene cluster from Mycoplasma mycoides and a portion of a cluster from B . subtilis showed an identical order of tRNA genes and the isoacceptors encoded . Such a striking comparison in gram-positive eubacteria suggests an important function for regulation and co-transcription of these tRNA genes.

Isr J Med Sci, 1987 May, 23(5), 347 - 51
Gene expression signals in Mycoplasma hyopneumoniae and Mycoplasma capricolum; Taschke C et al.; In Mycoplasma hyopneumoniae, the single genes for 16S and 23S rRNAs are clustered in one operon from which the 5S rRNA gene is separated by more than 4 kbp . This operon, gene 2413 and gene X from M . hyopneumoniae and the 5' ends of both rRNA operons from M . capricolum were cloned and used for analysis of the following gene expression signals: promoters and terminators of the DNA-directed RNA polymerase, ribosomal binding sites of mRNA, and sites for processing of precursor rRNA . The analyses were performed by nuclease S1 protection experiments, the primer extension technique, and DNA sequencing . From these studies we conclude that putative promoter sequences in M . hyopneumoniae deviate significantly from those in Escherichia coli and Bacillus subtilis in having its -35 consensus sequence replaced by A-T rich sequences, whereas the characterized M . capricolum promoter resembles more closely a typical E . coli promoter . The other expression signals show sequences or structures similar to those found in other eubacteria, indicating related underlying principles.

J Biol Chem, 1987 Apr 5, 262(10), 4701 - 7
Biosynthesis of a novel bile acid nucleotide and mechanism of 7 alpha-dehydroxylation by an intestinal Eubacterium species; Coleman JP et al.; Eubacterium species V.P.I . 12708 has inducible bile acid 7-dehydroxylase activity that can use either 7 alpha or 7 beta bile acids as substrates . Cell extracts prepared from bacteria grown in the presence of cholic acid catalyzed the rapid conversion of free bile acids into a highly polar bile acid metabolite (HPBA) . This conjugation activity co-eluted with bile acid 7-dehydroxylase activity on high performance gel filtration chromatography (GFC) . The HPBA was purified by a combination of high performance GFC and reverse-phase high performance liquid chromatography (HPLC) . The intact HPBA eluted earlier from reverse-phase HPLC than deoxycholyl-CoA and had a Mr of 1102 by Bio-Gel P-2 (GFC) . The HPBA had an absorption peak at 255 nm and was sensitive to treatment with phosphodiesterase I or nucleotide pyrophosphatase . The HPBA has a free phosphate as shown by an increase in elution volume on reverse-phase HPLC following treatment with alkaline phosphatase . Treatment of the purified HPBA with nucleotide pyrophosphate plus alkaline phosphatase yielded adenosine, whereas, treatment with nucleotide pyrophosphatase alone generated 5',3'-ADP . A bile acid metabolite was also generated by nucleotide pyrophosphatase treatment . The bile acid metabolite had different chromatographic properties (HPLC and TLC) than the corresponding free bile acid . Gas liquid chromatography-mass spectrometry showed the bile acid metabolite to be 12 alpha-hydroxy-3-oxo-4-cholenoic acid . We hypothesize that the HPBA is an intermediate in 7-dehydroxylation and consists of this compound linked at the C-24 with an anhydride bond to the beta phosphate (5') of ADP-3'-phosphate . These results suggest a novel mechanism of bile acid 7 alpha/7 beta-dehydroxylation in Eubacterium sp . V.P.I . 12708.

Appl Environ Microbiol, 1987 Apr, 53(4), 901 - 4
Reductive inactivation of digitoxin by Eubacterium lentum cultures; Chandrasekaran A et al.; The obligate anaerobe Eubacterium lentum inactivated the cardiac glycoside digitoxin by reducing the double bond in the lactone ring . This conversion was quantitative when the substrate was incubated at a concentration of 10 micrograms/ml . The reduction reaction coincided with the growth phase of the bacterium . The stereochemical configuration at C-20 of the reduction product dihydrodigitoxin was found to be R . Incubation of digitoxigenin and its mono- and bisdigitoxosides individually with E . lentum led to the formation of their respective dihydro derivatives . The configuration at C-20 of these reduced metabolites was also found to be R.

J Bacteriol, 1987 Apr, 169(4), 1516 - 21
Molecular cloning of bile acid 7-dehydroxylase from Eubacterium sp . strain VPI 12708; Coleman JP et al.; Eubacterium sp . strain VPI 12708 is a human intestinal bacterium which contains an inducible bile acid 7-dehydroxylase . Two-dimensional polyacrylamide gel electrophoresis showed that at least four new polypeptides were synthesized after exposure of growing cells to sodium cholate . One of these, of molecular weight 27,000 (PP-27), was implicated in 7-dehydroxylase catalysis . PP-27 was purified to greater than 95% homogeneity by DEAE-cellulose chromatography, high-pressure liquid chromatographic gel filtration, high-pressure liquid chromatography-DEAE chromatography, and preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis . The first 33 amino acid residues of the N terminus of PP-27 were determined with a gas-phase sequencer, and a corresponding mixed oligonucleotide (17-mer) was synthesized . Southern blot analysis of EcoRI total digests of chromosomal DNA showed a 2.2-kilobase fragment which hybridized to the 32P-labeled 17-mer . This fragment was enriched for by size fractionation of an EcoRI total digest of genomic DNA, ligated into the bacterial plasmid pUC8, and used to transform Escherichia coli HB101 . Transformants containing the putative 7-dehydroxylase gene were detected with the 32P-labeled 17-mer by colony hybridization techniques . The insert was 2.2 kilobases in length and contained the first 290 bases of the PP-27 gene . Preliminary nucleic acid sequence data correlate with the amino acid sequence . The entire gene was cloned on a 1,150-base-pair TaqI fragment . Western blot analysis of E . coli strains containing these plasmids indicated that PP-27 is expressed in E . coli but is not regulated by bile acids under the conditions used.

Acta Pathol Microbiol Immunol Scand {B}, 1987 Apr, 95(2), 151 - 2
Another polysaccharide antigen of Eubacterium saburreum with heptose as the main constituent; Hofstad T et al.; The polysaccharide antigen of Eubacterium saburreum strains L76, reacting by precipitation and complement-fixation, has D-glycero-D-galacto-heptose as the main component, and, in addition, O-acyl groups.

J Bacteriol, 1987 Apr, 169(4), 1691 - 701
In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli; Berg KL et al.; In this study we show that a segment of the Escherichia coli rrnB 16S gene can be translated in vivo . Other laboratories have previously reported that there are internal transcription and translation signals and open reading frames within the E . coli rrnB rRNA operon . Their studies revealed a translation start signal followed by a 252-base-pair open reading frame (ORF16) within the 16S gene and detected a promoter (p16) in the same general region by using in vitro RNA polymerase binding and transcription initiation assays . By using plasmid gene fusions of ORF16 to lacZ we showed that an ORF16'-'beta-galactosidase fusion protein was made in vivo . Transcripts encoding the fusion protein were expressed either from the rrnB p1p2 control region or from a hybrid trp-lac promoter (tacP), but the amount of expression was considerably less than for a lacZ control plasmid . We used fusions to the cat gene to show that p16 is one-half as active as lacP . Deletions were used to show that p16 is located within ORF16 and thus cannot promote a transcript encoding the ORF16 peptide . A comparison of sequences from different organisms shows that ORF16 and p16 lie in a highly conserved region of the procaryotic 16S RNA structure . The first 20 amino acids of ORF16 are conserved in most eubacterial and plant organellar sequences, and promoter activity has been detected in this region of the Caulobacter crescentus sequence by other workers.

Infect Immun, 1987 Apr, 55(4), 871 - 6
Chemical composition and immunological characterization of polysaccharide antigen from Eubacterium saburreum T18; Nakazawa F et al.; Two types of polysaccharide were obtained from the oral microorganism Eubacterium saburreum T18 by formamide extraction and subsequent gel filtration and ion-exchange chromatography . One polysaccharide, which was composed of D-glycero-D-galacto-heptose, had antigenic activity in an immunoprecipitation reaction with rabbit anti-T18 serum due to immunoglobulin M antibodies . The second polysaccharide was composed of D-glycero-D-manno-heptose and L-rhamnose, but it did not have immunoprecipitation activity . These polysaccharide antigens were not alkali labile and differed from E . saburreum L44 and T27 antigens, which were composed of D-glycero-D-galacto-heptose.

Eur J Biochem, 1987 Mar 2, 163(2), 397 - 405
A DNA polymerase with unusual properties from the slime mold Physarum polycephalum; Holler E et al.; Two forms of a DNA polymerase have been purified from microplasmodia of Physarum polycephalum by poly(ethyleneimine) precipitation and chromatography on DEAE-Sephacel, phosphocellulose, heparin Sepharose, hydroxyapatite, DNA-agarose, blue-Sepharose . They were separated from DNA polymerase alpha on phosphocellulose and from each other on heparin-Sepharose . Form HS1 enzyme was 30-40% pure and form HS2 enzyme 60% with regard to protein contents of the preparations . Form HS2 enzyme was generated from form HS1 enzyme on prolonged standing of enzyme preparations . The DNA polymerases were obtained as complexes of a 60-kDa protein associated with either a 135-kDa (HS1) or a 110-kDa (HS2) DNA-polymerizing polypeptide in a 1:1 molar stoichiometry . The biochemical function of the 60-kDa protein remained unknown . The complexes tended to dissociate during gradient centrifugation and during partition chromatography as well as during polyacrylamide gradient gel electrophoresis under nondenaturing conditions at high dilutions of samples . Both forms existed in plasmodia extracts, their proportions depending on several factors including those which promoted proteolysis . The DNA polymerases resembled eucaryotic DNA polymerase beta by several criteria and were functionally indistinguishable from each other . It is suggested that lower eucaryotes contain repair DNA polymerases, which are similar to those of eubacteria on a molecular mass basis.

Eur J Biochem, 1987 Mar 2, 163(2), 239 - 46
Structural analysis of 5S rRNA, 5S rRNA-protein complexes and ribosomes employing RNase H and d(GTTCGG); Lorenz S et al.; The hybridization of d(GTTCGG) to eubacterial 5S rRNAs, 5S rRNA-protein complexes, 70S ribosomes and 50S and 30S ribosomal subunits was investigated . This oligonucleotide, which may be considered to be an analogue of the T psi CG loop of tRNAs, was chosen in order to investigate a possible interaction between tRNAs with ribosomal components during protein synthesis . The hybridization was analysed by RNase H hydrolysis studies and, in the case of the ribosomes and ribosomal subunits, in addition with the radioactively labelled oligodeoxyribonucleotide in binding studies . The results obtained lead to the conclusion that nucleotides in loop c, i.e . positions 42-47, are available for oligonucleotide interaction in free Escherichia coli and Bacillus stearothermophilus 5S rRNAs and not available in the corresponding 5S rRNA-protein complexes . The 70S ribosomes and ribosomal subunits did not interact with the oligonucleotide . Under the assumption that d(GTTCGG) is an analogue of the T psi CG loop of tRNAs and in view of the results obtained, we conclude that in the unprogrammed ribosomes the T psi CG loop of tRNAs does not interact via standard Watson-Crick base pairs with the ribosomal 5S, 16S or 23S RNAs.

Mol Biol (Mosk), 1987 Mar-Apr, 21(2), 543 - 51
{The loss of CpG dinucleotides from DNA . I . Methylated and non-methylated genome compartments in eukaryotes with different levels of 5-methylcytosine in DNA}; Mazin AL et al.; The methylation of cytosine residues in CpG significantly increases the frequency of m5CpG----TpG transitions in DNA and CpG dinucleotides are eliminated from the genome (CpG-suppression) . In the millions of years of vertebrates evolution about 3 mol% of 5-methylcytosine have disappeared from their genome, i.e., 2-3-fold more than the amount persisting in the DNA of the now extant species . A computer analysis has been carried out of neighboring b.p . frequencies in more than 2500 sequenced genes of different species in the EMBL bank with an overall extension of over 3000 kb . It has been found that CpG methylated sites exhibit a highly irregular distribution pattern in the genome of eucaryotes . The majority of the vertebrate sequences (92%) bears the impress of a significant lack of CpG and an excess of TpG+CpA; therefore they may be referred to the genome methylated compartment . A group of genes has been discovered (about 8%) where CpG must have never been subjected to methylation . In invertebrates, such a nonmethylated compartment makes up 59% of the genome and in eubacteria--85% . A brief list of genes, belonging to the methylated and the non-methylated compartments of the invertebrate and yeast genome, is given . It has been established that the mean value of CpG-suppression in genes is directly proportional to the methylation level of total DNA in different species.

Appl Environ Microbiol, 1987 Mar, 53(3), 471 - 6
Additional characteristics of one-carbon-compound utilization by Eubacterium limosum and Acetobacterium woodii; Sharak Genthner BR et al.; Growth characteristics of Eubacterium limosum and Acetobacterium woodii during one-carbon-compound utilization were investigated . E . limosum RF grew with formate as the sole energy source . Formate also replaced a requirement for CO2 during growth with methanol . Growth with methanol required either rumen fluid, yeast extract, or acetate, but their effects were not additive . Cultures were adapted to grow in concentrations of methanol of up to 494 mM . Growth occurred with methanol in the presence of elevated levels of Na+ (576 mM) . The pH optima for growth with methanol, H2-CO2, and carbon monoxide were similar (7.0 to 7.2) . Growth occurred with glucose at a pH of 4.7, but not at 4.0 . The apparent Km values for methanol and hydrogen were 2.7 and 0.34 mM, respectively . The apparent Vmax values for methanol and hydrogen were 1.7 and 0.11 mumol/mg of protein X min-1, respectively . The Ks value for CO was estimated to be less than 75 microM . Cellular growth yields were 70.5, 7.1, 3.38, and 0.84 g (dry weight) per mol utilized for glucose, methanol, CO, and hydrogen (in H2-CO2), respectively . E . limosum was also able to grow with methoxylated aromatic compounds as energy sources . Glucose apparently repressed the ability of E . limosum to use methanol, hydrogen, or isoleucine but not CO . Growth with mixtures of methanol, H2, CO, or isoleucine was not diauxic . The results, especially the relatively high apparent Km values for H2 and methanol, may indicate why E . limosum does not usually compete with rumen methanogens for these energy sources.(ABSTRACT TRUNCATED AT 250 WORDS)

J Gen Microbiol, 1987 Feb, 133 ( Pt 2), 275 - 82
Systematic analysis of the long-chain components of Eubacterium lentum; Verhulst A et al.; The cellular long-chain component patterns of 33 strains of Eubacterium lentum were determined by gas chromatography . Two main types of long-chain component patterns were distinguished . The first (26 strains) was characterized by saturated branched-chain fatty acids (br14:0, br15:0, br16:0 and br17:0) . The second (7 strains) did not contain branched-chain fatty acids and was characterized by saturated straight-chain fatty acids (11:0, 12:0, 14:0 and 16:0) . Both types contained fatty aldehydes and their respective dimethyl acetals (14ald and 14dma, 16ald and 16dma) . br16dma was only found in the first type . The G + C content of the DNA (Tm) of the 33 strains varied between 63.7 and 69.1 mol % . Canonical correlation analysis distinguished three subtypes within the first main type.

Nucleic Acids Res, 1987 Jan 12, 15(1), 161 - 79
Evolutionary changes in the higher order structure of the ribosomal 5S RNA; McDougall J et al.; Comparative studies have been undertaken on the higher order structure of ribosomal 5S RNAs from diverse origins . Competitive reassociation studies show that 5S RNA from either a eukaryote or archaebacterium will form a stable ribonucleoprotein complex with the yeast ribosomal 5S RNA binding protein (YL3); in contrast, eubacterial RNAs will not compete in a similar fashion . Partial S1 ribonuclease digestion and ethylnitrosourea reactivity were used to probe the structural differences suggested by the reconstitution experiments . The results indicate a more compact higher order structure in eukaryotic 5S RNAs as compared to eubacteria and suggest that the archaebacterial 5S RNA contains features which are common to either group . The potential significance of these results with respect to a generalized model for the tertiary structure of the ribosomal 5S RNA and to the heterogeneity in the protein components of 5S RNA-protein complexes are discussed.

Proc Natl Acad Sci U S A, 1987 Jan, 84(1), 166 - 9
The guanine and cytosine content of genomic DNA and bacterial evolution; Muto A et al.; The genomic guanine and cytosine (G + C) content of eubacteria is related to their phylogeny . The G + C content of various parts of the genome (protein genes, stable RNA genes, and spacers) reveals a positive linear correlation with the G + C content of their genomic DNA . However, the plotted correlation slopes differ among various parts of the genome or among the first, second, and third positions of the codons depending on their functional importance . Facts suggest that biased mutation pressure, called A X T/G X C pressure, has affected whole DNA during evolution so as to determine the genomic G + C content in a given bacterium . The role of A X T/G X C pressure in diversification of bacterial DNA sequences and codon usage patterns is discussed in the perspective of the neutral theory of molecular evolution.

Cold Spring Harb Symp Quant Biol, 1987, 52, 805 - 24
The origin of cells: a symbiosis between genes, catalysts, and membranes; Cavalier-Smith T; The gap between early molecular evolution and the origin of the first cell may have been bridged by a photoheterotrophic obcell, consisting of genes and ribosomes attached to the outer surface of a phospholipid vesicle containing a light-driven proton pump and a proton-driven pyrophosphate synthase . I argue that the obcell was the substratum for the origin of DNA replication; DNA segregation by the growth and division of the peptidoglycan murein; periplasmic solute-binding proteins; bioenergetics, including the F0F1 proton-driven ATP synthase; active transport of calcium; and facilitated diffusion of nutrients across membranes, and that it played the major role in the replacement of ribozymes by protein catalysts . Curved growth of the peptidoglycan and a mutation causing septum formation produced the first true cell . Evolution of porins, sodium extrusion and potassium import, conversion of the facilitated diffusion proteins to active pumps, and the evolution of intermediary metabolism, carbon and nitrogen fixation, and of substrate level phosphorylation, completed the origin of the first negibacterial eubacterium, from which all other cells evolved, and from which they have inherited most of their major catalytic properties--with the notable exceptions of reverse transcriptase, RNA splicing, and methanogenesis, all of which I believe evolved very much later.

Cold Spring Harb Symp Quant Biol, 1987, 52, 769 - 76
Evolution of anticodons: variations in the genetic code; Jukes TH et al.; Clues to evolution of the genetic code can be found by comparing usage of anticodons in various organisms and organelles . GC content of DNA varies, as a result of directional mutation pressure (AT/GC pressure), especially in bacteria . Low GC in Mycoplasma is accompanied by use of UGA for tryptophan and, in ciliated protozoa, by use of UAA and UAG for glutamine . These are examples of "stop codon capture," which has been preceded by duplication of tRNA genes followed by nucleotide substitutions in their sequences, including mutational changes in their anticodons . Evolutionary changes in the code may have resulted from disappearance of codons and anticodons resulting from GC pressure and from their reappearance when the direction of the pressure was reversed . In this manner, codon UGA and anticodon UCA for tryptophan could have disappeared under GC pressure and reappeared in Mycoplasma under AT pressure . Stop codon UGA may have been the third of the three stop codons to appear, originating from mutations in UAA . Changes in the code are adaptive and nondeleterious . We propose that the number of anticodons has increased and that evolution continued until three existing forms of the universal code were produced: eukaryotic, eubacterial, and the code for halobacteria and methanococci . These three codes are distinguished from each other by their anticodon pattern . The eukaryotic code contains eight INN (ANN) anticodons that have replaced GNN anticodons as a result of AT pressure . Mitochondrial and chloroplast codes have evolved from the eubacterial code through genomic economization and AT pressure, leading to losses of GNN and CNN anticodons.(ABSTRACT TRUNCATED AT 250 WORDS)

Arch Microbiol, 1987, 149(2), 136 - 41
Methanogenic degradation of acetone by an enrichment culture; Platen H et al.; An anaerobic enrichment culture degraded 1 mol of acetone to 2 mol of methane and 1 mol of carbon dioxide . Two microorganisms were involved in this process, a filament-forming rod similar to Methanothrix sp . and an unknown rod with round to slightly pointed ends . Both organisms formed aggregates up to 300 micron in diameter . No fluorescing bacteria were observed indicating that hydrogen or formate-utilizing methanogens are not involved in this process . Acetate was utilized in this culture by the Methanothrix sp . Inhibition of methanogenesis by bromoethanesulfonic acid or acetylene decreased the acetone degradation rate drastically and led to the formation of 2 mol acetate per mol of acetone . Streptomycin completely inhibited acetone degradation, and neither acetate nor methane was formed . 14CO2 was incorporated exclusively into the C-1 atom of acetate indicating that acetone is degraded via carboxylation to an acetoacetate residue . It is concluded that acetone is degraded by a coculture of an eubacterium and an acetate-utilizing methanogen and that acetate is the only intermediate transferred between both . The energetical problems of the eubacterium converting acetone to acetate are discussed.

Ann N Y Acad Sci, 1987, 503, 125 - 39
Structural diversity of eukaryotic small subunit ribosomal RNAs . Evolutionary implications; Sogin ML et al.; The phylogenetic diversity of the eukaryotic kingdom was assessed by comparing the structural and evolutionary diversity of 18-20S ribosomal RNA genes . The coding regions for cytoplasmic small subunit ribosomal RNA genes vary in length from 1753 to 2305 nucleotides, and they appear to be evolutionary mosaics in which highly and partially conserved sequences are interspersed among regions that display very high rates of genetic drift . Structural similarities between these gene sequences were used to establish a phylogenetic framework for the eukaryotes . The extent of sequence variation within the eukaryotes exceeds that displayed within the eubacterial or archaebacterial lines of descent . The kinetoplastids and euglenoids represent the earliest branchings among the eukaryotes . These branchings preceded the divergence of lineages leading to the slime molds and apicomplexans and far antedate a radiative period that gave rise to the plants, animals, fungi, and other protists.

J Mol Evol, 1987, 26(4), 347 - 57
Characteristic views of prokaryotic 50S ribosomal subunits; Harauz G et al.; Multivariate statistical analysis and classification techniques are powerful tools in sorting noisy electron micrographs of single particles according to their principal features, enabling one to form average images with an enhanced signal-to-noise ratio and a better reproducible resolution . We apply this methodology here to determining the characteristic views of the large (50S) ribosomal subunits from the eubacterium Escherichia coli and the archaebacteria Methanococcus vannielii, Sulfolobus solfataricus, and Halobacterium marismortui . Average images were obtained of the subunit in the common crown and kidney projections, but views of the particle in orientations intermediate between these two extremes were also elucidated for all species . These averages show reproducible detail of up to 2.0 nm resolution, thus enabling the visualization and interspecies comparison of many structural features as a first step toward comparing the actual three-dimensional structures . Our results disprove evolutionary lineages recently postulated on the basis of electron microscopical images of ribosomal subunits.

J Mol Evol, 1987, 26(4), 341 - 6
Archetypical features in tRNA families; Nicoghosian K et al.; A compilation of known tRNA, and tRNA gene sequences from archaebacteria, eubacteria, and eukaryotes permits the construction of tRNA cloverleafs which show conserved structural elements for each tRNA family . Positions conserved across the three kingdoms are thought to represent archetypical features of tRNAs which preceded the divergence of these kingdoms.

J Mol Evol, 1987, 26(3), 226 - 51
Nonuniformity of nucleotide substitution rates in molecular evolution: computer simulation and analysis of 5S ribosomal RNA sequences; Manske CL et al.; The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed . Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs . New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates . These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities . It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA . A previous method (Farris et al . 1970; Klotz et al . 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites . Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution . Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.

J Mol Evol, 1987, 26(1-2), 74 - 86
Evolution in bacteria: evidence for a universal substitution rate in cellular genomes; Ochman H et al.; This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts . One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree . According to this approach, Salmonella typhimurium and Escherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago . The median extent of divergence between S . typhimurium and E . coli at synonymous sites for 21 kilobases of protein-coding DNA is 100% . This implies a silent substitution rate of 0.7-0.8%/Myr--a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants . Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions . The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants . Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes . For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence of S . typhimurium and E . coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons . Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate . By contrast, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.

J Mol Evol, 1987, 26(1-2), 59 - 73
Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics; Lake JA; Operator metrics are explicitly designed to measure evolutionary distances from nucleic acid sequences when substitution rates differ greatly among the organisms being compared, or when substitutions have been extensive . Unlike lengths calculated by the distance matrix and parsimony methods, in which substitutions in one branch of a tree can alter the measured length of another branch, lengths determined by operator metrics are not affected by substitutions outside the branch . In the method, lengths (operator metrics) corresponding to each of the branches of an unrooted tree are calculated . The metric length of a branch reconstructs the number of (transversion) differences between sequences at a tip and a node (or between nodes) of a tree . The theory is general and is fundamentally independent of differences in substitution rates among the organisms being compared . Mathematically, the independence has been obtained because the metrics are eigenvectors of fundamental equations which describe the evolution of all unrooted trees . Even under conditions when both the distance matrix method or a simple parismony length method are shown to indicate lengths that are an order of magnitude too large or too small, the operator metrics are accurate . Examples, using data calculated with evolutionary rates and branchings designed to confuse the measurement of branch lengths and to camouflage the topology of the true tree, demonstrate the validity of operator metrics . The method is robust . Operator metric distances are easy to calculate, can be extended to any number of taxa, and provide a statistical estimate of their variances . The utility of the method is demonstrated by using it to analyze the origins and evolution of chloroplasts, mitochondria, and eubacteria.

J Mol Evol, 1987, 25(4), 343 - 50
On the evolution of ribosomal RNA; Clark CG; Despite the availability of a rapidly growing ribosomal RNA database that now includes organisms in all three primary lines of descent (eubacteria, archaebacteria, and eukaryotes), theoretical treatment of the evolution of the ribosomal RNAs has lagged behind that of the protein genes . In this paper a theory is developed that applies current views of protein gene evolution to the ribosomal RNAs . The major topics addressed are the variability in size, gene arrangement, and processing of the rRNAs among the three primary lines of descent . Among the conclusions are that the rRNAs of eukaryotes retain some primitive features that were probably present in the rRNAs of the earliest cell (the progenote) and that the genes coding for the three major rRNA species were probably originally unlinked.

J Mol Evol, 1987, 25(3), 255 - 60
Structure of 5S rRNA in actinomycetes and relatives and evolution of eubacteria; Dams E et al.; The primary structure of 5S ribosomal RNA has been determined in five species belonging to the genus Mycobacterium and in Micrococcus luteus . The sequences of 5S RNAs from Actinomycetes and relatives point to the existence in this taxon of a bulge on the helix that joins the termini of the molecule . An attempt was made to reconstruct bacterial evolution from a sequence dissimilarity matrix based on 142 eubacterial 5S RNA sequences and corrected for multiple mutation . The algorithm is based on weighted pairwise clustering, and incorporates a correction for divergent mutation rates, as derived by comparison of sequence dissimilarities with an external reference group of eukaryotic 5S RNAs . The resulting tree is compared with the eubacterial phylogeny built on 16S rRNA catalog comparison . The bacteria for which the 5S RNA sequence is known form a number of clusters also discernible in the 16S rRNA phylogeny . However, the branching pattern leading to these clusters shows some notable discrepancies with the aforementioned phylogeny.

J Mol Evol, 1987, 25(2), 168 - 83
A view of early cellular evolution; Mikelsaar R; Some recent puzzling data on mitochondria put in question their place on the phylogenetic tree . A hypothesis, the archigenetic hypothesis, is presented, which generally agrees with Woese-Fox's concept of the common origin of eubacteria, archaebacteria, and eukaryotic hosts . However, for the first time, a case is made for the evolution of mitochondria from the ancient predecessors of pro- and eukaryotes (protobionts), not from eubacteria . Animal, fungal, and plant mitochondria are considered to be endosymbionts derived from independent free-living cells (mitobionts), which, having arisen at different developmental stages of protobionts, retained some of their ancient primitive features of the genetic code and the transcription-translation systems . The molecular-biological, bioenergetic, and paleontological aspects of this new concept of cellular evolution are discussed.

Ann N Y Acad Sci, 1987, 503, 103 - 24
Evolution of organisms and organelles as studied by comparative computer and biochemical analyses of ribosomal 5S RNA structure; Erdmann VA et al.; The results documented in this publication demonstrate that for evolutionary studies the ribosomal 5S rRNA is a suitable object for such an investigation and that as many methods as possible should be consulted . In this study the results of biochemical and chemical experiments were combined with those of computer sequence analyses, and they revealed that these methods complement each other nicely . We are currently at a state at which we are able to well define the secondary structures of the 5S rRNAs for eubacteria, organelles, archaebacteria, and eukaryotes and we are even able to propose a secondary structure for a Ur-5S rRNA . It is also clear that in the future the present studies should be continued and extended in such a way that the tertiary structures of these molecules will become known.

J Antibiot (Tokyo), 1987 Jan, 40(1), 7 - 13
The sorangicins, novel and powerful inhibitors of eubacterial RNA polymerase isolated from myxobacteria; Irschik H et al.; A new antibiotic, sorangicin, was isolated from the culture supernatant of the myxobacterium, Sorangium (Polyangium) cellulosum strain So cel2 . It is a macrocyclic lactone carbonic acid and is produced in two structural variants, sorangicins A and B . In addition small quantities of the respective glycosides, sorangiosids A and B, may be found . The antibiotic acts mainly against Gram-positive bacteria, including myocobacteria, with MIC values between 0.01 and 0.1 microgram/ml, but at higher concentrations (MIC 3 approximately 30 micrograms/ml) Gram-negatives are also inhibited . Yeasts and molds are completely resistant . The new antibiotic is a specific inhibitor of eubacterial RNA polymerase which it blocks, however, only if added before RNA polymerization has started.

Biochimie, 1987 Jan, 69(1), 11 - 23
Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure; Michot B et al.; All large rRNAs possess a common core of secondary structure . However, large variations in the size of the molecule have arisen during evolution, which are accommodated over a dozen rapidly evolving domains . Most of the enlargement of the eukaryotic molecules (as compared to prokaryotes) is in fact restricted over only two of these divergent domains, which are dramatically expanded in vertebrates . We have derived secondary structure models for these two domains through a systematic comparison of all the pro- and eukaryotic sequences published so far . Within each of these domains, a subset of secondary structure elements which are specific to eukaryotes is detected . Archaebacterial-specific secondary structures can also be identified which appear to be maintained through a strong selective constraint . The relative preservation of such group-specific structures raises the issue of their potential involvement in some diversification of ribosomal functions among the three fundamental phylogenetic groups, eubacteria, archaebacteria and eukaryotes . We also show that eukaryotic ribosomal RNAs are subjected, over their entire length, to a unique type of compositional constraint which may largely differ among the major eukaryotic taxa.

Gene, 1987, 58(2-3), 229 - 41
Nucleotide sequence analysis reveals similarities between proteins determining methylenomycin A resistance in Streptomyces and tetracycline resistance in eubacteria; Neal RJ et al.; Previous studies had localised the gene (mmr) for resistance to methylenomycin A (Mm) to a 2.5-kb PstI fragment in the middle of a cluster of Mm biosynthetic genes from the Streptomyces coelicolor plasmid SCP1 . In this paper, the gene has been more precisely located by sub-cloning, and the nucleotide sequence of the whole fragment has been determined . The predicted mmr-specified protein (Mr 49238) would be hydrophobic, with some homology at the amino acid level to tetracycline-resistance proteins from both Gram-positive and Gram-negative bacteria . Comparisons of hydropathy plots of the amino acid sequences reinforces the idea that the proteins are similar . It is suggested that Mm resistance may be conferred by a membrane protein, perhaps controlling efflux of the antibiotic . No significant homology was detected by hybridisation analysis between mmr and a cloned oxytetracycline (OTc)-resistance gene (tetB) of the OTc producer Streptomyces rimosus, and no cross-resistance was conferred by these genes . Sequences on both sides of mmr appear to encode proteins . The direction of translation in each case would be opposite to that of mmr translation . This suggests that mmr is transcribed as a monocistronic mRNA from a bidirectional promoter . An extensive inverted repeat sequence between the stop codons of mmr and the converging gene may function as a bidirectional transcription terminator.

NCI Monogr, 1987, (4), 3 - 6
DNA topoisomerases: from a laboratory curiosity to a subject in cancer chemotherapy; Wang JC; Recent studies indicate that the type II DNA topoisomerases of eubacteria and eukaryotes are structurally and evolutionarily related: the amino and carboxyl half of the single polypeptide eukaryotic enzyme are homologous to the B and A subunit of bacterial gyrase, respectively . The active site tyrosine of Escherichia coli DNA gyrase that becomes covalently linked to DNA during catalysis has been identified to be Tyr 122 of the A subunit . From a comparison of nucleotide sequences of the structural genes encoding several other type II topoisomerases, the active site tyrosine in these enzymes can be deduced . For the type I DNA topoisomerases, although the bacterial enzyme and the eukaryotic enzyme are very different in terms of their primary structures, substrate preferences, and mechanisms, it has been shown that the yeast DNA topoisomerase I can substitute for E . coli DNA topoisomerase I in vivo . The unique features of DNA topoisomerases as targets of antibiotics and anti-tumor drugs are discussed.

Eur J Biochem, 1986 Dec 15, 161(3), 681 - 7
Primary structure of the chromosomal protein HMb from the archaebacteria Methanosarcina barkeri; Laine B et al.; The amino acid sequence of the protein HMb, a protein of 93 residues (Mr 10757) which represents the major acid-soluble component of the Methanosarcina barkeri nucleoprotein complex, has been established from automated sequence analysis of the protein and from structural data provided by peptides derived from cleavage of the protein at aspartic acid, arginine and methionine residues . The protein HMb is mainly characterized by a high amount of charged residues (15% of acidic residues and 26.8% of basic residues) which are distributed all along the polypeptide chain . The amino acid sequence of the protein HMb is not homologous to any eubacterial, archaebacterial or eukaryotic chromosomal proteins known up to now.

Mol Gen Genet, 1986 Dec, 205(3), 434 - 41
Analysis of transcription and processing signals of the 16S-23S rRNA operon of Mycoplasma hyopneumoniae; Taschke C et al.; The 16S and 23S rRNA genes of Mycoplasma hyopneumoniae are closely spaced in one operon . The two genes are separated by a spacer region of 500 bp which shows no sequence homology to bacterial tRNA genes . Within this operon seven 5' and five 3' ends of various rRNA species were mapped and the corresponding DNA was sequenced . The results are consistent with the following model for synthesis of rRNAs: Transcription of the operon is initiated from either of two tandemly arranged promoters leading to a large precursor RNA consisting of both 16S and 23S rRNAs . This primary transcript is first cleaved within stem structures surrounding the two rRNAs to yield premature 16S and 23S rRNAs . By further processing events the mature 5' and 3' ends are generated . The promoter sequences of this operon differ from those of other eubacterial promoters in lacking the typical -35 region . The putative termination site at the 3' end of the operon is reminiscent of rho-independent terminators in Escherichia coli.

J Bacteriol, 1986 Dec, 168(3), 1147 - 54
Comparative action of glyphosate as a trigger of energy drain in eubacteria; Fischer RS et al.; Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa, each possessing a 5-enolpyruvylshikimate 3-phosphate synthase that is sensitive to inhibition by glyphosate {N-(phosphonomethyl)glycine}, provide a good cross-section of organisms exemplifying the biochemical diversity of the aromatic pathway targeted by this potent antimicrobial compound . The pattern of growth inhibition, the alteration in levels of aromatic-pathway enzymes, and the accumulation of early-pathway metabolites after the addition of glyphosate were distinctive for each organism . Substantial intracellular shikimate-3-phosphate accumulated in response to glyphosate treatment in all three organisms . Both E . coli and P . aeruginosa, but not B . subtilis, accumulated near-millimolar levels of shikimate-3-phosphate in the culture medium . Intracellular backup of common-pathway precursors of shikimate-3-phosphate was substantial in B . subtilis, moderate in P . aeruginosa, and not detectable in E . coli . The full complement of aromatic amino acids prevented growth inhibition and metabolite accumulation in E . coli and P . aeruginosa where amino acid end products directly control early-pathway enzyme activity . In contrast, the initial prevention of growth inhibition in the presence of aromatic amino acids in B . subtilis was succeeded by progressively greater growth inhibition that correlated with rapid metabolite accumulation . In B . subtilis glyphosate can decrease prephenate concentrations sufficiently to uncouple the sequentially acting loops of feedback inhibition that ordinarily link end product excess to feedback inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase by prephenate . The consequential unrestrained entry is an energy-rich substrates into the aromatic pathway, even in the presence of aromatic amino acid end products, is an energy drain that potentially accounts for the inability of end products to fully reverse glyphosate inhibition in B . subtilis . Even in E . coli after glyphosate inhibition and metabolite accumulation were allowed to become fully established, a transient period where end products were capable of only partial reversal of growth inhibition occurred . The distinctive metabolism produced by dissimilation of different carbon sources also profound effects upon glyphosate sensitivity.

Biochem Biophys Res Commun, 1986 Oct 15, 140(1), 38 - 42
A novel sulfotransferase sulfates tyrosine-containing peptides and proteins; Kobashi K et al.; The novel sulfotransferase (M.W . 315 kDa) obtained from Eubacterium A-44 catalyzed the sulfation of tyrosine residues of peptides and proteins such as kyotorphin, enkephalin, cholecystokinin-8 (non-sulfated form), trypsin inhibitor and insulin . Also, the enzyme sulfated tyrosine residues of protein fractions purified from Eubacterium A-44.

J Biol Chem, 1986 Oct 5, 261(28), 12942 - 7
Cloning, expression, and nucleotide sequence of the formate dehydrogenase genes from Methanobacterium formicicum; Shuber AP et al.; The genes for the two subunits of the formate dehydrogenase from Methanobacterium formicicum were cloned and their sequences determined . When expressed in Escherichia coli, two proteins were produced which had the appropriate mobility on an SDS gel for the two subunits of formate dehydrogenase and cross-reacted with antibodies raised to purified formate dehydrogenase . The genes for the two formate dehydrogenase subunits overlap by 1 base pair and are preceded by DNA sequences similar to both eubacterial and archaebacterial promoters and ribosome-binding sites . The amino acid sequences deduced from the DNA sequence were analyzed, and the arrangement of putative iron-sulfur centers is discussed.

J Periodontol, 1986 Oct, 57(10), 625 - 31
Systemic antibody response of clinically characterized patients with antigens of Eubacterium brachy initially and following periodontal therapy; Vincent JW et al.; Eubacterium brachy, a gram-positive anaerobic rod, has been implicated by cultural studies to be associated with the microflora of periodontal diseases . Serum samples from 184 clinically characterized patients were evaluated in a standardized enzyme-linked immunosorbent assay (ELISA) for reactivity to E . brachy antigens . Sera from clinically healthy subjects (HS) served as controls . Sera from rapidly progressive periodontitis (RP) patients demonstrated significantly greater reactivity by ELISA than did HS when reactivity with E . brachy antigens was determined (P less than 0.05) . Juvenile periodontitis (JP) and adult periodontitis (AP) patients did not differ in reactivity by ELISA from HS (P greater than 0.05) . Three to 4 years following successful periodontal therapy, reactivity was not significantly altered in any patient group (P greater than 0.05) . The possible significance of these findings and the importance of an extracellular antigen of E . brachy in the immunopathology of periodontal diseases are discussed.

Int Dent J, 1986 Sep, 36(3), 153 - 61
Current understanding of the aetiology and progression of periodontal disease; Page RC; There is overwhelming evidence that bacteria cause periodontitis and that they do so by extending apically along the surfaces of the tooth roots and creating pockets . A very complex mixture of microbial species, mostly although not exclusively gram-negative, anaerobic, and motile, is involved . Infection probably occurs in a progressive and sequential manner . The bacteria involved include various species of Bacteroides, Actinobacillus, Eikenella, Fusobacterium, Capnocytophaga, and Eubacterium . Local oral conditions such as tooth position play an aetiologic role by affecting plaque accumulation and retention . Host defence factors, particularly the phagocytic cells and the immune system, play a determinative role in the aetiology by monitoring, controlling, and regulating microbial colonization and infection . These diseases begin as an acute inflammation of the marginal gingiva, and they progress through orderly stages to the formation of a gingival pocket . Transition from gingivitis to periodontitis is not well-understood, but it probably involves colonization by additional microbial species or invasion of the periodontal tissue by species already present . Progression of periodontal destruction is episodic, possibly as a consequence of successful host defence . In most patients, periodontal destruction occurs more infrequently than previously suspected . In both treated and untreated patients, a small subgroup accounts for most of the disease activity . The most important problem we now face is to develop diagnostic methods to identify individuals in this subgroup and devise ways to prevent and control their diseases.

J Bacteriol, 1986 Sep, 167(3), 837 - 41
Characterization and purification of the membrane-bound ATPase of the archaebacterium Methanosarcina barkeri; Inatomi K; Membrane-bound ATPase was found in membranes of the archaebacterium Methanosarcina barkeri . The ATPase activity required divalent cations, Mg2+ or Mn2+, and maximum activity was obtained at pH 5.2 . The activity was specifically stimulated by HSO3- with a shift of optimal pH to 5.8, and N,N'-dicyclohexylcarbodiimide inhibited ATP hydrolysis . The enzyme could be solubilized from membranes by incubation in 1 mM Tris-maleate buffer (pH 6.9) containing 0.5 mM EDTA . The solubilized ATPase was purified by DEAE-Sepharose and Sephacryl S-300 chromatography . The molecular weight of the purified enzyme was estimated to be 420,000 by gel filtration through Sephacryl S-300 . Polyacrylamide gel electrophoresis in sodium dodecyl sulfate revealed two classes of subunit, Mr 62,000 (alpha) and 49,000 (beta) associated in the molar ratio 1:1 . These results suggest that the ATPase of M . barkeri is similar to the F0F1 type ATPase found in many eubacteria.

J Bacteriol, 1986 Aug, 167(2), 570 - 4
Eubacterial origin of chlamydiae; Weisburg WG et al.; The sequence of the 16S rRNA gene from Chlamydia psittaci was determined . Comparison of this sequence with other 16S rRNA sequences showed the organism to be eubacterial . The organism represents a hitherto unrecognized major eubacterial group . However, this group may be peripherally related to the planctomyces and relatives . Although these two groups seem to have very little in common phenotypically (they have been studied in very different ways), cell walls in both cases contain no peptidoglycan.

J Clin Periodontol, 1986 Aug, 13(7), 646 - 50
Serum antibody levels to 4 periodontal pathogens remain unaltered after mechanical therapy of juvenile periodontitis; Sandholm L et al.; Serum antibody titers to Actinobacillus actinomycetemcomitans (A.a.) Y4, Bacteroides gingivalis, Capnocytophaga ochracea and Eubacterium saburreum were determined with an enzyme immunoassay in 12 patients with juvenile periodontitis (JP) at the beginning of treatment and 16 to 32 months later after clinically successful mechanical therapy without antibiotics . The values were compared to corresponding data obtained from 26 age- and sex-matched individuals with a healthy periodontium . 6 JP patients had significantly increased levels of IgG and IgA antibodies to A.a . and 2 patients had increased IgG and IgA antibodies to C.ochracea . About 75% of the JP patients had a level of IgG antibody to B.gingivalis and E.saburreum which was more than one SD lower than the mean of the healthy controls, and in the IgA class 80-100% had such decreased levels of antibodies to these bacteria . In the IgM class, the JP patients by and large had normal levels of antibodies to the 4 bacteria . After treatment, antibodies to A.a . had decreased in only 3 patients, but the levels were still significantly higher than in healthy controls . Minimal alterations were observed in the levels of antibodies to B.gingivalis, C.ochracea and E.saburreum after treatment.

Mol Cell Biol, 1986 Aug, 6(8), 3010 - 3
The ubiquitous potential Z-forming sequence of eucaryotes, (dT-dG)n . (dC-dA)n, is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria; Gross DS et al.; The potential Z-forming sequence (dT-dG)n . (dC-dA)n is an abundant, interspersed repeat element that is ubiquitous in eucaryotic nuclear genomes . We report that in contrast to eucaryotic nuclear DNA, the genomes of eubacteria, archaebacteria, and mitochondria lack this sequence, since even a single tract of greater than or equal to 14 base pairs in length is not detectable through either hybridization or sequence analysis . Interestingly, the phylogenetic distribution of the (dT-dG)n . (dC-dA)n repeat exhibits a striking parallel to that of (dT-dC)n . (dG-dA)n, but not to other homocopolymeric sequences such as (dC-dG)n . (dC-dG)n or (dT-dA)n . (dT-dA)n.

Biochim Biophys Acta, 1986 Jul 25, 872(1-2), 33 - 41
Purification, characterization and reaction mechanism of novel arylsulfotransferase obtained from an anaerobic bacterium of human intestine; Kim DH et al.; A novel type of arylsulfotransferase was purified from Eubacterium A-44, one of the predominant bacteria of human intestine . The enzyme (Mr 315 000) was composed of four identical subunits (Mr 80 000) whose N-terminal amino acids were arginine . pI and optimal pH of the enzyme were 3.9 and 8-9, respectively . The apparent Km for p-nitrophenylsulfate using tyramine as an acceptor substrate and that for tyramine using p-nitrophenylsulfate as a donor substrate were determined to be 0.104 mM and 3.5 mM, respectively . The reaction mechanism of the enzyme was proposed as follows: a donor substrate, p-nitrophenyl {35S}sulfate, combines a histidine residue of the enzyme active site with concomitant release of a phenolic compound, p-nitrophenol . The sulfate group of the histidine residue transfers to a tyrosine group, and then to an acceptor with the binding of another donor to the histidine residue.

J Gen Microbiol, 1986 Jul, 132 ( Pt 7), 1939 - 49
Purification and partial characterization of DNA-dependent RNA polymerase from Rhodomicrobium vannielii; Scott NW et al.; DNA-dependent RNA polymerase has been isolated from Rhodomicrobium vannielii . Like those from other eubacteria, the enzyme contained four subunits: beta and beta prime (Mr 155,000), alpha (Mr 38,000), and sigma (Mr 98,000) . Analysis by isoelectric focussing showed that both alpha and sigma had several forms with different isoelectric pH values . The enzyme was sensitive to rifampicin (5 ng rifampicin ml-1 gave 50% inhibition) and capable of specific promoter selection with DNA from R . vannielii, calf thymus and phage T7D111.

Mol Gen Genet, 1986 Jul, 204(1), 133 - 40
Conservation of primary structure in the hisI gene of the archaebacterium, Methanococcus vannielii, the eubacterium Escherichia coli, and the eucaryote Saccharomyces cerevisiae; Beckler GS et al.; A 2.7 kilobase pair (Kb) fragment of DNA, which complements mutations in the hisI locus of Escherichia coli, has been cloned and sequenced from the genome of the methanogenic archaebacterium Methanococcus vannielii . The cloned DNA directs the synthesis of three polypeptides, with molecular weights of 71,000, 29,000 and 15,600 in minicells of E . coli . Subcloning and mutagenesis demonstrates that hisI complementation results from the activity of the 15,600 molecular weight polypeptide . The primary structure of this archaebacterial gene and its gene product have been compared with the functionally equivalent gene and protein from the eubacterium E . coli (hisI) (Chiariotti et al . 1986) and from the eucaryote Saccharomyces cerevisiae (his4A) (Donahue et al . 1982) . The DNA sequences of the archaebacterial and eubacterial genes are 40% homologous, the archaebacterial and eucaryotic DNA sequences are 47% homologous and, as previously reported (Bruni et al . 1986) the eubacterial and eucaryotic DNA sequences are 45% homologous . In E . coli the hisI locus is part of a bifunctional gene (hisI/E) within the single his operon . In S . cerevisiae the his4A locus is part of a multifunctional gene (his4) which encodes a protein with at least four enzymatic activities . The his genes of S . cerevisiae do not form an operon and are not physically linked . The M . vannielii hisI gene does not appear to be part of a multifunctional DNA sequence and, although it does appear to be within an operon, the open reading frames (ORFs) 5' and 3' to the M . vannielii hisI gene are not related to any published his sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

Appl Environ Microbiol, 1986 Jun, 51(6), 1300 - 3
Reduction of digoxin to 20R-dihydrodigoxin by cultures of Eubacterium lentum; Robertson LW et al.; The anaerobic bacterium Eubacterium lentum, a common constituent of the intestinal microflora, inactivates digoxin by reducing the unsaturated lactone ring . Reduction of the cardiac glycoside by growing cultures of E . lentum ATCC 25559 proceeded in a stereospecific manner, with the 20R-dihydrodigoxin constituting more than 99% of the product formed . This is in contrast to the 3:1 ratio of 20R and 20S epimers formed in the chemical catalytic hydrogenation . Formation of the reduced glycosides proceeded quantitatively when an overall concentration of 10 micrograms/ml was added to the cultures . E . lentum did not hydrolyze the digitoxose sugars from C-3 of the parent glycoside . However, the synthetically prepared sugar-hydrolyzed metabolites (digoxigenin, digoxigenin monodigitoxoside, and digoxigenin bisdigitoxoside) were reduced to the corresponding dihydro metabolites . Repetition of the experiments with a feces sample from a volunteer who was known to be a converter of digoxin to dihydrodigoxin gave results identical to those obtained with pure E . lentum cultures.

J Bacteriol, 1986 Jun, 166(3), 824 - 8
Probable insensitivity of mollicutes to rifampin and characterization of spiroplasmal DNA-dependent RNA polymerase; Gadeau AP et al.; The effect of rifampin on five mollicutes (Spiroplasma citri, Spiroplasma melliferum, Spiroplasma apis, Acholeplasma laidlawii, and Mycoplasma mycoides) was compared with that on Escherichia coli . We found that, in contrast to wild-type E . coli, mollicutes were insensitive to rifampin . DNA-dependent RNA polymerases from S . melliferum and S . apis were purified to the stage where the enzymes were dependent on the addition of exogenous templates for activity . The enzymes were then tested for their sensitivity to rifampin . Spiroplasmal enzymes were at least 1,000 times less sensitive to rifampin than the corresponding E . coli enzyme . This result provides a molecular basis for the resistance of mollicutes to rifampin . The RNA polymerase of S . melliferum was further purified and its subunit composition was investigated . The RNA polymerase has one small and two large subunits . The structure of S . melliferum RNA polymerase therefore resembles that of the eubacterial enzymes in spite of its insensitivity to rifampin.

J Otolaryngol, 1986 Jun, 15(3), 193 - 5
Fatal frontal sinusitis due to Neisseria sicca and Eubacterium lentum; Moon T et al.; Infectious sinusitis may on occasion be associated with meningitis, subdural empyema, epidural empyema, brain abscess, or osteomyelitis . We report a 29-year-old male patient with frontal sinusitis who developed all of these intracranial complications due to two previously unreported causative organisms, Neisseria sicca and Eubacterium lentum . The fulminant and fatal course resulting from locally invasive disease underscores the importance of early diagnosis and proper treatment of these complications . Possible exacerbating factors in this patient were sickle cell disease and immune compromise due to intravenous drug abuse.

J Biol Chem, 1986 Apr 15, 261(11), 5187 - 93
A discontinuous small subunit ribosomal RNA in Tetrahymena pyriformis mitochondria; Schnare MN et al.; We show here that in the mitochondria of Tetrahymena pyriformis, the small subunit (SSU) rRNA is discontinuous, being comprised of two separate components which we term "alpha" (a novel low molecular weight RNA, approximately equal to 200 nucleotides long) and "beta" (a previously described 14 S RNA) . The SSU alpha rRNA has been sequenced in its entirety; it represents the immediate 5'-terminal domain of conventional SSU rRNA . The sequences at the ends of the SSU beta rRNA have also been determined; they show that this molecule corresponds to the 3'-terminal 7/8 of conventional SSU rRNA . A 2.5-kilobase pair XbaI restriction fragment of T . pyriformis mitochondrial DNA which contains the SSU alpha and SSU beta rRNA genes was cloned and its complete nucleotide sequence was determined . This revealed that the genes encoding the two segments of SSU rRNA are separated by a 54-base pair (A + T)-rich spacer . The alpha and beta sequences can be fitted to a generalized secondary structure model for eubacterial 16 S rRNA, with the two RNA species associating through long range interactions to form base-paired regions characteristic of SSU rRNA . In this model, the spacer is situated in a region of pronounced primary and secondary structural variation among SSU rRNAs . The significance of these findings with respect to rRNA biosynthesis and processing and the possible evolutionary relationship between spacers and variable regions in rRNA genes is discussed.

Arch Biochem Biophys, 1986 Mar, 245(2), 537 - 9
A novel type of aryl sulfotransferase obtained from an anaerobic bacterium of human intestine; Kobashi K et al.; A novel type of aryl sulfotransferase is produced by an anaerobic bacterium of human intestine, Eubacterium A-44 . Aryl sulfotransferase separated from this bacterium differs from the sulfotransferase which uses 3'-phosphoadenosine 5'-phosphosulfate as a donor . The enzyme catalyzes stoichiometric transfer of a sulfate group from a phenol sulfate ester to other phenolic compounds, with strict specificity . The optimal pH and molecular weight were 8-9 and 315,000, respectively.

Proc Natl Acad Sci U S A, 1986 Mar, 83(5), 1383 - 7
Evolutionary diversity of eukaryotic small-subunit rRNA genes; Sogin ML et al.; The small-subunit rRNA gene sequences of the flagellated protists Euglena gracilis and Trypanosoma brucei were determined and compared to those of other eukaryotes . A phylogenetic tree was constructed in which the earliest branching among the eukaryotes is represented by E . gracilis . The E . gracilis divergence far antedates a period of massive evolutionary radiation that gave rise to the plants, animals, fungi, and certain groups of protists such as ciliates and the acanthamoebae . The genetic diversity in this collection of eukaryotes is seen to exceed that displayed within either the eubacterial or the archaebacterial lines of descent.

J Biol Chem, 1986 Feb 25, 261(6), 2912 - 7
Characterization of RNA-protein interactions in 7 S ribonucleoprotein particles from Xenopus laevis oocytes; Andersen J et al.; 5 S RNA interactions with transcription factor protein A (TFIIIA) in 7 S particles from Xenopus laevis oocytes (Xlo) have been characterized by the use of an in vitro RNA exchange assay . 32P-labeled Xlo 5 S RNA can rapidly be incorporated into 7 S particles by simple incubation of the RNA with intact particles . Incorporation of the labeled RNA during exchange reaches an equilibrium within 20 min at 20 degrees C . Labeled Xlo 5 S RNA already incorporated in 7 S particles can be chased out by an excess of unlabeled 5 S RNA . Nondenaturing gel electrophoresis of 7 S particle samples segregates several ribonucleoprotein particles containing TFIIIA and 5 S RNA . Time course experiments reveal incorporation of 32P-labeled 5 S RNA first in a higher molecular weight ribonucleoprotein particle before incorporation into the 7 S particle . In the exchange process, the integrity of the higher order structure of the RNA is essential for a recognition of the 5 S RNA by TFIIIA . Denatured Xlo 5 S RNA exchanges poorly in the presence of EDTA, but can exchange into the particle at a high level if sufficient divalent cations are present to allow the higher order structure of the RNA to reform . Xlo 5 S RNA fragments that have the 5' or 3' ends deleted past helix I markedly lose their ability to exchange . Heterologous eukaryotic and eubacterial 5 S RNAs can exchange into 7 S particles, although the eubacterial 5 S RNAs exchange at a low level.

J Bacteriol, 1986 Feb, 165(2), 638 - 43
Purification and characterization of glutamine synthetase from the archaebacterium Methanobacterium ivanovi; Bhatnagar L et al.; Glutamine synthetase (GS) was purified to electrophoretic homogeneity from the obligate anaerobic archaebacterium Methanobacterium ivanovi . The 130-fold-purified enzyme was obtained by heat treatment, ion-exchange chromatography, and gel filtration . Like all other eubacterial GSs known so far, the GS of M . ivanovi was found to be a dodecamer of about 600,000 daltons composed of a single type of subunit . The enzyme was stable at 63 degrees C for 10 min and was not sensitive to oxygen . The isoelectric point was 4.6, and the optimum pH of gamma-glutamyltransferase activity was 8.0 . The Km values for hydroxylamine, glutamine, and ADP in the transferase reaction were 6.8, 22.7, and 0.35 mM, respectively . L-Methionine-DL-sulfoximine strongly inhibited the activity . Like the GS from gram-positive bacteria, Anabaena sp., several yeasts, and mammals, the enzyme from M . ivanovi was not regulated by adenylylation as demonstrated by snake venom phosphodiesterase treatment . Inhibition of the transferase activity by L-alanine, glycine, L-histidine, and L-tryptophan was observed . L-Glutamine alone or in the presence of AMP did not inhibit the GS synthetic activity . The GS of Methanobacterium ivanovi did not cross-react with a variety of antisera against GS from Escherichia coli, Anabaena strain 7120, or Bacillus megaterium . Archaebacterial GS appears to be structurally and functionally similar to eubacterial GS in gram-positive bacteria.

Eur J Biochem, 1986 Jan 2, 154(1), 31 - 9
Improved procedure for the isolation of a double-strand-specific ribonuclease and its application to structural analysis of various 5S rRNAs and tRNAs; Digweed M et al.; An improved method for the isolation of a double-strand-specific RNase from snake venom is presented . This RNase, called CSV, was used to cleave yeast tRNAPhe and tRNA2Glu and tRNAfMet from Escherichia coli . In addition these RNAs and E . coli tRNAPhe were examined with the single-strand-specific nuclease S1 . The results are discussed in terms of the specificity of CSV RNase and the structure of tRNAs . S1 nuclease digestions at increasing temperatures allowed the melting of tertiary and secondary structure to be monitored . 5S rRNA from E . coli, Thermoplasma acidophilum and the chloroplasts of Spinacia oleracea were digested with CSV and S1 . The information these results give on the secondary-structural differences between different classes of 5S rRNA are discussed . Supporting evidence is found for tertiary interactions between hairpin loop c and internal loop d of eubacterial 5S rRNA.

J Biochem (Tokyo), 1986 Jan, 99(1), 1 - 8
ATP synthesis in cell envelope vesicles of Halobacterium halobium driven by membrane potential and/or base-acid transition; Mukohata Y et al.; Cell envelope vesicles active in ATP synthesis were prepared from Halobacterium halobium cells, which genetically lack bacteriorhodopsin, by sonication in the presence of substrates . ATP was synthesized when vesicles were illuminated to build up membrane potential through the action of halorhodopsin . The threshold value of membrane potential for ATP synthesis was about -100 mV relative to the external medium, i.e., inside-negative . ATP synthesis also occurred in the dark upon acidification of the external medium of a suspension of cell envelope vesicles . This base-acid transition ATP synthesis took place when the pH difference was greater than 1.6 units . The threshold pH difference was lowered when the base-acid transition was carried out under dim light which induced a membrane potential of about -100 mV . Regardless of the sort of driving force, ATP synthesis was optimum at the intravesicular pH of around 6.5 and almost nil at 8, where ATP syntheses by F0F1 type ATPases in other organisms are most active . The synthesis could be inhibited by N,N'-dicyclohexylcarbodiimide (DCCD) with a half-maximum inhibition at around 25 microM/2 mg protein/ml . These results strongly suggest that in halobacteria a DCCD-sensitive H+-translocating ATP synthase is in operation which is driven by membrane potential and/or pH gradient, and obeys chemiosmotic energetics . The results also suggest that the ATP synthase may not be identical to F0F1 type H+-translocating ATPases found in mitochondria, chloroplasts and eubacteria.

Mol Pharmacol, 1986 Jan, 29(1), 97 - 103
Cysteine conjugate beta-lyase in the gastrointestinal bacterium Eubacterium limosum; Larsen GL et al.; A cysteine conjugate beta-lyase (beta-lyase) from the gastrointestinal bacterium Eubacterium limosum has been isolated and characterized . This organism has the highest specific activity for cysteine conjugate beta-lyase of the gastrointestinal bacteria studied . The beta-lyase was found to cleave the thioether linkage of S-alkyl- and S-aryl-L-cysteine conjugates . Stoichiometric amounts of 2-mercaptobenzothiazole, pyruvic acid, and ammonia were produced from the beta-lyase cleavage of S-(2-benzothiazolyl)-L-cysteine . The enzyme activity was inhibited by hydroxylamine, iodoacetic acid, or KCN . The enzyme appears to be a 75,000-Da dimer of two 38,000-Da subunits . A natural substrate, cystathionine, was cleaved by this enzyme, indicating that this beta-lyase has beta-cystathionase activity . These data suggest that a beta-cystathionase from E . limosum may be an important enzyme in the metabolism of a wide range of cysteine conjugates of xenobiotics to thiol-containing products.

Biosystems, 1986, 19(3), 173 - 83
Phenylalanyl-tRNA synthetases as an example for comparative and evolutionary aspects of aminoacyl-tRNA synthetases; Rauhut R et al.; Aminoacyl-tRNA synthetases are indispensable components of protein synthesis in all three lines of evolutionary descent, eubacteria, archaebacteria and eukaryotes . Furthermore they are also present in the translational apparatus of the semi-autonomous organelles, mitochondria and chloroplasts, of the eukaryotic cell . Therefore aminoacyl-tRNA synthetases are appropriate objects for comparative molecular biology in order to obtain a comprehensive picture of the evolution of the translational process . The analysis of the phenylalanyl-tRNA synthetase in a large variety of organisms and organelles in this respect is the most advanced . In addition to comparison of quaternary structure, analysis includes functional aspects of accuracy mechanisms (proofreading) and comparison of structural features by means of substrate analogs . Evolutionary relationships are furthermore elucidated using the immunological approach and heterologous aminoacylation.

Biosystems, 1986, 19(3), 163 - 72
Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species; Hori H et al.; The secondary structure models of 5S rRNA have been constructed from the primary structure of 352 5S rRNA species available at present . All the 5S rRNAs examined can take essentially the same secondary structure, however they reveal characteristic differences between eukaryotes, metabacteria (= archaebacteria) and eubacteria . These three types of models can be further subgrouped by minor but characteristic differences . A phylogenic tree of organisms has been constructed using these 5S rRNA sequences by the weighted pairing method (WPG method) . The tree reveals that there exist several major groups of eubacteria which seem to have diverged into different directions in the early stages of bacterial evolution . After emergence of eubacteria, metabacteria and eukaryotes separated from each other from their common ancestor . In the eukaryotic evolution, red algae (Rhodophyta) emerged first, and thereafter, thraustocytrids-Proctista, Ascomycota, green plants (green algae and land plants), Basidiomycota, Chromophyta (brown algae, diatoms and golden-yellow algae), slime- and water molds, various protozoans, and animals emerged in this order.

Ann N Y Acad Sci, 1986, 463, 1 - 11
The evolutionary origins of intercellular communication and the Maginot Lines of the mind; Roth J et al.; By extending the evolutionary age of the vertebrate hormones from the vertebrates to include the metazoans, we expand their phyletic distribution about 30-fold . By tracing these molecules into the unicellular range including both eukaryotes and prokaryotes, the distribution of these molecules becomes very wide indeed . While "universal" or "ubiquitous" is probably not yet warranted, their recognition as "cosmic" molecules rather than "parochial" molecules does seem appropriate . Interestingly, the breakdown of the barriers for the hormonal molecules between the vertebrates and the rest of the metazoans, between the metazoans and the unicellular organisms, between the eukaryotes and prokaryotes, or the eubacteria and archebacteria is concordant with findings in multiple other systems . For example, hemoglobin or myoglobin is present in higher plants, Protozoa, and insects . The photosynthetic proteins of higher plants have their homologues in the photosynthetic bacteria, and the heat shock proteins of eukaryotes have their equivalents in the prokaryotes as well.

J S Afr Vet Assoc, 1985 Dec, 56(4), 195 - 7
Simultaneous isolation of anaerobic bacteria from udder abscesses and mastitic milk in lactating dairy cows; Greeff AS et al.; A variety of non-sporulating anaerobic bacterial species were isolated from udder abscesses in 10 lactating dairy cows . Fifty percent of the abscesses yielded multiple anaerobic species and the other 50% only 1 species . The anaerobic bacteria, however, were always accompanied by classical facultative anaerobic mastitogenic bacteria . In four of the five cows also afflicted with mastitis in the quarters with abscesses, the anaerobic and facultative anaerobic bacteria were identical . Peptococcus indolicus was the most commonly isolated organism followed by Eubacterium and Bacteroides spp . Bacteroides fragilis was resistant to penicillin, ampicillin and tetracycline.

Biochem Biophys Res Commun, 1985 Nov 27, 133(1), 322 - 8
Isolation and characterization of a novel vitamin-K from Eubacterium lentum; Collins MD et al.; A novel fat-soluble vitamin K like molecule was isolated from the prokaryote, Eubacterium lentum, and its structure investigated by mass spectrometry and proton nuclear magnetic resonance spectrometry . On the basis of these studies the novel quinone is shown to be 2,5 and 6- or 2,7 and 8-trimethyl-3-farnesylfarnesyl-1,4-naphthoquinone.

Biochim Biophys Acta, 1985 Nov 14, 837(2), 103 - 10
Purification and properties of 16 alpha-hydroxyprogesterone dehydroxylase from Eubacterium sp . strain 144; Glass TL et al.; Eubacterium sp . strain 144 converts 16 alpha-hydroxyprogesterone to 17-isoprogesterone . The first step of this reaction is catalyzed by 16 alpha-hydroxyprogesterone dehydroxylase (16 alpha-dehydroxylase) . This enzyme was purified 40-70-fold and characterized . 16 alpha-Dehydroxylase was found to be active in two molecular weight forms of Mr 181 000 and 326 000 . A subunit relative molecular weight of 42 400 was determined by sodium dodecyl sulfate gel electrophoresis of the purified enzyme . Although active with both 16 alpha-hydroxyprogesterone and 16 alpha-hydroxypregnenolone, the affinity of 16 alpha-dehydroxylase for the latter steroid was twice that of the former based on the apparent Km values . Evidence of possible substrate inhibition at high concentrations was seen with 16 alpha-hydroxypregnenolone . 16-Ketoprogesterone was found to be a competitive inhibitor of 16 alpha-dehydroxylase with respect to both steroid substrates . Although generally unaffected by low concentrations of non-ionic detergents, 16 alpha-dehydroxylase activity was stimulated 3-7-fold by sodium dodecyl sulfate and inhibited strongly by cetyltrimethylammonium bromide.

Carbohydr Res, 1985 Nov 1, 143, 185 - 90
Structural studies of the antigenic polysaccharide of Eubacterium saburreum, strain T17; Nakazawa F; The antigenic polysaccharide produced by Eubacterium saburreum, strain T17, is a homoglycan composed of D-glycero-D-galacto-heptose (Hep) residues having the pentasaccharide repeating-unit----6)-{alpha-Hepf-(1----4)} -beta-Hepp-(1----6)-{alpha-Hepf-(1----2), alpha-Hepf-(1----4)}-beta-Hepp-(1---- . The polysaccharide does not contain O-acetyl group.

J Bacteriol, 1985 Nov, 164(2), 914 - 7
Distribution of multicopy single-stranded DNA among myxobacteria and related species; Dhundale AR et al.; Multicopy single-stranded DNA (msDNA) is a short single-stranded linear DNA originally discovered in Myxococcus xanthus and subsequently found in Stigmatella aurantiaca . It exists at an estimated 500 to 700 copies per chromosome (T . Yee, T . Furuichi, S . Inouye, and M . Inouye, Cell 38:203-209, 1984) . We found msDNA in other myxobacteria, including Myxococcus coralloides, Cystobacter violaceus, Cystobacter ferrugineus (Cbfe17), Nannocystis exedens, and nine independently isolated strains of M . xanthus . The presence of msDNA in N . exedens would extend its phylogenetic distribution into another family of myxobacteria . Flexibacter elegans, a Cytophaga-like gliding bacteria which may be even more distantly related, also contained an msDNA but at a much lower copy number . msDNA was not detected in closely related strains of the myxobacteria Cystobacter fuscus and C . ferrugineus (Cbfe16 and Cbfe18) and the more distantly related eubacteria Herpetosiphon giganteus, Taxeobacter ocellatus, Lysobacter antibioticus, Lysobacter enzymogenes, Cytophaga johnsonae, Rhodopseudomonas sphaeroides, and Rhodospirillum rubrum . Thus far, msDNA has been found in certain gliding bacteria but not in others.

Nucleic Acids Res, 1985 Oct 11, 13(19), 6969 - 79
Characterization of the 7S RNA and its gene from halobacteria; Moritz A et al.; The 7S RNA is an abundant nonribosomal RNA in H . halobium and other halobacteria . A specific 7S RNA gene probe shows high homology to genomic DNA of all halobacteria tested but not to those of several other archaebacteria, eubacteria and eukaryotes . All halobacterial genomes seem to carry a single copy of the 7S RNA gene . The coding region of the 7S RNA gene is highly G+C rich whereas the 5'- and 3'-noncoding regions possess a rather low G+C content . An extended double stranded structure for the 7S RNA is deduced from its nucleotide sequence . The 7S RNA of H . halobium (304 nucleotides) resembles in size and structure the 7S-L RNA from mammalian cells and shares with it a sequence homology of about 50% when arranged in a colinear fashion . The similarities in sequence are found particularly at the 3'- and 5'-termini . No similarity was detected between the 7S RNA from H . halobium and the nonribosomal 6S RNA from Escherichia coli.

J Gen Microbiol, 1985 Oct, 131 ( Pt 10), 2659 - 63
16S ribosomal RNA analysis of Filibacter limicola indicates a close relationship to the genus Bacillus; Clausen V et al.; The phylogenetic relationship of the Gram-negative, filamentous gliding bacterium Filibacter limicola was analysed by 16S rRNA oligonucleotide cataloguing . In contrast to the proposed membership of this asporogenous species in the Flexibacteriaceae, Filibacter limicola clusters phylogenetically with the Gram-positive eubacteria Bacillus pasteurii, Sporosarcina ureae and the asporogenous species Planococcus citreus . The genetic relationship is supported by several common phenotypic properties.

Eur J Biochem, 1985 Sep 16, 151(3), 601 - 5
Characteristics of the binding of aminoglycoside antibiotics to teichoic acids . A potential model system for interaction of aminoglycosides with polyanions; Kusser W et al.; The binding of the aminoglycoside antibiotic dihydrostreptomycin to defined cell-wall teichoic acids and to lipoteichoic acid isolated from various gram-positive eubacteria was followed by equilibrium dialysis . Dihydrostreptomycin was used at a wide range of concentration under different conditions of ionic strength, concentration of teichoic acid, presence of cationic molecules like Mg2+, spermidine, other aminoglycoside antibiotics (gentamicin, neomycin, paromomycin) . Interaction of dihydrostreptomycin with teichoic acid was found to be a cooperative binding process . The binding characteristics seem to be dependent on structural features of teichoic acid and are influenced by cationic molecules . Mg2+, spermidine and other aminoglycosides antibiotics inhibit the binding of dihydrostreptomycin to teichoic acid competitively . The binding of aminoglycosides to teichoic acids is considered as a model system for the interaction of aminoglycoside antibiotics with cellular polyanions . Conclusions of physiological significance are drawn.

Afr J Med Med Sci, 1985 Sep-Dec, 14(3-4), 131 - 43
Review of group B streptococci and their infections; Onile BA; This review article discusses the stages in the development of research on group B streptococcus (GBS), otherwise called Streptococcus agalactiae . Emphasis was placed on the bacteriology, clinical spectrum of disease, immunity to GBS infections and antibiotic susceptibility of the causative organism . The organism, first recognized by Billroth in 1873, is classified into order Eubacteriales, family Lactobacillceae, class Schizomycetes and genus Streptococcus on the basis of its biochemical and physiological characteristics . It is subdivided into types Ia, Ib, Ic, II, III, X and R on the basis of carbohydrate and protein antigens present on its cell wall . Bovine strains of GBS are found in the bovine teat while human strains are present in the female vagina, the oro-pharynx, anorectum and the external auditory canal of newborns . It could be transmitted vertically from mother to child in-utero and during parturition . Cross infection by the nursery staff could also occur during the immediate post partum period . Two types of diseases are caused in the newborn: the early disease occurring within a week of birth; and the late disease presenting during the late neonatal period . The former usually presents in the form of septicaemia while the latter presents as meningitis . Adult infections include puerperal sepsis, pyelonephritis and a wide range of other infections . Usually they are associated with other underlying clinical conditions such as malignancy, diabetes mellitus and sickle cell disease . The organism is sensitive to penicillin which is the drug choice in treating established infections by GBS . Control measures are based on treatment of cases, eradication of vaginal colonization and chemoprophylaxis of infants at risk . An effective vaccine may become available in the near future.

Nucleic Acids Res, 1985 Aug 12, 13(15), 5697 - 706
Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E . coli tRNAs; Grosjean H et al.; We have determined the nucleotide sequence of the major species of E . coli tRNASer and of a minor species having the same GGA anticodon . These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E . coli . The two sequences differ in only one position of the D-loop . Neither tRNA has a modified adenosine in the position 3'-adjacent to the anticodon . This can be rationalized on the basis of a structural constraint in the anticodon stem and may be related to optimization of the codon-anticodon interaction . Comparison of all E.coli serine tRNAs (and that encoded by bacteriophage T4) reveals characteristic (possibly functional) features . Evolutionary analysis suggests an eubacterial origin of the T4 tRNASer gene and the existence of a recent common ancestor for the tRNASerGGA and tRNASerGUC genes.

Biochemistry, 1985 Jul 16, 24(15), 4052 - 7
Evolutionary aspects of accuracy of phenylalanyl-tRNA synthetase . Accuracy of the cytoplasmic and chloroplastic enzymes of a higher plant (Phaseolus vulgaris); Rauhut R et al.; The phenylalanyl-tRNA synthetases from cytoplasm and chloroplasts of bean (Phaseolus vulgaris) leaves employ different strategies with respect to accuracy . The chloroplastic enzyme that is coded for by the nuclear genome follows the pathway of posttransfer proofreading, also characteristic for enzymes from eubacteria and cytoplasm and mitochondria of lower eukaryotic organisms . In contrast, the cytoplasmic enzyme uses pretransfer proofreading in the case of noncognate natural amino acids, characteristic for higher eukaryotic organisms and archaebacteria . Dependent on the nature of the noncognate amino acid, pretransfer proofreading in this case occurs without tRNA stimulation or with tRNA stimulated with no or little effect of the nonaccepting 3'-OH group of the terminal adenosine . The fundamental mechanistic difference in proofreading between the heterotopic intracellular isoenzymes of the plant cell supports the idea of the origin of the chloroplastic gene by gene transfer from a eubacterial endosymbiont to the nucleus . Origin by duplication of the nuclear gene, as indicated for mitochondrial phenylalanyl-tRNA synthetases {Gabius, H.-J., Engelhardt, R., Schroeder, F.R., & Cramer, F . (1983) Biochemistry 22, 5306-5315}, appears unlikely . Further analyses of the ATP/PPi pyrophosphate exchange and aminoacylation of tRNAPhe-C-C-A(3'NH2), using 11 phenylalanine analogues, reveal intraspecies and interspecies variability of the architecture of the amino acid binding part within the active site.

Biochemistry, 1985 Jul 2, 24(14), 3667 - 72
Photoaffinity labeling of the pactamycin binding site on eubacterial ribosomes; Tejedor F et al.; Pactamycin, an inhibitor of the initial steps of protein synthesis, has an acetophenone group in its chemical structure that makes the drug a potentially photoreactive molecule . In addition, the presence of a phenolic residue makes it easily susceptible to radioactive labeling . Through iodination, one radioactive derivative of pactamycin has been obtained with biological activities similar to the unmodified drug when tested on in vivo and cell-free systems . With the use of {125I}iodopactamycin, ribosomes of Escherichia coli have been photolabeled under conditions that preserve the activity of the particles and guarantee the specificity of the binding sites . Under these conditions, RNA is preferentially labeled when free, small ribosomal subunits are photolabeled, but proteins are the main target in the whole ribosome . This indicates that an important conformational change takes place in the binding site on association of the two subunits . The major labeled proteins are S2, S4, S18, S21, and L13 . These proteins in the pactamycin binding site are probably related to the initiation step of protein synthesis.

J Bacteriol, 1985 Jul, 163(1), 75 - 81
Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences; Lane DJ et al.; 5S rRNA nucleotide sequences from Thiobacillus neapolitanus, Thiobacillus ferrooxidans, Thiobacillus thiooxidans, Thiobacillus intermedius, Thiobacillus perometabolis, Thiobacillus thioparus, Thiobacillus versutus, Thiobacillus novellus, Thiobacillus acidophilus, Thiomicrospira pelophila, Thiomicrospira sp . strain L-12, and Acidiphilium cryptum were determined . A phylogenetic tree, based upon comparison of these and other related 5S rRNA sequences, is presented . The results place the thiobacilli, Thiomicrospira spp., and Acidiphilium spp . in the "purple photosynthetic" bacterial grouping which also includes the enteric, vibrio, pseudomonad, and other familiar eubacterial groups in addition to the purple photosynthetic bacteria . The genus Thiobacillus is not an evolutionarily coherent grouping but rather spans the full breadth of the purple photosynthetic bacteria.

J Bacteriol, 1985 Jul, 163(1), 262 - 6
Chemotactic transducer proteins of Escherichia coli exhibit homology with methyl-accepting proteins from distantly related bacteria; Nowlin DM et al.; Transducers are transmembrane, methyl-accepting proteins central to the chemotactic systems of the enteric bacteria Escherichia coli and Salmonella typhimurium . Methyl-accepting proteins have been reported in a number of species in addition to these enteric bacteria . Those species include Bacillus subtilis and Spirochaeta aurantia, representatives of groups that diverged from ancestral enteric bacteria and from each other very early in bacterial evolution . An antiserum that reacts with all transducers of E . coli precipitated specifically methyl-accepting proteins from B . subtilis and S . aurantia, indicating that these proteins share antigenic determinants with transducers of E . coli . In addition, analysis of tryptic peptides by high-pressure liquid chromatography revealed similarities in the regions of methyl-accepting sites for proteins from all three species . These observations imply that structural features have been preserved in the three species from transducers contained in a common ancestor of eubacteria . It is thus reasonable to predict that other flagellated, chemotactic bacteria will be found to contain methyl-accepting proteins homologous to transducers of enteric bacteria.

Proc Natl Acad Sci U S A, 1985 Jul, 82(14), 4587 - 91
Initiator tRNA may recognize more than the initiation codon in mRNA: a model for translational initiation; Ganoza MC et al.; A special methionine tRNA (tRNAi) is universally required to initiate translation . Amongst species a tRNAi structural conservation is most apparent in the anticodon and T arms of the molecule but extends into the variable loop and the 3' strand of the D stem . This suggested that they could share a similar ancestral or current function in initiation of translation . We report that the sequence of bases neighboring the translational start codons of many eubacterial genes are complementary not only to the extended anticodon but also to the D and T loops of tRNAi . Study of the coding properties of tRNAi and of mutations that affect translation suggests that the translational start domain can be a mosaic of signals complementary to the loops of tRNAi . The hypothesis of multiple loop recognition suggests that unusual triplets can start prokaryotic and mitochondrial genes and predicts the occurrence of other reading frames . Furthermore, it suggests a unifying model for chain initiation based on RNA contacts and displacements.

Eur J Biochem, 1985 Jun 3, 149(2), 345 - 51
Transcription in methanogens . Evidence for specific in vitro transcription of the purified DNA-dependent RNA polymerase of Methanococcus thermolithotrophicus; Thomm M et al.; The purification of the DNA-dependent RNA polymerase of Methanococcus thermolithotrophicus is described . As the first step of purification the endogenous template was removed from the enzyme by hydrophobic interaction chromatography . The purified enzyme consists of seven components with different molecular masses . Transcription studies on T7 DNA and the recombinant plasmid pMV15, containing rRNA genes of Methanococcus vannielii, revealed that only the methanogen DNA is transcribed specifically, indicating a principal structural difference between archaebacterial and eubacterial promoters . This could be shown both by analysis of ternary transcription complexes and Southern hybridization . The site of initiation was found within a restriction fragment harbouring the first 390 nucleotides of the sequence coding for mature 16S rRNA and 1100 base pairs of upstream sequences . The specific initiation on this fragment strongly suggests that the enzyme can start in vitro transcription from the promoter(s) of rRNA synthesis.

Proc Natl Acad Sci U S A, 1985 Jun, 82(12), 4207 - 11
Structure and sequence divergence of two archaebacterial genes; Cue D et al.; The DNA sequences of a region that includes the hisA gene of two related methanogenic archaebacteria, Methanococcus voltae and Methanococcus vannielii, have been compared . Both organisms show a similar genome organization in this region, displaying three open reading frames (ORFs) separated by regions of very high A + T content . Two of the ORFs, including ORFHisA, show significant DNA sequence homology . As might be expected for organisms having a genome that is A + T-rich, there is a high preference for A and U as the third base in codons . Although the regions upstream of the structural genes contain prokaryotic-like promoter sequences, it is not known whether they are recognized as promoters in these archaebacterial cells . A ribosome binding site, G-G-T-G, is located 6 base pairs preceding the ATG translation initiation sequence of both hisA genes . The sequences upstream of the two hisA genes show only limited sequence homology . The M . voltae intergenic region contains four tandemly arranged repetitions of an 11-base-pair sequence, whereas the M . vannielii sequence contains both direct and inverted repetitive sequences . Based on the degree of hisA sequence homology, we conclude that M . voltae and M . vannielii are less closely related taxonomically than are members of the enteric group of eubacteria.

Proc Natl Acad Sci U S A, 1985 Jun, 82(11), 3716 - 20
Eubacteria, halobacteria, and the origin of photosynthesis: the photocytes; Lake JA et al.; The halobacteria and the photosynthetic members of the eubacteria have previously been classified in two separate urkingdoms--the archaebacteria and the eubacteria, respectively . They were thought to be no more closely related to each other than they each were to the eukaryotes . In accord with this earlier classification, photosynthesis was thought to have originated twice by independent events--once within the eubacteria and once within the archaebacteria . In this paper, however, using three-dimensional ribosome structure as a probe of evolutionary divergences, we show that the eubacteria and the halobacteria are more closely related to each other than they are to any other known organisms . The simplest interpretation of our data is that all extant photosynthetic cells are descended from a single common ancestor that possessed a primeval photosynthetic mechanism . Numerous data on the occurrence of related biochemical processes in halobacteria and eubacteria support this theory . Essential components of the photosynthetic apparatus, such as carotenoids, are present in both halobacteria and in eubacteria, including the nonphotosynthetic eubacteria, suggesting that photosynthesis could be a primitive property of both groups . Our data indicate that together the eubacteria and the halobacteria form a monophyletic group for which we propose the name "photocytes." If other techniques of phylogenetic analysis confirm this evolutionary tree, we propose that the photocytes be given urkingdom status.

J Bacteriol, 1985 Jun, 162(3), 909 - 17
Polyadenylated, noncapped RNA from the archaebacterium Methanococcus vannielii; Brown JW et al.; Polyadenylated {poly(A)+} RNA molecules have been isolated from Methanococcus vannielii by oligodeoxythymidylate-cellulose affinity chromatography at 4 degrees C . Approximately 16% of the label in RNA isolated from cultures allowed to incorporate {3H}uridine for 3 min at 37 degrees C was poly(A)+ RNA . In contrast, less than 1% of the radioactivity in RNA labeled over a period of several generations was contained in poly(A)+ RNA molecules . Electrophoretic separation of poly(A)+ RNA molecules showed a heterogeneous population with mobilities indicative of sizes ranging from 900 to 3,000 bases in length . The population of poly(A)+ RNA molecules was found to have a half-life in vivo of approximately 12 min . Polyadenylate {poly(A)} tracts were isolated by digestion with RNase A and RNase T1 after 3' end labeling of the poly(A)+ RNA with RNA ligase . These radioactively labeled poly(A) oligonucleotides were shown by electrophoresis through DNA sequencing gels to average 10 bases in length, with major components of 5, 9, 10, 11, and 12 bases . The lengths of these poly(A) sequences are in agreement with estimates obtained from RNase A and RNase T1 digestions of {3H}adenine-labeled poly(A)+ RNA molecules . Poly(A)+ RNA molecules from M . vannielii were labeled at their 5' termini with T4 polynucleotide kinase after dephosphorylation with calf intestine alkaline phosphatase . Pretreatment of the RNA molecules with tobacco acid pyrophosphatase did not increase the amount of phosphate incorporated into poly(A)+ RNA molecules by polynucleotide kinase, indicating that the poly(A)+ RNA molecules did not have modified bases (caps) at their 5' termini . The relatively short poly(A) tracts, the lack of 5' cap structures, and the instability of the poly(A)+ RNA molecules isolated from M . vannielii indicate that these archaebacterial poly(A)+ RNAs more closely resemble eubacterial mRNAs than eucaryotic mRNAs.

Appl Environ Microbiol, 1985 Jun, 49(6), 1379 - 84
Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences; Stahl DA et al.; The microorganisms inhabiting a 91 degrees C hot spring in Yellowstone National Park were characterized by sequencing 5S rRNAs isolated from the mixed, natural microflora without cultivation . By comparisons of these sequences with reference sequences, the phylogenetic relationships of the hot spring organisms to better characterized ones were established . Quantitation of the total 5S-sized rRNAs revealed a complex microbial community of three dominant members, a predominant archaebacterium affiliated with the sulfur-metabolizing (dependent) branch of the archaebacteria, and two eubacteria distantly related to Thermus spp . The archaebacterial and the eubacterial 5S rRNAs each constituted about half the examined population.

Infect Immun, 1985 May, 48(2), 303 - 11
Serum antibody reactive with predominant organisms in the subgingival flora of young adults with generalized severe periodontitis; Tew JG et al.; In the present study we sought to determine whether serum antibody was present against microorganisms which predominate in the subgingival flora of young adults with generalized severe periodontitis (SP) . Subjects with SP were often seropositive for Eubacterium brachy, Fusobacterium nucleatum E3C22, and Peptostreptococcus micros, whereas subjects with juvenile periodontitis (JP) and subjects with healthy periodontium (HP) were not . Both SP and JP subjects were more frequently seropositive for Bacteroides gingivalis, F . nucleatum D52B16, and F . nucleatum E1D1 than were HP subjects . The data were most striking for B . gingivalis, for which both the incidence and the magnitude of specific antibody was clearly elevated for SP and JP subject groups . However, SP subjects generally had either a high antibody titer or no detectable titer . In contrast, JP and HP subjects generally had at least very small amounts of antibody . Except at very low levels of antibody, neither SP nor JP groups differed significantly from the HP group for antibody to Eubacterium nodatum, Bacteroides intermedius (homology group 4197 or 8944), or Lactobacillus minutus antibody . There was a high frequency of antibody to E . nodatum, with very high titers in all groups despite the fact that this organism is rarely found in HP subjects . For Eubacterium timidum, the JP group was clearly more frequently seropositive than the HP group . Despite high levels of L . minutus in subgingival flora, none of the 50 SP subjects had a detectable antibody titer, and only four of the HP and JP subjects had detectable antibody . These results indicate that many organisms in the subgingival flora elicit antibody responses . B . gingivalis is probably the best example among the species tested . However, some organisms that are present in high concentration, e.g., L . minutus, apparently fail to induce significant antibody responses.

Appl Environ Microbiol, 1985 May, 49(5), 1146 - 53
Stimulation of 16-dehydroprogesterone and progesterone reductases of Eubacterium sp . strain 144 by hemin and hydrogen or pyruvate; Glass TL et al.; Suspensions of Eubacterium sp . strain 144, prepared from cells grown with 16-dehydroprogesterone, catalyzed the reduction of this steroid to 17-isoprogesterone at a very low rate . Modifications of the assay to optimize the pH (5.5) and increase the steroid solubility (10% {vol/vol} methanol) did not significantly enhance the reaction . However, growth of strain 144 in the presence of hemin was found to stimulate 16-dehydroprogesterone reductase during the initial 30 min of incubation, giving a biphasic time course . These biphasic kinetics could be eliminated by providing the cells with an exogenous electron donor . Strain 144 used either H2 or pyruvate for this purpose, and 17-isoprogesterone formation was nearly complete after 20 to 30 min of incubation . However, under these conditions, strain 144 further converted 17-isoprogesterone to products which lacked UV absorbance (254 nm) . When progesterone was used as a substrate, it was found that strain 144 could reduce the C4-C5 double bond of this steroid by a progesterone reductase to give mostly 5 beta-pregnadione and some 5 alpha-pregnadione . Furthermore, the 3-keto group of 5 beta-pregnadione steroid was also reduced to a hydroxy function . The maximum activities of both 16-dehydroprogesterone and progesterone reductases in cell suspensions required the growth of strain 144 with hemin and 16-dehydroprogesterone and the presence of H2 or pyruvate.

Zentralbl Bakteriol Mikrobiol Hyg {A}, 1985 May, 259(3), 359 - 66
{Gnotobiotic studies on SPF mice in relation to a study of tumor development in the colon after cholecystectomy}; Haralambie E et al.; The relation between cholecystectomy and colon carcinogenesis has not been fully elucidated . As bacteria may be involved in the carcinogenic process, we investigated the effect of cholecystectomy and dimethylhydrazine (DMH) administration to SPF NMRI mice with regard to tumour genesis and bacterial colonisation of the intestine . It results from this study that cholecystectomy does not influence tumour genesis and that 6-7 months post operationem and DMH administration tumours and bacteria originally not found in the animals develop: clostridia, eubacteria spec . which cannot be differentiated and E . lentum . Theses changes appear in group II of mice (laparotomy and DMH) and group III (cholecystectomy and DMH), but not in group I (controls) . From the results of this study we cannot conclude whether the tumours or the new bacteria appeared first . Biochemical investigations of C . innocuum, C . paraputrificum and C . tertium indicated that these bacteria metabolised bile acids by a specific metabolic step only but not produced carcinogenic substances themselves . If bacteria are involved in tumorgenesis, different species may be involved producing a carcinogenic environment by metabolic chain reactions . We know of such a bacterial collaboration in anaerobic infections.

Proc Natl Acad Sci U S A, 1985 Apr, 82(8), 2437 - 41
Pattern analysis of 5S rRNA; Eigen M et al.; Some 200 different 5S rRNA sequences from eubacteria, chloroplasts, mitochondria, archaebacteria, and eukaryotes were analyzed for evolutionary kinship relationships and associated sequential features . Group-specific occupation schemes for the 149 positions of an overall alignment were established . Eubacterial, archaebacterial, and intermediate occupation schemes all yield a strongly biased base triplet pattern in one of the three possible reading frames strongest for eubacterial, chloroplastic, and archaebacterial, but still detectable for mitochondrial and eukaryotic cytoplasmic sequences . The frequency of triplets decays in the order RNY greater than RNR greater than YNY greater than YNR; R being a purine (guanine or adenine), Y is a pyrimidine (cytosine or uracil), and N is any base . A strong preference for guanine or cytosine was found in all triplet positions . The effects show no exceptions and are clearly above the level of statistical fluctuations.

Xenobiotica, 1985 Mar, 15(3), 199 - 209
Distribution of cysteine conjugate beta-lyase in gastrointestinal bacteria and in the environment; Larsen GL; A cysteine conjugate beta-lyase was detected in 24 of 43 gastrointestinal bacteria tested, and from mixed populations of bacteria obtained from lake, river and soil samples . These bacterial cysteine conjugate beta-lyases catalyse the cleavage of the thioether linkage of both an S-alkyl- and an S-aryl-linked cysteine conjugate (2-S-cysteinyl-N-isopropylacetanilide (cysteine conjugate of propachlor) and S-(2-benzothiazolylcysteine), respectively) . A cysteine conjugate beta-lyase was isolated from Eubacterium limosum at levels at least 16-fold greater than those from any other gastrointestinal bacterial tested . This enzymic activity was present from the late lag phase through the stationary phase of growth of the bacteria . Maximum activity occurred in the mid log phase . A cysteine conjugate beta-lyase isolated from animal and plant tissues cleaved only the S-aryl-linked cysteine conjugate (S-(2-benzothiazolyl)cysteine) and generally had less enzymic activity than enzymes isolated from the bacteria . Glutathione-S-transferase activity was not detected in the 43 gastrointestinal bacteria tested, except for a low level (0.6 nmol/min per mg) of activity in Escherichia coli . No S-methyl transferase activity was detected in the gastrointestinal bacteria or mixed populations of bacteria tested.

Infect Immun, 1985 Mar, 47(3), 592 - 7
Reaction of human sera with Eubacterium brachy: isolation and characterization of an extracellular antigen; Vincent JW et al.; Recent studies have demonstrated an association of Eubacterium sp . with the subgingival microflora of patients with chronic periodontitis . One species, Eubacterium brachy, was evaluated to determine the possible mechanisms by which this microorganism may contribute to these diseases . Of 167 sera evaluated by double diffusion in agar, 20.8% displayed reactivity with a sonicated preparation of E . brachy . An extracellular antigen was identified in the culture supernatant fluid which reacted with antibodies in human sera . This antigen was isolated by methanol precipitation and purified by gel filtration . When tested by an enzyme-linked immunosorbent assay, all sera displayed some reactivity . Lines of identity were not shared with other species of Eubacterium, but were shared with other clinical isolates of E . brachy . The reactive antibody was identified as immunoglobulin G by immunoelectrophoresis, verified by enzyme-linked immunosorbent assay, and found to be capable of complement fixation . The monosaccharides and amino acids of the extracellular antigen were identified by high-pressure liquid chromatography . This antigen was shown to have a molecular weight of 170,000 and to share a line of identity with the sonicated preparation of E . brachy . The possible role of the organism in the immunopathology of periodontal diseases is discussed.

Proc Natl Acad Sci U S A, 1985 Feb, 82(4), 1180 - 3
Mutagenic DNA repair in Streptomyces; Stonesifer J et al.; Streptomyces fradiae JS6 (mcr-6) is defective in the repair of potentially lethal damage to DNA induced by mitomycin C (MC), hydroxylamine (NH2OH), methyl methanesulfonate (MMS), 4-nitroquinoline 1-oxide (NQO), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), and ultraviolet light (UV), but it exhibits nearly normal sensitivity to ethyl methanesulfonate (EMS)-induced lethality . JS6 is substantially less mutable by MNNG, MMS, NQO, UV, NH2OH, and also EMS than is the parental strain . A spontaneous revertant of JS6 showed wild-type levels of resistance to all of these agents and wild-type levels of induced mutagenesis, indicating that a single mutation caused the multiple traits displayed by JS6 . The mcr-6 gene product thus appears to control an error-prone (mutagenic) DNA repair system . Mediation of EMS mutagenesis by an error-prone repair pathway in S . fradiae, rather than by direct mispairing as in Escherichia coli, suggests that the streptomycetes have evolved more efficient error-avoidance mechanisms than those commonly observed in the single-celled eubacteria.

Arch Microbiol, 1985 Feb, 141(1), 70 - 4
A simple and rapid method for screening bacteria for type II restriction endonucleases: enzymes in Aphanothece halophytica; Whitehead PR et al.; A method is described which allows a large number of bacterial strains to be rapidly and easily screened for the presence of site-specific endonucleases . The method involves selective permeabilization of the bacterial cell and analysis of the exuded material . Type II restriction endonucleases from cyanobacteria and Gram-negative eubacteria have been detected and new enzymes have been found . The method should be widely applicable and easy to modify for use in genera other than those tested . Three-site-specific endonuclease activities, detected by this method in Aphanothece halophytica PCC 7412, were purified and their recognition and cleavage specificities were determined AhaI and AhaII recognise and cleave the same DNA sequences as CauII and AcyI respectively; the specificity of AhaIII (TTT decreases AAA) has been reported previously (Whitehead and Brown, 1982, FEBS Letters 143:296-300).

J Antibiot (Tokyo), 1985 Feb, 38(2), 145 - 52
The corallopyronins, new inhibitors of bacterial RNA synthesis from Myxobacteria; Irschik H et al.; From the culture broth of the myxobacterium, Corallococcus (Myxococcus) coralloides, three new antibiotics have been isolated: corallopyronin A, B and C . The compounds, which are chemically related to the recently discovered myxopyronins, act mainly on Gram-positive bacteria, with MIC values between 0.1 and 10 micrograms/ml, and only exceptionally or at much higher concentrations (MIC values; 100 and more micrograms/ml) on Gram-negatives . They do not inhibit eukaryotic organisms and show no toxicity for mice (sc) . The corallopyronins appear to block specifically eubacterial RNA polymerase.

J Biol Chem, 1985 Jan 25, 260(2), 899 - 906
Characterization of the ribosomal RNA gene clusters in Halobacterium cutirubrum; Hui I et al.; We present a comprehensive and detailed analysis of the structure and organization of a cloned ribosomal RNA gene cluster from the archaebacterial species Halobacterium cutirubrum . With the exception of a region in the middle of the 23 S rRNA gene, the DNA sequence of the entire gene cluster has been determined . The gene organization is similar to that found in typical eubacteria with the 16, 23, and 5 S genes occupying the proximal, middle, and distal positions, respectively . There appears to be no equivalent to the eucaryotic 5.8 S gene in H . cutirubrum . The cluster also contains two putative tRNA genes, an alanine tRNA gene in the 16-23 S intergenic space, and a cysteine tRNA gene distal to the 5 S rRNA gene . The 16 and 23 S rRNA genes are surrounded by long nearly perfect inverted repeat sequences which are presumably utilized along with other structural features of the RNA for the processing of 16 and 23 S rRNA from a large precursor transcript . The 5' sequence flanking the 16 S rRNA gene contains two imperfect copies, followed by three perfect copies of a bipartite direct-repeat unit . The sequence AAGTAA, believed to be an important component of the Halobacterium promotor, is present in the highly conserved portion of the direct repeat unit . In the 3' region flanking the 5 S rRNA gene there are sequences, a short inverted repeat followed by T5, and a G/C-rich region followed by an A/T-rich region, which may function in transcription termination . Genomic southern hybridization experiments clearly indicate that the ribosomal RNA genes are unique single-copy DNA in H . cutirubrum.

Biochemistry, 1985 Jan 15, 24(2), 241 - 50
Comparison of eubacterial and eukaryotic 5S RNA structures: a chemical modification study; Kjems J et al.; The 5S RNAs from Bacillus stearothermophilus and Saccharomyces cerevisiae were probed by nucleotide-specific reagents, with a view to compare and contrast their higher order structures . The progressive unfolding of the RNAs during heating, in the presence and absence of magnesium, was monitored . Evidence was provided for the double-helical segments which occur in the secondary structural models of both RNAs . The results also placed constraints on the possible structuring of the remainder of the RNA and yielded some insight into ways of folding up the molecule . Together with the data from our earlier studies, employing ribonucleases, these results provide a detailed picture of the structuring and topography of the 5S RNAs . The main structural differences between the eubacterial and eukaryotic RNAs occur throughout the loop D/helix IV/loop E/helix V arm; in particular strong evidence is provided for loop D of the eukaryotic RNA being involved in a tertiary interaction.

J Biol Chem, 1985 Jan 10, 260(1), 182 - 7
Archaebacterial phenylalanyl-tRNA synthetase . Accuracy of the phenylalanyl-tRNA synthetase from the archaebacterium Methanosarcina barkeri, Zn(II)-dependent synthesis of diadenosine 5',5'''-P1,P4-tetraphosphate, and immunological relationship of OFFnylalanyl-tRNA synthetases from different urkingdoms; Rauhut R et al.; Phenylalanyl-tRNA synthetase from the archaebacterium Methanosarcina barkeri activates a number of phenylalanine analogues (methionine, p-fluorophenylalanine, beta-phenylserine, beta-thien-2-ylalanine, 2-amino-4-methylhex-4-enoic acid and ochratoxin A) in the absence of tRNA, as demonstrated by Km and kcat of the ATP/PPi exchange reaction . Upon complexation with tRNA, AMP formation from the enzyme X tRNA complex in the presence of ATP, one of the above analogues or tyrosine, leucine, mimosine, N-benzyl-L- or N-benzyl-D-phenylalanine indicates activation of the analogues under conditions of aminoacylation . Natural noncognate amino acids are not transferred to tRNAPhe-C-C-A or tRNAPhe-C-C-A-(3'-NH2) . This pretransfer proofreading mechanism, together with the comparatively low ratio of synthetic to successive hydrolytic steps, resembles the mechanism of liver enzymes of vertebrates . In contrast, eubacterial phenylalanyl-tRNA synthetases achieve the necessary fidelity by post-transfer proofreading, a corrective hydrolytic event after transfer to tRNAPhe . Diadenosine 5',5'''-P1,P4-tetraphosphate synthesis is shown to be a common feature for phenylalanyl-tRNA synthetases from all three lineages of descent . The immunological approach demonstrates that aminoacyl-tRNA synthetases do not belong to the group of enzymes in gene expression with high structural conservation.

Med Microbiol Immunol (Berl), 1985, 174(1), 25 - 8
Anaerobic bacteria in urine before and after prostatic massage of infertile men; Moberg PJ et al.; In the present study 25 infertile men delivered urine before and after prostatic massage . Expressed prostatic secretion (EPS) was obtained from 11 men . Aerobic and anaerobic bacterial analyses showed that a total of 33 isolates was found in samples of urine voided before massage as compared to 59 isolates after massage of the prostate . There was an increase in the number of anaerobes whereas there was no change in the number of aerobes . The occurrence of EPS did not influence the number of aerobic and anaerobic isolates in urine voided after massage of the prostate . The most often isolated anaerobes in urine voided after prostatic massage were Eubacterium lentum, Peptococcus asaccharolyticus and Bacteroides species and the most common anaerobe in EPS was Peptostreptococcus micros.

Curr Genet, 1985, 9(6), 517 - 9
Identification of an aspartate transfer RNA gene in maize mitochondrial DNA; Parks TD et al.; A gene for a transfer RNA (tRNA) specific for aspartic acid was identified in maize mitochondrial DNA . The nucleotide sequence and predicted secondary structure of this tRNA more closely resemble eubacterial and chloroplast aspartate tRNA genes than other mitochondrial aspartate tRNA genes . This gene is located on a 3,123 base pair EcoRI DNA fragment that also contains an elongator methionine tRNA gene . These two tRNA genes are separated by 726 nucleotides and are located on opposite strands of DNA.

Curr Genet, 1985, 9(6), 505 - 15
Primary and secondary structure of 26S ribosomal RNA of Oenothera mitochondria; Manna E et al.; The primary structure of 26S ribosomal RNA from mitochondria of the dicotyledoneous plant Oenothera berteriana is inferred from the sequence of a cloned rDNA restriction fragment . A tentative secondary structure model valid for Oenothera and for the major part of maize mitochondrial 26S rRNA has been constructed in analogy to the refined german model for E . coli L-rRNA (Maly and Brimacombe 1983) . The derived structure generally matches the eubacterial model providing further support to the E . coli consensus structure . Some structural features however show eukaryotic characteristics . Possible interactions between L-rRNA, 5S rRNA and initiator-tRNA are discussed.

J Mol Evol, 1985, 22(3), 237 - 42
Nuclease S1 analysis of eubacterial 5S rRNA secondary structure; MacDonell MT et al.; Single-strand-specific nuclease S1 was employed as a structural probe to confirm locations of unpaired nucleotide bases in 5S rRNAs purified from prokaryotic species of rRNA superfamily I . Limited nuclease S1 digests of 3'- and 5'-end-labeled {32P}5S rRNAs were electrophoresed in parallel with reference endoribonuclease digests on thin sequencing gels . Nuclease S1 primary hydrolysis patterns were comparable for 5S rRNAs prepared from all 11 species examined in this study . The locations of base-paired regions determined by enzymatic analysis corroborate the general features of the proposed universal five-helix model for prokaryotic 5S rRNA, although the results of this study suggest a significant difference between prokaryotic and eukaryotic 5S rRNAs in the evolution of helix IV . Furthermore, the extent of base-pairing predicted by helix IV needs to be reevaluated for eubacterial species . Clipping patterns in helices II and IV appear to be consistent with a secondary structural model that undergoes a conformational rearrangement between two (or more) structures . Primary clipping patterns in the helix II region, obtained by S1 analysis, may provide useful information concerning the tertiary structure of the 5S rRNA molecule.

Clin Invest Med, 1985, 8(4), 286 - 95
Does cytomegalovirus play a role in community-acquired pneumonia?
Marrie TJ, Janigan DT, Haldane EV, Faulkner RS, Kwan C, Durant H.
Cytomegalovirus (CMV) is recognized as an important pathogen in the immuno-suppressed patient . Sporadic case reports of cytomegalovirus community-acquired pneumonia have appeared . We studied 443 patients with community-acquired pneumonia requiring hospitalization to define the role of cytomegalovirus in this illness . Four patients (0.9%) had good evidence that cytomegalovirus caused their pneumonia: 2 had the virus isolated from pulmonary tissue and 2 had cytomegalovirus inclusion bodies visualized in this tissue . An additional 14 patients had serologic evidence (a fourfold rise in the complement fixation tests) of cytomegalovirus infection . Analysis of these 18 patients suggest, that cytomegalovirus plays a role in community-acquired pneumonia . Six (33%) of the patients were immunosuppressed . Six others had concomitant infections: Chlamydia trachomatis (3); Epstein-Barr virus and M . pneumoniae (1); and bacteremia with Group B streptococcus and Bacteroides fragilis plus Eubacterium lentum (1 each) . Seven patients (39%) required assisted ventilation, four of whom developed secondary bacterial pneumonia . Five (28%) died . Only two patients had a clinical and radiographic picture suggestive of a viral illness as a cause of the pneumonia . Three patients had atypical lymphocytes in their peripheral blood film . We found that the prevalence of complement fixing antibody to cytomegalovirus increased with age . Such antibody was lacking among those in the 16-20 year group while it peaked at 65% for males and at 78% for females ages 91-100 years . Despite the fact that 42.2% of the adults lacked antibody to cytomegalovirus, community-acquired pneumonia due to this virus is uncommon and does not justify routine serological testing for such infection among patients with community-acquired pneumonia.

J Bacteriol, 1985 Jan, 161(1), 231 - 7
Generation of a large, protonophore-sensitive proton motive force and pH difference in the acidophilic bacteria Thermoplasma acidophilum and Bacillus acidocaldarius; Michels M et al.; The mechanism by which acidophilic bacteria generate and maintain their cytoplasmic pH close to neutrality was investigated . For this purpose we determined the components of proton motive force in the eubacterium Bacillus acidocaldarius and the archaebacterium Thermoplasma acidophilum . After correction for probe binding, the proton motive force of untreated cells was 190 to 240 mV between external pH 2 and 4 . Anoxia diminished total proton motive force and the transmembrane pH difference by 60 to 80 mV . The protonophore 2,4-dinitrophenol abolished the total proton motive force almost completely and diminished the transmembrane pH difference by at least two units . However, even after correction for probe binding, protonophore-treated cells maintained a pH difference of approximately one unit.

Gene, 1985, 37(1-3), 181 - 9
The nucleotide sequence of the gene coding for the 16S rRNA from the archaebacterium Halobacterium halobium; Mankin AS et al.; The complete 1473-bp sequence of the 16S rRNA gene from the archaebacterium Halobacterium halobium has been determined . Alignment with the sequences of the 16S rRNA gene from the archaebacteria Halobacterium volcanii and Halococcus morrhua reveals similar degrees of homology, about 88% . Differences in the primary structures of H . halobium and eubacterial (Escherichia coli) 16S rRNA or eukaryotic (Dictyostelium discoideum) 18S rRNA are much higher, corresponding to 63% and 56% homology, respectively . A comparison of the nucleotide sequence of the H . halobium 16S rRNA with those of its archaebacterial counterparts generally confirms a secondary structure model of the RNA contained in the small subunit of the archaebacterial ribosome.

Nucleic Acids Res, 1984 Dec 11, 12(23), 8749 - 68
Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs; Nelles L et al.; The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined . The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin . Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment . Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures.

J Lipid Res, 1984 Dec 1, 25(12), 1343 - 9
HPLC purification and preparation of antibodies to cholic acid-inducible polypeptides from Eubacterium sp . V.P.I . 12708; Paone DA et al.; The role of bile acid-inducible polypeptides in 7-dehydroxylation was investigated in Eubacterium sp . V.P.I . 12708 . Cholic acid-inducible bile acid 7 alpha-, 7 beta-dehydroxylase, and delta 6 reductase activities co-eluted from a gel filtration high performance liquid chromatography (HPLC) column . Antibody (Ab) was prepared to these enzymatically active fractions, immunoadsorbed with uninduced cell extract coupled to Sepharose 4B, and used for immunoprecipitation of {35S}-methionine-labeled polypeptides . Ab immunoprecipitated polypeptides with molecular weights of 45,000, 27,000, and 23,500 from induced but not uninduced cell extracts . Immunoinhibition experiments showed that this Ab preparation inhibited (60%) bile acid 7 alpha-dehydroxylase activity in cell extracts . The 45,000 mol wt polypeptide was purified by (NH4)2SO4 fractionation, HPLC gel filtration, and HPLC-DEAE chromatography . Ab prepared to the 45,000 mol wt polypeptide immunoprecipitated only that polypeptide . This Ab, however, did not inhibit bile acid 7 alpha-dehydroxylase activity . Ab specific for the 27,000 mol wt polypeptide was prepared by partial purification and immunoadsorption with uninduced cell extracts . Immunochemical staining, following SDS-PAGE of crude cell extracts, shows a single immunoreactive protein band at 27,000 daltons . This Ab immunoprecipitated the 27,000 mol wt polypeptide as well as small amounts of the 45,000 and 23,000 mol wt polypeptides . Immunoinhibition studies showed that this Ab preparation inhibited (25%) 7 alpha-dehydroxylase activity . These data suggest that the 27,000 mol wt polypeptide is involved in enzyme catalysis . This does not, however, eliminate some role for the 45,000 and 23,500 mol wt polypeptides in bile acid metabolism in this organism.

Mol Biol Rep, 1984 Dec, 10(2), 75 - 8
Functional implication of the sole arginine residue of ribosomal proteins L7/L12; Hernandez F et al.; Modification of the only arginine residue present in proteins L7/L12 from Escherichia coli with phenylglyoxal, 2,3-butanedione and 1,2-cyclohexanedione is accompanied by functional alterations . The capacity of these proteins to promote polyphenylalanine synthesis and elongation factor G-dependent hydrolysis of GTP in L7/L12-depleted ribosomal cores is significantly decreased (more than 50%) on modification . Incubation of the butanedione- and cyclohexanedione-modified L7/L12 under regenerating conditions is accompanied by recovery of the original activity in polyphenylalanine synthesis . These results and the conservation of the arginine residue in eubacterial L7/L12-type proteins point to the functional implication of this arginine residue.

Nucleic Acids Res, 1984 Nov 26, 12(22), 8393 - 406
Structural requirements for the interaction of 5S rRNA with the eukaryotic transcription factor IIIA; Pieler T et al.; In order to study the binding of the eukaryotic transcription factor IIIA to heterologous 5S rRNAs with a low degree of overall sequence conservation (less than 20%) we have utilized a transcription competition assay involving eubacterial, archaebacterial and eukaryotic 5S rRNAs . All the molecules inhibit Xenopus 5S rRNA transcription specifically, which suggests that only a small amount of specific conserved RNA sequences, if indeed any, are essential for the interaction of the transcription factor with the 5S rRNA molecule, whereas universal 5S rRNA secondary structure elements seem to be required . A fragment of Xenopus laevis oocyte 5S rRNA (nucleotides 41-120), which partially maintains the original 5S rRNA structure, also competes for TF III A . In vitro transcription of a naturally occurring mutant of the Xenopus laevis oocyte 5S rRNA gene, the pseudogene, which carries several point mutations within the TF III A binding domain is equally inhibited by exogenous Xenopus 5S rRNA.

FEBS Lett, 1984 Nov 19, 177(2), 189 - 94
A ribosomal protein that is immunologically conserved in archaebacteria, eubacteria and eukaryotes; Schmid G et al.; A ribosomal protein which exhibits cross-reaction between organisms belonging to the eubacterial, archaebacterial and eukaryotic groups was studied by immunoblotting analysis . It was identified as the equivalent of the E . coli ribosomal protein L2.

Steroids, 1984 Oct, 44(4), 329 - 36
Effect of bile acid analogs on 7 alpha-dehydroxylase activity in Eubacterium sp . V.P.I . 12708; Hylemon PB et al.; 7 beta-Methyl-chenodeoxycholic acid (7-MeCDC, 3 alpha, 7 alpha-dihydroxy-7 beta-methyl-5 beta-cholan-24-oic acid), 7 alpha-methyl-ursodeoxycholic acid (7-MeUDC, 3 alpha, 7 beta-dihydroxy-7 alpha-methyl-5 beta-cholan-24-oic acid), 7 xi-methyl-lithocholic acid (7-MeLC, 3 alpha-hydroxy-7 xi-methyl-5 beta-cholan-24-oic acid) and ursodeoxycholylsarcosine (UDCS) were tested as inhibitors of bacterial bile acid 7 alpha-dehydroxylase activity . At a concentration of 50 microM, 7-MeCDC and 7-MeUDC inhibited enzyme activity by 66% and 12%, respectively . 7 alpha-Dehydroxylase activity was not inhibited in the presence of 7-MeLC and UDCS . None of the four bile acid analogs tested inhibited the growth of Eubacterium sp . V.P.I . 12708 at concentrations up to 100 microM.

Infect Immun, 1984 Oct, 46(1), 1 - 6
Bacteriology of experimental gingivitis in children; Moore WE et al.; Children are more resistant to gingivitis than are adults . To determine possible differences in their periodontal floras, an experimental gingivitis study, identical in design to one reported earlier with young adults, was conducted with four 4- to 6-year-old children . The incidence of sites that developed gingival index scores of 2 in children was less than one-third of the incidence observed in adults . The composition of the flora of each child was statistically significantly different from that of any other child or adult . The floras of the children as a group were statistically significantly different from those of the adults . Children had 3-fold greater proportions of Leptotrichia species, 2.5-fold greater proportions of Capnocytophaga species, 2.3-fold greater proportions of Selenomonas species, 2-fold greater proportions of bacterial species that require formate and fumarate, and 1.5-fold greater proportions of Bacteroides species . Adults had greater proportions of Fusobacterium, Eubacterium, and Lactobacillus species . Fusobacterium nucleatum, Actinomyces WVa 963, Selenomonas D04, and Treponema socranskii were predominant species that correlated with increasing gingival index scores in both children and adults.

Isr J Med Sci, 1984 Sep, 20(9), 758 - 61
Mycoplasmal ribosomal RNA genes and their use as probes for detection and identification of Mollicutes; Razin S et al.; The number and organization of ribosomal RNA (rRNA) genes in the genome of Mycoplasma, Ureaplasma, Acholeplasma and Spiroplasma species were studied by the Southern hybridization technique . Restriction endonuclease-digested DNAs of the organisms were hybridized with nick-translated probes consisting of defined portions of the rrnB rRNA operon of Escherichia coli and with a recombinant plasmid pMC5 constructed of pBR325 and an insert containing M . capricolum genes for 23S, 5S and most of the 16S rRNA gene . The hybridization data indicate the presence of only one or two sets of rRNA genes in the mollicutes tested, a number lower than in eubacteria . The rRNA genes in mollicutes appear to be organized as clusters (acting apparently as operons) in the typical prokaryotic fashion, 5'-16S-23S-5S-3' . Despite the marked sequence homology shared by the rRNA operons of the different mollicutes and of E . coli, the operons are not identical . Thus, there is an EcoRI restriction site in the 16S rRNA genes in only 8 of the 13 species tested . The recombinant plasmid pMC5 has provided a sensitive probe for detection and identification of mollicutes in contaminated cell cultures . The purified DNA of the tested cell culture, or its supernatant fluid, was digested by EcoRI, and Southern blot hybridization of the products was performed with nick-translated pMC5 . The probe did not hybridize with eukaryotic DNA . Each of the mollicutes species examinated exhibited a species-specific hybridization pattern . The hybridization tests enabled the identification of the four most prevalent mycoplasma contaminants of cell cultures, M . orale, M . hyorhinis, M . arginini and A . laidlawii . The test is capable of detecting 1 ng of mycoplasmal DNA, roughly equivalent to the DNA content of 10(5) mycoplasmas . The possibility of using this approach for detection and identification of noncultivable mycoplasmas in plant and insect tissues is under investigation.

Isr J Med Sci, 1984 Sep, 20(9), 762 - 4
Comparative analysis of mycoplasma ribosomal RNA operons; Gobel U et al.; Using differential probes derived from the Escherichia coli rrnB operon, we were able to map the ribosomal operons of Mycoplasma pneumoniae, M . hyorhinis, and M . arthritidis . All organisms contained only one ribosomal RNA operon, and the genes were linked in the eubacterial order, 16S-23S-5S . The HindIII sites in M . hyorhinis and M . pneumoniae were highly conserved.

Nucleic Acids Res, 1984 Aug 24, 12(16), 6629 - 44
Nucleotide sequence and evolution of the 18S ribosomal RNA gene in maize mitochondria; Chao S et al.; The nucleotide sequence of the gene coding for the 18S ribosomal RNA of maize mitochondria has been determined and a model for the secondary structure is proposed . Dot matrix analysis has been used to compare the extent and distribution of sequence similarities of the entire maize mitochondrial 18S rRNA sequence with that of 15 other small subunit rRNA sequences . The mitochondrial gene shows great similarity to the eubacterial sequences and to the maize chloroplast, and less similarity to mitochondrial rRNA genes in animals and fungi . We propose that this similarity is due to a slow rate of nucleotide divergence in plant mtDNA compared to the mtDNA of animals . Sequence comparisons indicate that the evolution of the maize mitochondrial 18S, chloroplast 16S and nuclear 17S ribosomal genes have been essentially independent, in spite of evidence for DNA transfer between organelles and the nucleus.

Eur J Biochem, 1984 Aug 15, 143(1), 175 - 82
Equilibria in 5-S ribosomal RNA secondary structure . Bulges and interior loops in 5-S RNA secondary structure may serve as articulations for a flexible molecule; De Wachter R et al.; The basic assumption in this paper is that the secondary structure of a 5-S ribosomal RNA cannot be represented by a single model . We propose that the molecule can adopt, at least within the ribosome, a series of slightly different structures of nearly equal stability . The different structures arise from the existence of ambiguous base-pairing opportunities in bulged helices and the adjacent interior loops . In eubacterial 5-S RNAs there is one such an area, in eukaryotic 5-S RNAs two such areas that can give rise to structural switches . We explain how a change in secondary structure in these areas may influence the relative orientation of the surrounding helices, in other words how bulges and interior loops may serve as articulations and give rise to a flexible tertiary structure.

J Biol Chem, 1984 Aug 10, 259(15), 9461 - 71
Halobacterium volcanii tRNAs . Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs; Gupta R; Transfer RNAs of Halobacterium volcanii, an archaebacterium, were separated by two-dimensional gel electrophoresis and sequenced by a combination of methods . A total of 41 tRNAs, at least one for each amino acid, were identified . These are five tRNAs for Leu, four for Gly, three each for Ala, Arg, Pro, and Ser, two each for Glu, Ile, Lys, Met (initiator and noninitiator), Thr, and Val, and one each for the remaining eight amino acids . As in eucaryotes, only Leu and Ser tRNAs are class II (large extra arm) . The sequences of the 33 class I tRNAs, for the remaining 18 amino acids, are presented here . These cover at least 44 codons out of a possible 49 codons for the 18 amino acids . Although these archaebacterial tRNAs follow general tRNA patterns, they are in detail distinct from both eucaryotic and eubacterial tRNAs . Moreover, the initiator tRNA is unique in having a 5'-triphosphorylated end.

Science, 1984 Aug 3, 225(4661), 510 - 2
A new ribosome structure; Henderson E et al.; Ribosomes derived from the sulfur-dependent archaebacteria are structurally distinct from those types found in ribosomes from eubacteria, eukaryotes, and other archaebacteria . All four ribosome types share a common structural core, but each type also has additional independent structural features . In the smaller subunit derived from sulfur-dependent archaebacteria ("eocytes"), lobes, similar to those found at the base of the eukaryotic small subunits, and an archaebacterial bill, similar to those found on the smaller subunit of archaebacteria and eukaryotes, are present . On the larger subunit from sulfur-dependent archaebacteria, an eocytic lobe, eocytic gap, and eocytic bulge are present . These features, with the exception of the eocytic gap, are found in a slightly modified form on eukaryotic large subunits . These novel ribosomal properties are in general consistent with other molecular biological properties peculiar to these organisms.

Microbiol Sci, 1984 Aug, 1(5), 117 - 22
The phylogeny of prokaryotes; Stackebrandt E et al.; Data from methods such as 5S RNA sequencing have enabled phylogenetic relationships within the prokaryotes to be determined . A basic evolutionary dichotomy is suggested by the diversion of the archaebacteria and the eubacteria . Possible inter-relationships of the former and eukaryotic organisms are discussed.

J Gen Microbiol, 1984 Aug, 130 ( Pt 8), 1911 - 20
The ribonucleotide sequence of 5s rRNA from two strains of deep-sea barophilic bacteria; Deming JW et al.; Deep-sea bacteria were isolated from the digestive tract of animals inhabiting depths of 5900 m in the Puerto Rico Trench and 4300 m near the Walvis Ridge . Growth of two bacterial strains was measured in marine broth and in solid media under a range of pressures and temperatures . Both strains were barophilic at 2 degrees C (+/- 1 degrees C) with an optimal growth rate of 0.22 h-1 at a pressure 30% lower than that encountered in situ . At 1 atm they grew at temperatures ranging from 1.2 to 18.2 degrees C (+/- 0.3 degrees C), while in situ pressures increased the upper temperature limit to 23.3 degrees C . Both strains were identified as members of the genus Vibrio, based on standard taxonomic tests and mol% G + C values (47.0 and 47.1) . Ribonucleotide sequences determined for 5S ribosomal RNA from each strain confirmed relationship to the Vibrio-Photobacterium group, as represented by V . harveyi and P . phosphoreum, but the barophiles were clearly distinct from these species . Secondary structure conformed to the established model for eubacterial 5S rRNA.

Nucleic Acids Res, 1984 Jul 25, 12(14), 5837 - 52
On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA; Gray MW et al.; To probe the earliest evolutionary events attending the origin of the five known genome types (archaebacterial, eubacterial, nuclear, mitochondrial and plastid), we have analyzed sequences corresponding to a ubiquitous, highly conserved core of secondary structure in small subunit rRNA . Our results support (i) the existence of three primary lineages (archaebacterial, eubacterial, and nuclear), (ii) a specific eubacterial ancestry for plastids and mitochondria (plant, animal, fungal), and (iii) an endosymbiotic, evolutionary origin of the two types of organelle from within distinct groups of eubacteria (blue-green algae (cyanobacteria) in the case of plastids, nonphotosynthetic aerobic bacteria in the case of mitochondria) . In addition, our analysis suggests (iv) a biphyletic origin of mitochondria, with animal and fungal mitochondria branching together but separately from plant mitochondria, and (v) a monophyletic origin of plastids . The method described here provides a powerful and generally applicable molecular taxonomic approach towards a global phylogeny encompassing all organisms and organelles.

J Steroid Biochem, 1984 Jul, 21(1), 65 - 72
Biotransformation of 16-dehydroprogesterone by the intestinal anaerobic bacterium, Eubacterium sp . 144; Glass TL et al.; Eubacterium sp . 144 biotransformed 16-dehydroprogesterone by initially hydrating approx 50% to 16 alpha-hydroxyprogesterone . The detection of this reaction was dependent, in part, on the solubility state of 16-dehydroprogesterone and was less extensive when the concentration of methanol was insufficient to solubilize the steroid . Cultures containing a mixture of 16-dehydroprogesterone and 16 alpha-hydroxyprogesterone formed isoprogesterone as a final steroid end product . However, the extent of the reductive reaction was influenced by culture age at the time of 16-dehydroprogesterone addition and decreased in older cultures . Moreover, both mid- and late-log phase cells also formed progesterone as a reduced steroid end product . The enzyme(s) responsible for isoprogesterone formation (16-dehydroprogesterone reductase) appeared to be inducible because activity was not evident until 3-6 h after the addition of 16-dehydroprogesterone to early log-phase cultures . Growth inhibitory concentrations of chloramphenicol or rifampin prevented isoprogesterone formation, but not the production of progesterone . At lower concentrations, chloramphenicol delayed both growth and isoprogesterone formation by strain 144 . Interestingly, rifampin partially inhibited the 16 alpha-hydroxyprogesterone dehydratase (hydration reaction) in cultures of strain 144, but did not affect the enzyme's activity in cell extracts.

J Bacteriol, 1984 Jul, 159(1), 233 - 7
Secondary structure and phylogeny of Staphylococcus and Micrococcus 5S rRNAs; Dekio S et al.; Nucleotide sequences of 5S rRNAs from four bacteria, Staphylococcus aureus Smith (diffuse), Staphylococcus epidermidis ATCC 14990, Micrococcus luteus ATCC 9341 and Micrococcus luteus ATCC 4698, were determined . The secondary structural models of S . aureus and S . epidermidis sequences showed characteristics of the gram-positive bacterial 5S rRNA (116-N type {H . Hori and S . Osawa, Proc . Natl . Acad . Sci . U.S.A . 76:381-385, 1979}) . Those of M . luteus ATCC 9341 and M . luteus ATCC 4698 together with that of Streptomyces griseus (A . Simoncsits, Nucleic Acids Res . 8:4111-4124, 1980) showed intermediary characteristics between the gram-positive and gram-negative (120-N type {H . Hori and S . Osawa, 1979}) 5S rRNAs . This and previous studies revealed that there exist at least three major groups of eubacteria having distinct 5S rRNA and belonging to different stems in the 5S rRNA phylogenic tree.

EMBO J, 1984 Jul, 3(7), 1613 - 9
The nucleotide sequence of the 16S ribosomal RNA gene of the archaebacterium Halococcus morrhua; Leffers H et al.; The sequence of the 16S rRNA gene from the archaebacterium Halococcus morrhua was determined by the dideoxynucleotide sequencing method . It is 1475 nucleotides long . This is the second archaebacterial sequence to be determined and it provides sequence comparison evidence for the secondary structural elements confined to the RNAs of this kingdom and, also, support for controversial or additional base pairing in the eubacterial RNAs . Six structural features are localized that have varied during the evolution of the archaebacteria, eubacteria and eukaryotes . Moreover, although the secondary structures of both sequenced archaebacterial RNAs strongly resemble those of eubacteria, they contain sufficient eukaryotic-like structural characteristics to reinforce the view that they belong to a separate line of evolutionary descent.

EMBO J, 1984 Jul, 3(7), 1603 - 8
Queuosine modification in tRNA and expression of the nitrate reductase in Escherichia coli; Janel G et al.; In eubacteria the modified nucleoside queuosine is present in tRNAAsn, tRNAAsp, tRNAHis and tRNATyr . A precursor of queuine, pre-queuine, is synthesized from GTP, inserted into the first position of the anticodon of the corresponding tRNAs by a specific tRNA-guanine transglycosylase and further modified to queuosine . Isogenic pairs of Escherichia coli, containing or lacking the tRNA-transglycosylase (JE 7335, tgt+ lacZ+ and JE 7337, tgt- lacZ+; JE 7334, tgt+ lacZ- and JE 7336, tgt- lacZ-), have been employed to study the function of queuosine in tRNA . Compared with the tgt+ strain (JE 7335), the tgt- mutant (JE 7337) grown under anaerobic conditions, is defective with respect to the nitrate respiration system, in which electrons are transported from D(-)-lactate via quinone and cytochrome bNO3-(556) to nitrate . Low temperature cytochrome spectra of the anaerobically grown tgt- mutant show a lowered amount of type b cytochromes involving the spectrum of cytochrome bNO3-(556) . In the case of the anaerobically grown tgt- mutant three proteins are missing in the protein pattern of cytoplasmic membranes . Their mol . wts . correspond to those of the subunits of the nitrate reductase complex . In contrast to the tgt+ strains (JE 7334, JE 7335) both tgt- mutants (JE 7336, JE 7337) cannot grow on lactate under anaerobic conditions with nitrate offered as electron acceptor and NO3- is not reduced to NO2- . A possible link between Q-modification of tRNAs, the synthesis of proteins of the nitrate reductase complex and the synthesis of menaquinone or ubiquinone is discussed.

Eur J Biochem, 1984 Jun 15, 141(3), 453 - 9
Synthesis of RNA I by the RNA polymerase from Micrococcus luteus on the Escherichia coli plasmid pBR322; Brack RP et al.; Incubation of DNA-dependent RNA polymerase from Micrococcus luteus (gram-positive) with the plasmid pBR322 under transcription conditions in vitro leads to the formation of a rather short-chained RNA . This transcript is initiated at the same site on pBR322 as RNA I, a defined Escherichia coli RNA polymerase product . M . luteus RNA polymerase initiates transcription at the RNA I site much more efficiently than the E . coli enzyme, using either a plasmid preparation of pBR322 or an appropriate linear restriction fragment as template . In the latter case, cleavage of the restriction fragment 24 or 71 nucleotides (but not 91 nucleotides) upstream of the initiation site destroys template activity . By sequence analysis it was determined that the 3' terminus of the M . luteus RNA polymerase transcription product is identical with that known for RNA I . Moreover, in agreement with synthesis of RNA I by E . coli RNA polymerase in vitro, termination by the M . luteus enzyme is also a stutter process characterized by the same dependence on the available UTP concentration . These observations lead to the hypothesis that termination by eubacterial RNA polymerases might not be species-specific.

Proc Natl Acad Sci U S A, 1984 Jun, 81(12), 3786 - 90
Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes; Lake JA et al.; Ribosomal large and small subunits are organized in four general structural patterns . The four types are found in ribosomes from eubacteria, archaebacteria, eukaryotes, and a group of sulfur-dependent bacteria ( eocytes ), respectively . All four ribosomal types share a common structural core, but each type also has additional independent structural features . The independent features include the eukaryotic lobes and the archaebacterial bill on the smaller subunit . On the larger subunit, they include the eocytic lobe, eocytic gap, and eocytic bulge and a modified central protuberance . These data are most parsimoniously fit by a single unrooted evolutionary tree . In this tree eocytes are closely related to eukaryotes, while archaebacteria and eubacteria are closest neighbors . The tree is consistent with currently known molecular biological properties and indicates that eocytes have a phylogenetic importance equal to that of the three known kingdoms . When other properties and molecular mechanisms of these organisms are better defined, we suggest that an appropriate kingdom name for this group would be the Eocyta .

Quad Sclavo Diagn, 1984 Jun, 20(2), 212 - 25
{Cervicovaginal cytology in women wearing intrauterine devices}; Stella F et al.; PIP: Cervical and vaginal smears in 300 women using IUDs and in 300 age matched control subjects were examined . In women using the IUD, endometrial cells have been observed also in the 2nd half of the menstrual cycle . Conversely, these cells are present in women belonging to the control group, just in the 1st half of the cycle . A pattern of cervico-vaginitis due to Chlamydiae, Actinomyces and Eubacteria have been observed in higher percentage in women IUD wearers -- 58% of the 300 women using the IUD and 19.3% of the control group subjects (P0.005) . These patterns often have been characterized by the presence of repair cells . Implications in the evaluation of vaginal smears are discussed . author's modified

Can J Biochem Cell Biol, 1984 Jun, 62(6), 426 - 33
Purification, properties, and N-terminal amino acid sequence of certain 50S ribosomal subunit proteins from the archaebacterium Halobacterium cutirubrum; Matheson AT et al.; Sixteen ribosomal proteins (r-proteins) from the 50S ribosomal subunit of the archaebacterium Halobacterium cutirubrum have been purified and their amino acid composition and partial N-terminal amino acid sequence have been determined . These proteins as a group are much more acidic than the large subunit r-proteins from eubacteria or eukaryotes . Little sequence homology is evident between the 50S subunit archaebacterial r-proteins and the equivalent proteins from the eubacterium Escherichia coli.

Jpn J Antibiot, 1984 Jun, 37(6), 1058 - 69
{Antibacterial activity of MT-141 against anaerobic bacteria}; Watanabe T et al.; In vitro and in vivo antibacterial activities of MT-141, a new cephamycin, against anaerobic bacteria were compared with those of cefmetazole (CMZ), cefoxitin, cefotaxime, ceftizoxime, latamoxef and cefazolin to obtain the following results . MT-141 showed high activity against a wide variety of anaerobic bacteria including B . fragilis and C . difficile except for Eubacterium lentum, E . aerofaciens and B . furcosus . Antibacterial activity of MT-141 against anaerobic bacteria was almost independent of inoculum size, medium, pH and serum addition . In vitro development of resistance of MT-141 against P . variabilis and B . fragilis was comparable to that of CMZ . Successive parenteral administration of MT-141 into mice did not cause abnormal proliferation of C . difficile . MT-141 showed excellent therapeutic effect against experimental subcutaneous abscess in mice caused by B . fragilis.

J Biol Chem, 1984 May 25, 259(10), 6340 - 5
Phenylalanyl-tRNA synthetase from the archaebacterium Methanosarcina barkeri; Rauhut R et al.; Phenylalanyl-tRNA synthetase from the archaebacterium Methanosarcina barkeri was purified 1620-fold with 24% overall yield . It appears to be a tetrameric enzyme with a molecular mass of 270 kDa, as determined by gel filtration, with a subunit structure of alpha 2 beta 2 (alpha = 63 kDa, beta = 70 kDa), as determined by sodium dodecyl sulfate gel electrophoresis . No conservation of common antigenic determinants is noted with polyclonal antibodies raised against the enzymes of Escherichia coli, yeast, and hen liver . Heterologous aminoacylation of tRNA with high selectivity for archaebacterial tRNA and substrate properties of ATP analogues reveals a unique pattern, reflecting the supposed genealogical difference between the urkingdoms of archaebacteria, eubacteria, and eukaryotes.

FEBS Lett, 1984 Apr 9, 169(1), 67 - 72
Reconstitution of 50 S ribosomal subunits from Bacillus stearothermophilus with 5 S RNA from spinach chloroplasts and low-Mr RNA from mitochondria of Locusta migratoria and bovine liver; Vogel DW et al.; Reconstitution experiments with 50 S ribosomal subunits from Bacillus stearothermophilus demonstrate that spinach chloroplast 5 S rRNA can be incorporated into the bacterial ribosome and yield biologically active particles, thereby establishing the eubacterial nature of chloroplast 5 S rRNA . In contrast, mitochondria from Locusta migratoria or bovine liver do not appear to contain discrete, low-Mr RNAs, which can replace 5 S rRNA in the functional reconstitution of B . stearothermophilus ribosomes.

Appl Environ Microbiol, 1984 Apr, 47(4), 735 - 9
7 alpha-Dehydroxylation of bile acids by resting cells of a Eubacterium lentum-like intestinal anaerobe, strain c-25; Masuda N et al.; 7 alpha-Dehydroxylation of cholic acid and chenodeoxycholic acid by whole cells of strain c-25, a Eubacterium lentum-like intestinal anaerobe, was studied . 7 alpha-Dehydroxylase activity was observed only in whole cells grown in the presence of the primary bile acid (cholic acid or chenodeoxycholic acid) . Chenodeoxycholic acid was twice as effective as cholic acid as an inducer . Although cells grown in the presence of chenodeoxycholic acid had no significant substrate specificity for the two primary bile acids, cells grown in the presence of cholic acid showed two times greater activity against cholic acid than chenodeoxycholic acid . Exposure of cell suspensions to atmospheric oxygen resulted in little loss of the 7 alpha-dehydroxylase activity . The induced enzyme had an optimal pH range of 7.3 to 7.7 . Although adding flavin mononucleotide to the growth medium significantly increased the 7 alpha-dehydroxylation of bile acids without an increase in cell growth, inhibition of the enzyme activity was observed in the resting cell system when flavin mononucleotide was included in the reaction mixture.

J Med Microbiol, 1984 Apr, 17(2), 207 - 9
Agglutinins to anaerobic bacteria in Crohn's disease and in Indian patients with diarrhoea; Howells B et al.; Agglutinins to certain species of Eubacterium and Peptostreptococcus have been reported in sera from a high proportion of patients with Crohn's disease . Because this might be a non-specific finding common to patients with diarrhoea associated with damaged intestinal mucosa, we have compared the incidence of such agglutinins in patients with Crohn's disease with that seen in patients in North-East India with acute or chronic diarrhoea . The incidence of agglutinins in Crohn's disease was 44%, compared with 11% in acute and 17% in chronic diarrhoea . These figures suggest that mucosal damage alone does not explain the high incidence of agglutinins in Crohn's disease.

J Biochem (Tokyo), 1984 Apr, 95(4), 1179 - 86
Binding sites of rat liver 5S RNA to ribosomal protein L5; Aoyama K et al.; The ribonucleoprotein complex consisting of 5S RNA and the protein L5 was prepared from the large subunit of rat liver ribosomes . The RNA in the complex was digested in situ with RNase A or RNase T1 . The RNase-resistant RNA fragments bound to the protein were recovered and purified by 2D-PAGE, and their nucleotide sequences were determined in order to elucidate the binding sites of the RNA to the protein . The results showed that the fragments had arisen from the 5'-end region (residues 1-21), from the second hairpin loop (residues 77-102) and from the 3'-end region (residues 106-120) . Harsher digestion trimmed these fragments to shorter fragments . It was concluded that the minimal interactive sequences of 5S RNA to the protein L5 were residues 13-21, residues 85-102, and residues 106-114 . A part of the first hairpin loop, residues 41-52, was also suspected to interact with the protein . These protein-binding sites of rat liver 5S RNA were compared with those of Escherichia coli, Halobacterium cutirubrum and yeast, and their probable conservation from eubacteria to eukaryotes is discussed.

J Bacteriol, 1984 Apr, 158(1), 84 - 93
Methylation of ribosomal proteins in bacteria: evidence of conserved modification of the eubacterial 50S subunit; Amaro AM et al.; Methylation of the 50S ribosomal proteins from Bacillus stearothermophilus, Bacillus subtilis, Alteromonas espejiana, and Halobacterium cutirubrum was measured after the cells were grown in the presence of {1-14C}methionine or {methyl-3H}methionine or both . Two-dimensional polyacrylamide gel electrophoretic analysis revealed, in general, similar relative electrophoretic mobilities of the methylated proteins from each eubacterium studied . Proteins known to be structurally and functionally homologous in several microorganisms were all methylated . Thus, the following group of proteins, which appear to be involved in peptidyltransferase or in polyphenylalanine-synthesizing activity in B . stearothermophilus (P.E . Auron and S . R . Fahnestock, J . Biol . Chem . 256:10105-10110, 1981), were methylated (possible Escherichia coli methylated homologs are indicated in parentheses): BTL5(EL5), BTL6(EL3), BTL8(EL10), BTL11(EL11), BTL13(EL7L12) and BTL20b(EL16) . In addition, the pentameric ribosomal complex BTL13 X BTL8, analogous to the complex EL7L12 X EL10 of E . coli, contained methylated proteins . Analysis of the methylated amino acids in the most heavily methylated proteins, BSL11 from B . subtilis and BTL11 from B . stearothermophilus, showed the presence of epsilon-N-trimethyllysine as the major methylated amino acid in both proteins, in agreement with known data for E . coli . In addition, BSL11 appeared to contain trimethylalanine, a characteristic, modified amino acid previously described only in EL11 from E . coli . These results and those previously obtained from other bacteria indicate a high degree of conservation for ribosomal protein methylation and suggest an important, albeit unknown, role for the modification of these components in eubacterial ribosomes.

J Bacteriol, 1984 Apr, 158(1), 286 - 95
Cloning and manipulation of the Escherichia coli cyclopropane fatty acid synthase gene: physiological aspects of enzyme overproduction; Grogan DW et al.; Like many other eubacteria, cultures of Escherichia coli accumulate cyclopropane fatty acids (CFAs) at a well-defined stage of growth, due to the action of the cytoplasmic enzyme CFA synthase . We report the isolation of the putative structural gene, cfa, for this enzyme on an E . coli-ColE1 chimeric plasmid by the use of an autoradiographic colony screening technique . When introduced into a variety of E . coli strains, this plasmid, pLC18-11, induced corresponding increases in CFA content and CFA synthase activity . Subsequent manipulation of the cfa locus, facilitated by the insertion of pLC18-11 into a bacteriophage lambda vector, allowed genetic and physiological studies of CFA synthase in E . coli . Overproduction of this enzyme via multicopy cfa plasmids caused abnormally high levels of CFA in membrane phospholipid but no discernable growth perturbation . Infection with phage lambda derivatives bearing cfa caused transient overproduction of the enzyme, although pL-mediated expression of cfa could not be demonstrated in plasmids derived from such phages . CFA synthase specific activities could be raised to very high levels by using cfa runaway-replication plasmids . A variety of physiological factors were found to modulate the levels of CFA synthase in normal and gene-amplified cultures . These studies argue against several possible mechanisms for the temporal regulation of CFA formation.

Rev Infect Dis, 1984 Mar-Apr, 6 Suppl 1, S107 - 14
Anaerobic oral and dental infection; Newman MG; Anaerobes make up a significant part of the oral and dental indigenous and pathogenic flora . Their role in periodontal disease, root canal infections, infections of the hard and soft oral tissue, as well as their importance as foci for disseminated infectious disease is well established . Despite the ubiquitous involvement of bacteria, significant progress in our understanding of specific microbial etiologies has occurred only in the past decade . Estimates of the number of species recovered from samples of subgingival plaque range from 250 to 400, a large portion made up by anaerobes . Common anaerobic isolates include Fusobacterium, Bacteroides, Actinomyces, Peptococcus, Peptostreptococcus, Selenomonas, Eubacterium, Propionibacterium, and Treponema . Recently, several significant advances in our knowledge have set the stage for future research . First, circulating levels of hormones in pregnant women were shown to be stimulatory to Bacteroides species, which were associated with increased levels of gingival infection . Second, bacterial invasion of the soft and hard periodontal tissues has been documented in gingivitis, advanced periodontitis, and localized juvenile periodontitis . The frequency and identity of invading bacteria will determine the implications for diagnosis and treatment . Third, antibacterial "probes" aimed at anaerobic (and capnophilic) bacteria have had promising results in controlling and arresting oral, dental, and peridontal anaerobic infections.

Nature, 1984 Feb 23-29, 307(5953), 735 - 7
Molecular genetic evidence for early evolutionary origin of budding peptidoglycan-less eubacteria; Stackebrandt E et al.; Recent studies on the cell wall composition of budding, non-prosthecate bacteria have shown that representatives of the genera Planctomyces and Pasteuria (sensu Staley, 1973) lack the peptidoglycan moiety, which is the characteristic feature of eubacterial cell walls, but possess an as yet unidentified protein sheet instead; in this respect Planctomyces and Pasteuria strains resemble certain archaebacteria more than eubacteria . To determine their phylogenetic positions, the 16S ribosomal RNAs of three budding, peptidoglycan-less strains with and without stalks were subjected to partial sequence analyses . As we report here, the comparison of data with those obtained from about 320 eubacterial and 40 archaebacterial strains revealed that the strains investigated are not members of the archaebacterial kingdom but represent an ancient line of descent of the eubacterial kingdom . Furthermore the diphtheria toxin reaction of Planctomyces and Pasteuria shows that they behave like eubacteria.

Can J Microbiol, 1984 Feb, 30(2), 251 - 9
Preliminary characterization of inhibitors of Neisseria gonorrhoeae produced in vitro by Eubacterium limosum; Morin A et al.; Among anaerobic bacteria normally found in the urogenital flora, Eubacterium limosum was found to inhibit the in vitro growth of Neisseria gonorrhoeae . The antigonococcal activity produced by E . limosum was soluble in methanol and in a chloroform--methanol mixture (30:70) . The fraction soluble in chloroform--methanol (30:70) yielded eight absorbance peaks when chromatographed on Bio-Gel P-2 and the inhibitory activity was found in the first two peaks . This activity was not absorbed on DEAE Sephacel and was eluted with distilled water in a peak considered as peak 1, on which preliminary characterization was done . The inhibitory activity of peak 1 was found to be heat and pH resistant and not susceptible to proteases, lipase, or amylases . When peak 1 was chromatographed on cellulose paper using a butanol--acetic acid (4:1) solvent system, eight different spots were detected upon spraying the paper with ninhydrin . No spot was detected with anthrone, bromothymol, nor Sudan black reagents used for the detection of carbohydrates and lipids . Based on sodium dodecyl sulfate-urea polyacrylamide gel electrophoresis and gel chromatography on Sephadex G-25, peak 1 appeared either as a diffuse band and as a single peak, respectively . The molecular weight of the inhibitory complex was estimated to be 2400 . All these results suggest that the antigonococcal activity produced by E . limosum is composed of more than one low molecular weight amino compound.

J Periodontol, 1984 Feb, 55(2), 93 - 7
Eubacterium brachy . Reactivity in in vitro bone resorptive bioassay; Vincent JW et al.; Recent studies have demonstrated an association of Eubacterium sp . with the subgingival microflora of patients with chronic periodontitis . One species, Eubacterium brachy, was evaluated to determine the possible mechanisms by which this microorganism may contribute to this disease . An extracellular antigen was identified in the culture supernatant which reacted with antibodies in human sera . This antigen was isolated by methanol precipitation and purified by gel filtration . The purified extracellular antigen was reacted in vitro with 45CaCl2-labeled fetal rat bone in a bone resorptive bioassay . This antigen was shown to have a molecular weight of 170,000, to share a line of identity with a sonicated preparation of E . brachy whole cells and to result in increased 45CaCl2 release from fetal rat bones when cultures were exposed to the purified extracellular antigen at concentrations of 10 to 53 micrograms/ml.

Proc Natl Acad Sci U S A, 1984 Feb, 81(3), 848 - 52
Major heat shock gene of Drosophila and the Escherichia coli heat-inducible dnaK gene are homologous; Bardwell JC et al.; The Escherichia coli dnaK gene is homologous to the major heat shock-induced gene in Drosophila (Hsp70) . The primary DNA sequence of the entire protein-coding region of the dnaK gene was determined and compared with that of the Hsp70 gene of Drosophila . The two sequences are homologous; the dnaK gene could encode a 69,121-Da polypeptide, 48% identical to the hsp70 protein of Drosophila . The homology between the Hsp70 gene of Drosophila and the E . coli dnaK gene illustrates the remarkable conservation of the heat shock genes in evolution . In contrast to Drosophila and Saccharomyces cerevisiae, both of which contain multigene families related to the Hsp70 gene, hybridization analyses indicate that E . coli contains only a single Hsp70-related gene, dnaK . Hybridization between the DNA of an archaebacterium Methanosarcina barkeri and the Hsp70 genes of Drosophila, Saccharomyces, and E . coli has been detected, suggesting the existence of Hsp70-related genes in the three "primary kingdoms": eukaryotes, eubacteria, and archaebacteria.

J Biol Chem, 1984 Jan 10, 259(1), 224 - 30
The nucleotide sequence of a rat 18 S ribosomal ribonucleic acid gene and a proposal for the secondary structure of 18 S ribosomal ribonucleic acid; Chan YL et al.; The nucleotide sequence of a rat 18 S rRNA gene was determined . The 18 S rRNA encoded in the gene contains 1874 nucleotides, and the molecular weight estimated from the sequence is 6.09 X 10(5) . The sequences of rat and Xenopus laevis 18 S rRNAs are very similar; the only differences of consequence are the insertions between nucleotides 197 and 206 and between 258 and 279 of the rat nucleic acid of sequences rich in guanine and cytosine . A proposal is presented for the secondary structure of rat 18 S rRNA based on a comparison with the sequences of 17 other small ribosomal subunit RNAs . While the primary sequences of rat and eubacterial RNAs are different, the deduced secondary structures are remarkably similar.

Mol Gen Genet, 1984, 196(1), 146 - 51
Apparent operon for a 5S ribosomal RNA gene and for tRNA genes in the archaebacterium Methanococcus vannielii; Wich G et al.; The nucleotide sequence of the chromosomal segment from Methanococcus vannielii previously shown to encode a gene for 5S ribosomal RNA (rRNA) unlinked to any other rRNA genes (Jarsch et al . 1983) was determined . It was found that the 5S rRNA gene is flanked by seven genes for tRNA (tRNAPro, tRNAThr, tRNATyr, tRNALys and tRNAAsp) . Two of the tRNA genes (tRNAAsp and tRNALys) are repeated in the cluster . Only the tRNAPro cistron encodes the 3'-CCA tRNA sequence . The 5S rRNA/tRNA gene cluster probably represents one transcriptional unit . The 5'- and 3'-flanking sequences of the tRNA/5S rRNA gene cluster bear some similarity with initiation and termination signals in eubacteria . There is indication that the different 5S rRNA genes from Methanococcus exhibit sequence polymorphism.

Appl Environ Microbiol, 1984 Jan, 47(1), 39 - 43
Biotransformation of linoleic acid and bile acids by Eubacterium lentum; Eyssen H et al.; Eubacterium lentum is a gram-positive, nonsporeforming, nonmotile, asaccharolytic anaerobe . In the present investigations, 3 E . lentum strains (group E) isolated from rat feces were compared with 30 E . lentum strains (groups A, B, C, and D) previously studied by Macdonald et al . (I . A . Macdonald, J . F . Jellet, D . E . Mahony, and L . V . Holdeman, Appl . Environ . Microbiol . 37:992-1000, 1979) . All strains alkalized (pH 8 to 8.5) arginine-containing (2 to 15 mg/ml) culture media, and growth of the majority of the strains was stimulated by arginine . All strains converted linoleic acid into transvaccenic acid by shifting the 12,13-cis double bond of linoleic acid into an 11,12-trans(?) double bond followed by biohydrogenation of the 9,10-cis double bond . Hence, biohydrogenation of linoleic acid is a new general characteristic of E . lentum . The 33 strains were also studied for bile acid deconjugase and hydroxysteroid dehydrogenase (HSDH) activities . The 6 strains in group D were steroid inactive; the 27 strains in groups A, B, C, and E were steroid active . The steroid-active group contained bile acid deconjugase-producing strains (groups C and E, plus strain 116 in group A) and nondeconjugating strains . All nondeconjugating strains of groups A and B developed 7 alpha- and 12 alpha-HSDH activities and contained 3 alpha-HSDH-positive strains and 3 alpha-HSDH-negative strains . Deconjugating strains varied in HSDH activities.

J Mol Evol, 1984-85, 21(4), 334 - 7
Phylogeny of the 5S ribosomal RNA from Synechococcus lividus II: the cyanobacterial/chloroplast 5S RNAs form a common structural class; Delihas N et al.; The complete nucleotide sequence of the 5S ribosomal RNA from the cyanobacterium Synechococcus lividus II has been determined . The sequence is (sequence in text) This 5S RNA has the cyanobacterial- and chloroplast-specific nucleotide insertion between positions 30 and 31 (using the numbering system of the generalized eubacterial 5S RNA) and the chloroplast-specific nucleotide-deletion signature between positions 34 and 39 . The 5S RNA of S . lividus II has 27 base differences compared with the 5S RNA of the related strain S . lividus III . This large difference may reflect an ancient divergence between these two organisms . The electrophoretic mobilities on nondenaturing polyacrylamide gels of renatured 5S RNAs from S . lividus II, S . lividus III, and spinach chloroplasts are identical, but differ considerably from that of Escherichia coli 5S RNA . This most likely reflects differences in higher-order structure between the 5S RNA of E . coli and these cyanobacterial and chloroplast 5S RNAs.

Proc Natl Acad Sci U S A, 1984 Jan, 81(2), 493 - 7
Pronounced structural similarities between the small subunit ribosomal RNA genes of wheat mitochondria and Escherichia coli; Spencer DF et al.; We present here the nucleotide sequence of the small subunit (18S) rRNA gene from wheat mitochondria . Aside from five discrete variable domains, this gene and the analogous (16S) rRNA gene in Escherichia coli show essentially a one-to-one correspondence in their potential secondary structures, with regions accounting for 86% of the bacterial 16S rRNA having a strict secondary structure counterpart in the mitochondrial 18S rRNA . Primary sequence identity between the two rRNAs ranges from 73% to 85% (76% overall) within regions of conserved secondary structure . Within a smaller secondary structure core common to all small subunit rRNAs, the wheat mitochondrial sequence shares substantially more primary sequence identity with the E . coli (eubacterial) sequence (88%) than with the small subunit rRNA sequences of Halobacterium volcanii (an archaebacterium) (71%) or Xenopus laevis cytoplasm (61%) . Moreover, the wheat mitochondrial sequence contains a very high proportion of certain lineage-specific residues that distinguish eubacterial/plastid 16S rRNAs from archaebacterial 16S and eukaryotic cytoplasmic 18S rRNAs . These data establish that the ancestry of the wheat mitochondrial 18S rRNA gene can be traced directly and specifically to the eubacterial primary kingdom, and the data provide compelling support for a relatively recent xenogenous (endosymbiotic) origin of plant mitochondria from eubacteria-like organisms.

Ann Microbiol (Paris), 1984 Jan-Feb, 135A(1), 9 - 15
Molecular and biological features of mollicutes (mycoplasmas); Razin S et al.; The small size of the mollicute genome considerably restricts the amount of genetic information available to the organisms . This is reflected in the relatively small number of cell proteins synthesized, the lack of many biosynthetic pathways and the marked dependence on exogenous nutrients for growth . The protein synthesizing machinery of mollicutes resembles that of eubacteria and is sensitive to the same antibiotics, except for rifampicin, to which RNA polymerases of mollicutes appear resistant . The mollicute ribosomes are built of 50 S and 30 S subunits and contain about 50 different proteins and 5 S, 16 S and 23 S rRNA, as in eubacteria . However, the 5 S rRNA in mollicutes appears shorter (107-112 nucleotides) than in eubacteria (116-120 nucleotides) . We hybridized restriction endonuclease-digested DNA from a variety of Mycoplasma, Ureaplasma, Acholeplasma and Spiroplasma species with nick-translated probes consisting of defined portions of the rrnB rRNA operon of Escherichia coli and the rRNA operon of M . capricolum . The results suggest the presence of only one or two sets (operons) of rRNA genes in the genome of Mollicutes, a number falling considerably below that of the eubacteria examined so far but resembling that found in archaebacteria . Our data also indicate a marked nucleotide sequence homology along the rrnB rRNA operon of E . coli and the rRNA operons of the various mollicutes, indicating that the rRNA genes in mollicutes are linked in the classical prokaryotic fashion 16 S-23 S-5 S . Each mollicute appeared to possess, on its genome, different flanking sequences adjacent to the rRNA operon(s), resulting in species-specific hybridization patterns.(ABSTRACT TRUNCATED AT 250 WORDS)

J Mol Evol, 1984-85, 21(4), 305 - 16
What are mycoplasmas: the relationship of tempo and mode in bacterial evolution; Woese CR et al.; In phenotype the mycoplasmas are very different from ordinary bacteria . However, genotypically (i.e., phylogenetically) they are not . On the basis of ribosomal RNA homologies the mycoplasmas belong with the clostridia, and indeed have specific clostridial relatives . Mycoplasmas are, however, unlike almost all other bacteria in the evolutionary characteristics of their ribosomal RNAs . These RNAs contain relatively few of the highly conserved oligonucleotide sequences characteristic of normal eubacterial ribosomal RNAs . This is interpreted to be a reflection of an elevated mutation rate in mycoplasma lines of descent . A general consequence of this would be that the variation associated with a mycoplasma population is augmented both in number and kind, which in turn would lead to an unusual evolutionary course, one unique in all respects . Mycoplasmas, then, are actually tachytelic bacteria . The unusual evolutionary characteristics of their ribosomal RNAs are the imprints of their rapid evolution.

J S Afr Vet Assoc, 1983 Dec, 54(4), 243 - 5
The effect of lincomycin-neomycin treatment on experimental anaerobic bacterial bovine mastitis; Du Preez JH et al.; Three healthy lactating quarters of a Friesland cow were each experimentally infected with a pure culture of a strain of either Bacteroides fragilis, Eubacterium lentum or a Peptostreptococcus sp . respectively . The onset and progression to clinical mastitis was monitored 12 hourly by examination for clinical signs of inflammation, bacterial culture, somatic cell counts and with a strip cup . All infected quarters developed clinical mastitis within 24 hours . The 2 quarters infected with B . fragilis and E . lentum respectively were treated 4 times consecutively at 12 hour intervals, commencing at 24 h by intramammary instillation of 10 ml of a mixture containing 200 mg lincomycin hydrochloride, 200 mg neomycin sulphate and 5 mg methylprednisolone (Lincocin Forte, Upjohn) . Both quarters became clinically normal and no bacteria could be detected in the secretions 12 hours after the first treatment . At 36 hours the strip cup became negative, and the somatic cell count dropped to less than 500 X 10(3) at 72 hours after the initial treatment . The quarter infected with a Peptostreptococcus sp . was unable to overcome the infection by natural means when intramammary treatment was delayed for the first 36 hours after the onset of clinical mastitis . Subsequent treatment of this quarter gave results similar to those treated earlier.

Eur J Biochem, 1983 Nov 2, 136(2), 241 - 4
Purification of the elongation factor Tu (EF-Tu) from the cyanobacterium Spirulina platensis; Tiboni O et al.; Elongation factor Tu (EF-Tu) has been purified from the cyanobacterium Spirulina platensis . By gel electrophoresis the Mr of the purified protein appears to be 49 000, a value close to that reported for the EF-Tu isolated from a number of bacteria but higher than that reported for the protein isolated from Escherichia coli (43 000) . Functionally, however, S . platensis EF-Tu may replace the E . coli protein in a protein-synthesizing system in vitro . In addition, its activity is affected by kirromycin, an antibiotic that specifically interacts with eubacterial EF-Tu.

J Bacteriol, 1983 Oct, 156(1), 375 - 85
In vivo metabolic intermediates of phospholipid biosynthesis in Rhodopseudomonas sphaeroides; Cain BD et al.; The in vivo metabolic pathways of phospholipid biosynthesis in Rhodopseudomonas sphaeroides have been investigated . Rapid pulse-chase-labeling studies indicated that phosphatidylethanolamine and phosphatidylglycerol were synthesized as in other eubacteria . The labeling pattern observed for N-acylphosphatidylserine (NAPS) was inconsistent with the synthesis of this phospholipid occurring by direct acylation of phosphatidylserine (PS) . Rather, NAPS appeared to be kinetically derived from an earlier intermediate such as phosphatidic acid or more likely CDP-diglyceride . Tris-induced NAPS accumulation specifically reduced the synthesis of PS . Treatment of cells with a bacteriostatic concentration of hydroxylamine (10 mM) greatly reduced total cellular phospholipid synthesis, resulted in accumulation of PS, and stimulated the phosphatidylglycerol branch of phospholipid metabolism relative to the PS branch of the pathway . When the cells were treated with a lower hydroxylamine dosage (50 microM), total phospholipid synthesis lagged as PS accumulated, however, phospholipid synthesis resumed coincident with a reversal of PS accumulation . Hydroxylamine alone was not sufficient to promote NAPS accumulation but this compound allowed continued NAPS accumulation when cells were grown in medium containing Tris . The significance of these observations is discussed in terms of NAPS biosynthesis being representative of a previously undescribed branch of the phospholipid biosynthetic sequence.

J Mol Biol, 1983 Sep 5, 169(1), 249 - 79
Higher order structure in the 3'-minor domain of small subunit ribosomal RNAs from a gram negative bacterium, a gram positive bacterium and a eukaryote; Douthwaite S et al.; An experimental approach was used to determine and compare the highest order structure within the 150 to 200 nucleotides at the 3'-ends of the RNAs from the small ribosomal subunits of Escherichia coli, Bacillus stearothermophilus and Saccharomyces cerevisiae . Chemical reagents were employed to establish the degree of stacking and/or accessibility of each adenosine, guanosine and cytidine . The double helices were probed with a cobra venom ribonuclease from Naja naja oxiana, and the relatively unstructured and accessible sequences were localized with the single strand-specific ribonucleases A, T1, T2 and S1 . The data enabled the various minimal secondary structural models, proposed for the 3'-regions of the E . coli and S . cerevisiae RNAs, to be critically examined, and to demonstrate that the main common features of these models are correct . The results also reveal the presence and position of additional higher order structure in the renatured free RNA . It can be concluded that a high level of conservation of higher order structure has occurred during the evolution of the gram negative and gram positive eubacteria and the eukaryote in both the double helical regions and the "unstructured" regions . Several unusual structural features were detected . Multiple G X A pairings in two of the putative helices, which are compatible with phylogenetic sequence comparisons, are strongly supported by the occurrence of cobra venom ribonuclease cuts adjacent to, and in one case between, these pairings . Evidence is also provided for the stacking of an A X A pair within a double helix of the yeast RNA . Other special structural features include adenosines bulged out from double helices; such nucleotides, which are hyper-reactive, have been implicated in protein recognition in 5 S ribosomal RNA . The 3'-terminal regions of the RNAs are particularly important for the functioning of the ribosome . They are involved in mRNA, tRNA and ribosomal factor binding . The results reveal that while the functionally important RNA sequences tend to be conserved, they are not always accessible in the free RNA; the pyrimidine-rich "Shine and Dalgarno" sequence, for example, which is involved in mRNA recognition, occurs in a double helix in both eubacterial RNAs.

Yale J Biol Med, 1983 Sep-Dec, 56(5-6), 373 - 6
The ribosomal genes of Mycoplasma capricolum; Muto A et al.; The nucleotide sequence of 5S rRNA from Mycoplasma capricolum is more similar to that of the gram-positive bacteria than that of the gram-negative bacteria . The presence of two copies of rRNA genes in M . capricolum genome has been demonstrated . The two different rRNA gene clusters have been cloned in E . coli plasmid vectors and analyzed for the rRNA gene organizations, demonstrating that the gene arrangement is in the order of 16S, 23S, and 5S rDNA . The ribosomes of M . capricolum contain about 30 species of proteins in 50S and 20 in 30S subunits . The number and size of the ribosomal proteins are not significantly different from those of other eubacterial ribosomes.

Yale J Biol Med, 1983 Sep-Dec, 56(5-6), 367 - 72
Mycoplasma evolution: a review of the use of ribosomal and transfer RNA nucleotide sequences in the determination of phylogenetic relationships; Walker RT; Comparison of the nucleotide sequences of "structural" RNAs (ribosomal and transfer RNA) has enabled the construction of phylogenetic trees to be achieved . Data from 16S rRNA, 5S rRNA, and tRNA from a total of eight Mollicutes (excluding T . acidophilum) including representatives of the families Mycoplasmataceae, Spiroplasmataceae, and Acholeplasmataceae, show that these families share a close relationship and a common ancestor with the gram-positive eubacteria . Thermoplasma acidophilum is a member of the kingdom Archaebacteriae and has no relationship to the other Mollicutes.

Dtsch Med Wochenschr, 1983 Aug 19, 108(33), 1242 - 6
{Serodiagnosis of Crohn's disease}; Auer IO et al.; Three serological tests, recommended as being of diagnostic value for Crohn's disease, were evaluated in 39 patients with Crohn's disease and--as controls--in 27 patients with ulcerative colitis, 45 healthy persons and 65 patients with inflammatory diseases other than Crohn's disease or ulcerative colitis . The tests were the determination of (1) serum antibodies to pseudomonas-like organisms (PLO) by means of indirect immunofluorescence; (2) agglutinating serum antibodies to 4 strains of anaerobic gram-positive coccoid rods (species of Eubacterium, Peptostreptococcus and Coprococcus); and (3) serum antibodies to perinuclear antigens in buccal mucosa of Crohn's disease patients by immunofluorescence . The results indicate that the occurrence of high-titer antibodies to PLO is reasonably sensitive for Crohn's disease, but has a low specificity, and that antibodies to perinuclear antigens in buccal mucosa have both low sensitivity and specificity . However, the occurrence of agglutinins to 4 strains of anaerobic grampositive coccoid rods is significantly higher in Crohn's disease than in ulcerative colitis, patients with other diseases and healthy controls . Thus the determination of these agglutinins does not discriminate between Crohn's disease and ulcerative colitis; but it is a serodiagnostic adjunct in the diagnosis of chronic inflammatory bowel diseases.

J Bacteriol, 1983 Aug, 155(2), 900 - 2
Chloroflexus aurantiacus has 30S ribosomal subunits of the eubacterial type; Henderson E et al.; Ribosomal subunits from Chloroflexus aurantiacus were isolated and examined by sucrose gradient sedimentation, gel electrophoresis, and electron microscopy . The 30S subunits had all the characteristic structural features of other eubacterial 30S subunits . The data support the proposal that the absence of the archaebacterial bill is a valid phylogenetic marker of the eubacterial lineage.

Steroids, 1983 Jul, 42(1), 105 - 14
Metabolism of bile acid oxazoline derivatives by hepatocyte monolayer cultures and intestinal anaerobic bacteria; Hylemon PB et al.; Certain bile acid oxazoline derivatives (100 microM), but not corresponding unconjugated bile acids (100 microM), were found to inhibit the growth of Eubacterium sp . V.P.I . 12708 . The growth inhibition was correlated with the polarity of the steroid portion of the bile acid oxazoline . Primary cultures of adult rat hepatocyte monolayer cultures converted {7 epsilon-14C}methylchenooxazoline3 into MeOH-H2O soluble derivatives . Certain intestinal bacteria were capable of metabolizing {17 epsilon-14C}methylchenooxazoline as well as the MeOH-soluble hepatocyte derivative(s) . These results suggest that bile acid oxazoline derivatives may undergo hepatic, as well as bacterial metabolism during enterohepatic circulation.

Nucleic Acids Res, 1983 Jun 25, 11(12), 4195 - 9
Structure of the archaebacterial transposable element ISH50; Xu WL et al.; We have sequenced in its entirety a new transposable element from the archaebacterium Halobacterium halobium . This 996 bp element shows some features not unlike those of insertion sequences from eubacteria, although it clearly differs from them in sequences which may be involved in transcription and or translation initiation.

Carbohydr Res, 1983 Jun 16, 117, 125 - 31
Structural studies of the antigenic polysaccharide of Eubacterium saburreum, strain T27; Kondo W et al.; The antigenic polysaccharide produced by Eubacterium saburreum, strain T27, is a homoglycan composed of D-glycero-D-galacto-heptose (Hep) residues having a nonasaccharide repeating-unit with the structure (leads to 6)-{alpha-Hepf-(1 leads to 4)}-beta-Hepp-(1) leads to (3)6)-{alpha-Hepf-(1 leads to 2), alpha-Hepf-(1 leads to 4)}-beta-Hepp-(1 leads to . The polysaccharide contains acetyl groups linked to O-2 (except to the 2,4,6-linked heptopyranosyl residue), O-3 and O-7 of part of both heptopyranosyl and heptofuranosyl residues . The assignment of an acetyl group at O-3 of part of the terminal heptofuranosyl and 4,6-linked heptopyranosyl groups is tentative.

Can J Microbiol, 1983 May, 29(5), 612 - 8
{Studies of mixed anaerobic infections involving Bacteroides gingivalis}; Grenier D et al.; The infectiousness of several combinations of bacteria containing Bacteroides gingivalis and other bacteria associated with periodontal diseases was evaluated by subcutaneous injection to guinea pigs . Among the seven mixtures studied, only one permitted the development of an infection easily transmissible to a second guinea pig; this bacterial mixture was composed of B . gingivalis, Fusobacterium nucleatum, Eubacterium saburreum, and Capnocytophaga ochracea (formerly Bacteroides ochraceus) . Owing to its ability to synthesize many lytic enzymes and potentially cytotoxic products, B . gingivalis represented the most virulent species of the mixture . Results from in vitro studies suggest that the development of B . gingivalis in the infected animal depends on the growth of C . ochracea . Succinic acid produced in large amount by C . ochracea seems to be one of the growth factors used by B . gingivalis.

Science, 1983 Apr 15, 220(4594), 325 - 7
Digoxin-inactivating bacteria: identification in human gut flora; Saha JR et al.; Digoxin, the most widely used cardiac glycoside, undergoes significant metabolic conversion in many patients to cardioinactive metabolites in which the lactone ring is reduced . This appears to occur within the gastrointestinal tract . An attempt was made to isolate and identify the organisms capable of reducing digoxin from stool cultures obtained from human volunteers . Of hundreds of isolates studied, only Eubacterium lentum, a common anaerobe of the human colonic flora, converted digoxin to reduced derivatives . Such organisms were also isolated in high concentrations from the stools of individuals who did not excrete these metabolites when given digoxin in vivo . When the growth of E . lentum was stimulated by arginine, inactivation of digoxin was inhibited . Neither the presence of these organisms alone nor their concentration within the gut flora appeared to determine whether digoxin would be inactivated by this pathway in vivo.

J Comp Pathol, 1983 Apr, 93(2), 235 - 42
Infectious necrotic hepatitis caused by an unclassified anaerobic bacillus in the water snake; Chiodini RJ et al.; Necrotic hepatitis resembling black disease of ruminants is described in a group of five water snakes (Natrix sipedon pictiventirs) . Lesions varied from multifocal granulomas to massive coagulation necrosis . A bacterium recovered from the livers could not be classified, but closely resembled Eubacterium tarantellus . The bacterium was isolated from all snake livers and from snake mites (Ophionyssus natricis) which were probably implicated in the transmission of the disease and it is possible that trematodes were concerned in producing the initial damage to the liver.

Poult Sci, 1983 Apr, 62(4), 675 - 82
Cecal microflora of turkeys fed low or high fiber diets: enumeration, identification, and determination of cellulolytic activity; Bedbury HP et al.; Examination of cecal contents or bacterial cultures thereof from turkeys fed either a high fiber (HF) or low fiber (LF) ration indicated that direct microscopic counts of microbes were significantly higher in HF-fed than in LF-fed birds . There was no significant difference in mean colony counts between the two groups of turkeys . In both LF and HF-fed birds, 77% of the microbes were Gram-positive rods, 14% Gram-negative rods, and 9% Gram-positive cocci . The predominant microorganism was Eubacterium, but Lactobacillus, Peptostreptococcus, Escherichia coli, Propionibacterium, and Bacteriodes were also isolated . Percentages of Peptostreptococcus were significantly greater in HF-fed turkeys and of E . coli were significantly greater in LF-fed turkeys . Yeasts were routinely found in both LF and HF-fed birds, but protozoa were not isolated . Turkeys fed the HF diet harbored significantly higher numbers of facultative microorganisms than did LF-fed birds . In pure cultures from turkeys preconditioned to a HF diet, there was a nonsignificant trend toward greater cellulolysis than in pure cultures from LF-fed turkeys . In contrast, cellulolysis by mixed cultures from HF-fed birds was significantly greater than that in mixed cultures from LF-fed turkeys.

Scand J Gastroenterol, 1983 Mar, 18(2), 217 - 23
Selected bacterial antibodies in Crohn's disease and ulcerative colitis; Auer IO et al.; Agglutinins to four strains of anaerobic gram-positive coccoid rods (species of Eubacterium, Peptostreptococcus and Coprococcus) were found in significantly higher frequency in Crohn's disease (CD) than in ulcerative colitis (UC) and in other diseased control subjects and were virtually absent in apparently healthy subjects . When the posterior probability of having CD was calculated on the basis of these agglutination reactions, 64% of patients with CD and 34% of patients with UC but only 10% of diseased controls and none of the healthy controls were regarded as 'probable' or 'definite' cases of CD . However, the posterior probability of CD did not sharply differentiate between CD and UC but indicated chronic inflammatory bowel disease . Factors contributing to the appearance of these agglutinins in CD were also evaluated . The findings would indicate the importance of a damaged intestinal mucosal barrier for the production of these agglutinins, provided the antigens are present in the intestine . No significant differences were observed between the occurrence of antibodies to pseudomonas-like organisms (PLO) in CD and the various control groups . The study could not add further evidence to the hypothesis of a possible aetiopathogenic role of PLO in CD.

Regul Toxicol Pharmacol, 1983 Mar, 3(1), 82 - 99
Further studies on environmental factors that modify the toxicity of nickel to microbes; Babich H et al.; The toxicity of nickel (Ni) to mycelial growth of filamentous fungi and to replication of eubacteria, an actinomycete, and yeasts was influenced by various environmental abiotic factors . Sulfide and phosphate reduced the toxicity of Ni by the formation of insoluble salts . The clay minerals, montmorillonite and, to a much lesser extent, kaolinite, and the hydrous oxides of aluminum or manganese reduced the toxicity, presumably by the adsorption of cationic Ni to their net negatively charged surfaces . Amino acids, such as aspartic acid, complex organics, such as tryptone, casamino acids, and yeast extract, and chelating agents, such as citrate, 2,6-pyridine dicarboxylic acid, nitrilotriacetic acid, and ethylenediaminetetraacetic acid, significantly reduced the toxicity of Ni, presumably as the result of decreased attraction between the net negatively charged cell surfaces and the complexed Ni . The toxicity of Ni varied in different commercial media, with greater toxicities occurring in nutrient broth and MR-VP medium and lower toxicities occurring in lauryl tryptone, Elliker, microinoculum, and tryptic soy broths . Nickel had a lower toxicity in solid media gelled with Gelrite than with Bacto-agar.

J Bacteriol, 1983 Mar, 153(3), 1342 - 7
Occurrence of diphthamide in archaebacteria; Pappenheimer AM Jr et al.; We examined the nature of the diphtheria toxin fragment A recognition site in the protein synthesis translocating factor present in cell-free preparations from the archaebacteria Thermoplasma acidophilum and Halobacterium halobium . In agreement with earlier work (M . Kessel and F . Klink, Nature (London) 287:250-251, 1980), we found that extracts from these organisms contain a protein factor which is a substrate for the ADP-ribosylation reaction catalyzed by diphtheria toxin fragment A . However, the rate of the reaction was approximately 1,000 times slower than that typically observed with eucaryotic elongation factor 2 . We also demonstrated the presence of diphthine (the deamidated form of diphthamide, i.e., 2-{3-carboxyamide-3-(trimethylammonio)propyl}histidine) in acid hydrolysates of H . halobium protein in amounts comparable to those found in hydrolysates of similar preparations from eucaryotic cells (Saccharomyces cerevisiae and HeLa) . Diphthine could not be detected in hydrolysates of protein from the eubacterium Escherichia coli . Whereas both archaebacterial and eucaryotic elongation factors contain diphthamide, they differ importantly in other respects.

Nucleic Acids Res, 1983 Feb 11, 11(3), 591 - 604
Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach; Pieler T et al.; 5S rRNAs from Spinacea oleracea cytoplasmic and chloroplastic ribosomes have been subjected to digestion with the single strand specific nuclease S1 and to chemical modification of cytidines by sodium bisulphite in order to probe the RNA structure . According to these data, cytoplasmic 5S rRNA can be folded as proposed in the general eukaryotic 5S rRNA structure (1) and 5S rRNA from chloroplastides is shown to be more related to the general eubacterial structure (2).

Xenobiotica, 1983 Feb, 13(2), 115 - 26
Metabolism of mercapturic acid-pathway metabolites of 2-chloro-N-isopropylacetanilide (propachlor) by gastrointestinal bacteria; Larsen GL et al.; 1 . Mercapturic acid pathway metabolites of propachlor, labelled with 14C, were incubated with pig caecal contents, small and large intestinal contents, and pure cultures of gastrointestinal bacteria . 2 . The glutathione, cysteine, N-acetylcysteine, and the S-oxide of the N-acetylcysteine conjugates of propachlor (2-chloro-N-isopropylacetanilide) were each metabolized by mixed pig caecal micro-organisms to 2-mercapto-N-isopropylacetanilide . 3 . The extent of formation of 2-mercapto-N-isopropylacetanilide by mixed pig caecal micro-organisms from mercapturic acid-pathway metabolites of 14C-propachlor was as follows: glutathione (43.4%), cysteine (32.6%), N-acetylcysteine (5.2%), and the S-oxide of the N-acetylcysteine conjugate of propachlor (6.1%) . The S-oxide of the N-acetylcysteine conjugate of propachlor was converted by the mixed pig caecal micro-organisms to N-acetylcysteine and cysteine conjugates of propachlor . 4 . Small intestinal contents metabolized the glutathione conjugate of propachlor to the cysteine conjugate; little C-S lyase activity was present in the small intestinal contents . 5 . The cysteine conjugate of propachlor was metabolized to 2-mercapto-N-isopropylacetanilide by Fusobacterium necrophorum, Bacteroides vulgatus, Megasphaera elsdenii and Eubacterium aerofaciens.

Am J Gastroenterol, 1983 Feb, 78(2), 90 - 3
The significance of eubacterium bacteremia; Eng RH et al.; Eubacterium is a commensal of the human gastrointestinal tract . In rare instances this organism can become blood-borne . Nine cases of bacteremia were described and eight cases were found in the medical literature . Thirteen of the 17 cases (76%) had active gastrointestinal disease leading to the Eubacterium bacteremia . It is suggested that recovery of Eubacterium in blood culture should alert the clinician to the possibility of active gastrointestinal disease including occult neoplasms.

Biochem J, 1983 Feb 1, 209(2), 461 - 70
Particle weights and protein composition of the ribosomal subunits of the extremely thermoacidophilic archaebacterium Caldariella acidophila; Londei P et al.; 1 . The ribosomal subunits of one thermoacidophilic archaebacterium (Caldariella acidophila) and of two reference eubacterial species (Bacillus acidocaldarius, Escherichia coli) were compared with respect to ribosome mass and protein composition by (i) equilibrium-density sedimentation of the particles in CsCl and (ii) gel-electrophoretic estimations of the molecular weights of the protein and the rRNA . 2 . By either procedure, it is estimated that synthetically active archaebacterial 30S subunits (52% protein by wt.) are appreciably richer in protein than the corresponding eubacterial particles (31% protein by wt.) 3 . The greater protein content of the archaebacterial 30S subunits is accounted for by both a larger number and a greater average molecular weight of the subunit proteins; specifically, C . acidophila 30S subunits yield 28 proteins whose combined mass is 0.6 X 10(6) Da, compared with 20 proteins totalling 0.35 X 10(6) Da mass for eubacterial 30S subunits . 4 . No differences in protein number are detected among the large subunits, but C . acidophila 50S subunits exhibit a greater number-average molecular weight of their protein components than do eubacterial 50S particles . 5 . Particle weights estimated by either buoyant-density data, or molecular weights of rRNA plus protein, agree to within less than 2% . By either procedure C . acidophila 30S subunits 1.15 X 10(6) Da mass) are estimated to be about 300 000 Da heavier than their eubacterial counterparts (0.87 X 10(6) Da mass); a smaller difference . 0.15 X 10(6) Da, exists between the archaebacterial and the eubacterial 50S subunits (respectively 1.8 X 10(6) and 1.65 X 10(6) Da) . It is concluded that the heavier-than-eubacterial mass of the C . acidophila ribosomes resides principally in their smaller subunits.

Chemotherapy, 1983, 29(4), 289 - 93
Penicillin failure in the treatment of Bacteroides fragilis lung abscess . Experimental study in rabbits; Thadepalli H et al.; Carbenicillin, chloramphenicol, doxycycline, and clindamycin were compared with penicillin for the treatment of lung abscess in an animal model produced by transtracheal inoculation of a mixture of anaerobes: Bacteroides fragilis, Peptococcus morbillorum, Eubacterium lentum and Fusobacterium nucleatum . Both chloramphenicol and doxycycline eliminated the bacteria but failed to close the abscess cavity . Carbenicillin, although it eradicated B . fragilis, failed to close the abscess cavity in 3 of 6 animals . In all animals tested, clindamycin sterilized the abscess cavities and healed the lung abscesses, while penicillin failed to eradicate the infection . Clindamycin was significantly more effective than penicillin in the elimination of anaerobic bacteria from the lung (p less than 0.05) . Clindamycin also closed the abscess cavity faster than penicillin (p less than or equal to 0.02) . The superior efficacy of clindamycin may have been the result of accumulation in the lung tissue in concentrations four- to eightfold higher than in the serum.

Vet Pathol, 1983 Jan, 20(1), 80 - 9
Pathology of liver granulomas in turkeys; Arp LH et al.; Liver granulomas from five- and seven-week-old turkeys were studied by light and electron microscopy and by bacterial culture . Granulomas of five-week-old poults were composed of a caseous, necrotic center surrounded by consecutive zones of heterophils, giant cells, macrophages, and finally by lymphocytes . Tissue Gram and modified Dieterle stains demonstrated numerous gram-positive, filamentous bacteria in necrotic centers with radial extension of the bacteria to the zone of giant cells . Electron microscopic examination revealed septate, filamentous bacteria within an electron-dense milieu between heterophils, macrophages, and giant cells . An anaerobic, gram-positive bacillus and a staphylococcus were isolated from most granulomas examined . In broth, the bacillus formed long filaments or chains morphologically similar to those in tissue sections . The bacillus was identified tentatively as Eubacterium tortuosum . The staphylococcus had cultural reactions typical for Staphylococcus epidermidis . Intravenous inoculation of three-week-old poults with a mixture of E . tortuosum and S . epidermidis produced granulomas in liver and spleen and multiple mucosal ulcers in the duodenum and colon.

Recent Results Cancer Res, 1983, 84, 255 - 63
Alteration of tRNA modification in eukaryotes: causes and consequences; Kersten H; To evaluate the role of the modified nucleosides in tRNA function, especially their involvement in regulatory mechanisms of development, differentiation, or neoplastic transformation we use the following organisms: eubacteria, the slime mold D . discoideum, the topminnow Xiphophorus, and mice . Ribosylthymine, a common modified nucleoside at position 54 in tRNAs of prokaryotes and the major class of eukaryotic elongator tRNAs, is involved in the binding to the ribosomal A-site and is important for the proper functioning of tRNA during translation . Alterations in the extent of this modification occur early in the development of D . discoideum . The fully methylated species are found on polysomes, actively synthesizing protein . The partially methylated tRNAs accumulate in the nuclei, and might be involved in regulatory mechanisms at the transcriptional level . The Q base, a modified deazaguanine derivative, is present at position 34, the first position of the anticodon of tRNAAsn, tRNATyr, and tRNAHis . Alterations in the extent of this modification occur in corresponding tRNAs during the first minutes after the onset of development in D . discoideum and before final differentiation into spores, indicating that Q is important for developmental processes . Changes in the modification of G34 to Q34 in specific tRNAs of the melanophoric system of the topminnow Xiphophorus further support the view that Q is necessary in differentiation . In plasmacytomas and in Ehrlich ascites tumor cells of mice, the amount of unmodified G34 in corresponding tRNAs is correlated to the growth rate, density, or age of the tumor cells.

J Lipid Res, 1983 Jan, 24(1), 20 - 7
Regulation of bile acid 7-dehydroxylase activity by NAD+ and NADH in cell extracts of Eubacterium species V.P.I . 12708; White BA et al.; The 7 alpha-dehydroxylation of primary bile acids by Eubacterium sp . V.P.I . 12708 required a cell extract prepared from a cholic acid-induced culture and NAD+ . NADH (0.5 mM) inhibited bile acid 7-dehydroxylase activity more than 50% when added to reaction mixtures containing NAD+ (0.5 mM) . Saturation kinetics and double reciprocal plots of NADH inhibition were consistent with negative cooperativity . 7-Dehydroxylase activity was modulated by the molar ratio of NAD+-NADH with maximal activity at a NAD+ mole fraction of 0.75 to 0.85 . NADH stimulated 7-dehydroxylase activity (30% to 50%) at low concentration (less than 0.15 mM) and inhibited at higher concentrations . Reduction of the proposed delta 6-intermediate (3 alpha-hydroxy-5 beta-6-cholen-24-oic acid) to lithocholic acid required a cell extract from a cholic acid-induced culture and was stimulated by the addition of NAD+ . Reduced flavin nucleotides stimulated (32% to 62%) and NADH (0.5 mM) inhibited (78%) the reduction of the delta 6-intermediate to lithocholic acid . 7-Dehydroxylase was highly specific for bile acid substrates and required a free C-24 carboxyl group and an unhindered 7 alpha- or 7 beta-hydroxy group on the B-ring of the steroid nucleus for activity . Bile acid 7 alpha- and 7 beta-dehydroxylase and delta 6-reductase activities all co-eluted from an anaerobic high performance liquid chromatography gel filtration column . However, approximately 80% to 96% of the total units of activity were lost . A substantial portion (20% to 30%) of the total activity was recovered when material from low molecular weight (8,000 to 14,000 Mr) eluting fractions was added back to fractions containing enzyme activity . These studies show that 7-dehydroxylase is highly specific for substrates and its activity may be regulated by the NAD+-NADH ratio in the bacterial cell.

Digestion, 1983, 27(2), 63 - 9
An international study of agglutinins to Eubacterium, Peptostreptococcus and Coprococcus species in Crohn's disease, ulcerative colitis and control subjects; Wensinck F et al.; The world-wide occurrence of agglutinating antibodies to four coccoid anaerobes belonging to Eubacterium, Peptostreptococcus and Coprococcus spp . was investigated in 937 coded sera from patients suffering from Crohn's disease, ulcerative colitis, various other diseases and from healthy controls . Positive results were found in 59% of patients with Crohn's disease, 29% of patients with ulcerative colitis, and 8% of both diseased and healthy control subjects . Patients with Crohn's disease of the colon had more positive tests (67%) than patients with disease confined to the small bowel (46%) . The results show that agglutinating antibodies to the coccoid anaerobes occur more frequently in patients with Crohn's disease than in other subjects in widely varying geographic regions.

Scand J Infect Dis Suppl, 1983, 40, 41 - 6
Gardnerella vaginalis and anaerobic bacteria in the etiology of bacterial (nonspecific) vaginosis; Spiegel CA et al.; G . vaginalis was originally described as the etiologic agent of bacterial vaginosis (nonspecific vaginitis) because it was recovered only from women with signs and symptoms of "bacterial vaginitis" and not from normal controls . Recent data have shown that G . vaginalis is present in normal women but at concentrations lower than the limit of sensitivity of the media formerly used . Detection of low concentrations of G . vaginalis in normal controls has been made possible by development of a selective and differential medium (HBT) . Anaerobically performed studies of the vaginal flora have indicated that while lactobacilli predominate in the normal vagina with or without G . vaginalis, anaerobic bacteria including Bacteroides spp., Peptococcus spp., Eubacterium spp . and curved rods as well as G . vaginalis predominate in bacterial vaginosis . Anaerobic bacteria and G . vaginalis are decreased after appropriate therapy . After treatment with metronidazole, lactobacilli again predominate . Lactobacilli are less prevalent after treatment with ampicillin or amoxicillin . These data suggest that as in infections at other mucous membrane sites, bacterial vaginosis is a mixed infection involving a finite number of facultative and anaerobic species . The data also suggest an important role for facultative lactobacilli.

Biosystems, 1983-84, 16(3-4), 217 - 25
Studies on dinoflagellate chromosomal basic protein; Li JY; Routine cytochemical methods proved useless in demonstrating basic protein in dinoflagellate chromosomes because when the DNA was removed, these chromosomes dissolved away just as eubacterial nucleoids . However, with ammoniacal silver technique or alkaline Biebrich scarlet, DNA could be kept intact, all the dinoflagellate chromosomes examined gave positive reaction . The acid-soluble proteins were extracted from methanol-fixed Amphidinium carterae and methanol-fixed isolated nuclei of Noctiluca miliaris, and subjected to urea polyacrylamide gel electrophoresis . Only one band of basic protein co-migrating with histone H4 was found . The chromosomes of Oxyrrhis marina can retain their original forms after the removal of DNA . Their chromosomal basic protein can be demonstrated by various cytochemical methods . This protein co-migrates with histone H4 in urea gel too . Its amino acid composition has been determined . This protein can combine with DNA fibril to form a nucleosome-like structure which seems to be corresponding to two of the archaebacterial nucleosome-like structures and may represent the primitive nucleosome.

J Biol Chem, 1982 Dec 10, 257(23), 14192 - 7
Amino acid sequence of a 3Fe:3S ferredoxin from the "archaebacterium" Methanosarcina barkeri (DSM 800); Hausinger RP et al.; The complete amino acid sequence for a 3Fe:3S ferredoxin from the "archaebacterium" Methanosarcina barkeri (DSM 800) was determined by repetitive Edman degradation on the whole protein and peptides derived from trypsin, thermolysin, and Staphylococcus aureus protease digestion . The protein has 59 residues of which 8 are cysteines . The latter have the same spacing and distribution as found for the clostridial-type 2 x 4Fe:4S ferredoxins . Also, the sequence had evidence of internal homology which is indicative of gene duplication prior to the divergence of the archaebacteria and the eubacteria . This is the first sequence to be reported for a methanogen ferredoxin and only the fourth for a 3Fe:3S ferredoxin from any source.

Nucleic Acids Res, 1982 Nov 25, 10(22), 7231 - 45
Organization of rRNA structural genes in the archaebacterium Thermoplasma acidophilum; Tu J et al.; In the archaebacterium Thermoplasma acidophilum, each of the structural genes for 5S, 16S and 23S rRNA occur once per genome . In contrast to those of eubacteria and eukaryotes, they appear unlinked . The distance between the 16S and the 23S rDNA is at least 7.5 Kb, that between 23S and 5S rDNA at least 6 Kb and that between 16S and 5S rDNA at least 1.5 Kb . No linkage between those genes has been found by the analysis of recombinant plasmids carrying Bam HI and Hind III rDNA fragments as by hybridizing those plasmids to fragments of Thermoplasma DNA generated by 6 individual restriction endonucleases, recognizing hexanucleotide sequences.

Nucleic Acids Res, 1982 Nov 11, 10(21), 6671 - 4
Nucleotide sequence of Streptomyces griseus initiator tRNA; Kuchino Y et al.; The primary structure of initiator tRNA from Streptomyces griseus was determined by post-labeling procedures . The nucleotide sequence is pC-G-C-G-G-G-G-U-G-G-A-G-C-A-G-C-U-C-G-G-D-A-G-C-U-C-G-C-U-G-G-G-C-U-C-A-U-A-A-C-C- C-A-G-A-G-G-U-C-G-C-A-G-G-U-psi-C-A-m1A-A-U-C-C-U-G-U-C-C-C-C-G-C-U-A-C-C-A0H . The unique feature of the sequence of this tRNA is that residue 54 is occupied by unmodified U, while ribothymidine is located in that position in most initiator tRNAs from eubacteria.

FEBS Lett, 1982 Nov 8, 148(2), 255 - 9
Archaebacterial elongation factor Tu insensitive to pulvomycin and kirromycin; Cammarano P et al.; A spermine-dependent, polyphenylalanine-synthesizing cell-free system having an optimum activity at 75-85 degrees C, has been developed from the extremely thermoacidophilic archaebacterium Caldariella acidophila . The C . acidophila system is totally insensitive to the EF-Tu targeted antibiotics pulvomycin (at 40 degrees C) and kirromycin (at 47-72 degrees C) contrary to control systems derived from both mesophilic (Escherichia coli) and thermoacidophilic (Bacillus acidocaldarius) eubacteria . The archaebacterial EF-Tu-equivalent factor is also immunologically unrelated to eubacterial EF-Tu and does not cross react with antibodies against Escherichia coli EF-Tu . The pulvomycin and kirromycin reactions thus provide new phyletic markers for archaebacterial ancestry.

J Lipid Res, 1982 Nov, 23(8), 1152 - 8
Enhancement of the 7 alpha-dehydroxylase activity of a gram-positive intestinal anaerobe by Bacteroides and its significance in the 7-dehydroxylation of ursodeoxycholic acid; Hirano S et al.; The 7 alpha-dehydroxylation of chenodeoxycholic acid (CDCA) and cholic acid (CA) by a Eubacterium lentum-like intestinal anaerobe was specifically enhanced by the bacteroides present in mixed cultures and also by the addition to the growth medium of cell extracts from the bacteroides . The 7 alpha-dehydroxylating organism also possessed 7 alpha-hydroxysteroid dehydrogenase activity, and, in collaboration with a 7 beta-dehydrogenating organism, converted ursodeoxycholic acid (UDCA) into CDCA . Large quantities of lithocholic acids were produced from UDCA as well as CDCA in in vitro cocultures of these three kinds of microorganisms.

Appl Environ Microbiol, 1982 Nov, 44(5), 1187 - 95
Formation of ursodeoxycholic acid from chenodeoxycholic acid by a 7 beta-hydroxysteroid dehydrogenase-elaborating Eubacterium aerofaciens strain cocultured with 7 alpha-hydroxysteroid dehydrogenase-elaborating organisms; MacDonald IA et al.; A gram-positive, anaerobic, chain-forming, rod-shaped anaerobe (isolate G20-7) was isolated from normal human feces . This organism was identified by cellular morphology as well as fermentative and biochemical data as Eubacterium aerofaciens . When isolate G20-7 was grown in the presence of Bacteroides fragilis or Escherichia coli (or another 7 alpha-hydroxysteroid dehydrogenase producer) and chenodeoxycholic acid, ursodeoxycholic acid produced . Time course curves revealed that 3 alpha-hydroxy-7-keto-5 beta-cholanoic acid produced by B . fragilis or E . coli or introduced into the medium as a pure substance was reduced by G20-7 specifically to ursodeoxycholic acid . The addition of glycine- and taurine-conjugated primary bile acids (chenodeoxycholic and cholic acids) and other bile acids to binary cultures of B . fragilis and G20-7 revealed that (i) both conjugates were hydrolyzed to give free bile acids, (ii) ursocholic acid (3 alpha, 7 beta, 12 alpha-trihydroxy-5 beta-cholanoic acid) was produced when conjugated (or free) cholic acid was the substrate, and (iii) the epimerization reaction was at least partially reversible . Corroborating these observations, an NADP-dependent 7 beta-hydroxysteroid dehydrogenase (reacting specifically with 7 beta-OH-groups) was demonstrated in cell-free preparations of isolate G20-7; production of the enzyme was optimal at between 12 and 18 h of growth . This enzyme, when measured in the oxidative direction, was active with ursodeoxycholic acid, ursocholic acid, and the taurine conjugate of ursodeoxycholic acid (but not with chenodeoxycholic, deoxycholic, or cholic acids) and displayed an optimal pH range of 9.8 to 10.2

Nucleic Acids Res, 1982 Oct 25, 10(20), 6363 - 7
The nucleotide sequence of the 5S rRNA from Spiroplasma species BC3 and Mycoplasma mycoides sp . capri PG3; Walker RT et al.; Using in vitro labelling techniques, the complete nucleotide sequence of the 5S ribosomal RNAs isolated from the honeybee pathogen, Spiroplasma species BC3 and Mycoplasma mycoides sp . capri PG3, have been determined . The latter shows only 3 differences from the reported sequence of M . capricolum 5S rRNA, indicating that these two species are very closely related . The Spiroplasma sequence is also 107 nucleotides long and a comparative analysis of the sequence confirms that this Spiroplasma species is closely related to the Mycoplasma species and that they and the Gram-positive eubacteria have descended from a common ancestor and in the process the cell wall-less organisms have lost a large percentage of their genome.

Proc Natl Acad Sci U S A, 1982 Oct, 79(19), 5948 - 52
Mapping evolution with ribosome structure: intralineage constancy and interlineage variation; Lake JA et al.; Ribosomal small subunits are organized in three general structural patterns that correspond to the eubacterial, archaebacterial, and eukaryotic lineages . Within each of these lineages, ribosomal structure is highly conserved . Small subunits from all three lineages share a common overall structure except for the following differences: (i) small subunits from archaebacteria and from the cytoplasmic component of eukaryotes both contain a feature on the head of the subunit, the archaebacterial bill, that is absent in eubacteria, and (ii) eukaryotic small subunits contain additional regions of density at the base of the subunit, the eukaryotic lobes, that are absent in archaebacteria and in eubacteria . We interpret the intralineage conservation of ribosomal three-dimensional structure as forming a phylogenetic basis for regarding archaebacteria, eubacteria, and eukaryotes as primitive lines . Although our data are separate and independent from those of Woese and Fox, they lend further support to their proposal {Woese, C . R . & Fox, G . E . (1977) Proc . Natl . Acad . Sci . USA 74, 5088-5090} . These data also provide a simple, rapid, and accurate method for classifying organisms and for identifying new lineages . Finally, interlineage variation of ribosomal structure is used to establish a rigorous framework for considering the evolution of these three lines.

J Clin Microbiol, 1982 Sep, 16(3), 437 - 42
Controlled evaluation of the effect of atmosphere of incubation on detection of bacteremia and fungemia in supplemented peptone broth; Tenney JH et al.; To evaluate the role of atmosphere of incubation in the detection of clinically important bacteremia and fungemia in adults, we compared the yield of microorganisms from 10,541 paired 5-ml samples of blood incubated aerobically and anaerobically . The medium, supplemented peptone broth (SPB) with 0.03% sodium polyanetholesulfonate, and the ratio of blood to broth (1:10) were the same for all cultures . Only cultures with adequate blood samples (greater than or equal to 80% of stated volume) were compared statistically . More fungi (P less than 10(-7) ) grew in continuously vented bottles of SPB . Aerobic incubation also favored (P less than 0.01) isolation of Neisseria gonorrhoeae and Eubacterium; more than 80% of these bacterial organisms were detected only in vented bottles . Anaerobic incubation (plugged venting units) did not significantly favor the isolation of any genus of microorganisms, although an estimated 11% more Bacteroidaceae grew in the unvented bottle of SPB . By comparison of our data with published results for other media, we conclude that the need for both aerobic and anaerobic incubation of blood cultures is dependent upon the medium used and the microorganisms likely to be encountered . Vented incubation of blood cultured in SPB is crucial for detection of fungi and some bacteria . Routine use of an unvented bottle of SPB may not be worthwhile for patients in whom Bacteroidaceae cause bacteremia infrequently . However, when Bacteroidaceae are suspected as the cause of sepsis, use of an unvented bottle of SPB is prudent.

Proc Natl Acad Sci U S A, 1982 Aug, 79(15), 4599 - 603
Three-dimensional structural model of eubacterial 5S RNA that has functional implications; Pieler T et al.; Escherichia coli 5S RNA and its specific protein complexes were hydrolyzed with the single-strand-specific nuclease S1 . Based on the results, a tertiary structural model for E . coli 5S RNA is proposed in which ribosomal proteins E-L5, E-L18, and E-L25 influence the conformation of the RNA . This may be of significance for ribosomal function . Comparison of the proposed E . coli 5S RNA structure with those of 18 other prokaryotic 5S RNAs led to a generalized eubacterial 5S RNA tertiary structure in which the majority of the conserved nucleotides are in non-base-paired regions and several conserved "looped-out" adenines (in E . coli, adenines -52, -53, -57, -58, and -66) are implied to be important for protein recognition or interaction or both.

Nucleic Acids Res, 1982 Jul 10, 10(13), 3921 - 32
3'-Terminal sequence of wheat mitochondrial 18S ribosomal RNA: further evidence of a eubacterial evolutionary origin; Schnare MN et al.; We have determined the sequences of the 3'-terminal approximately 100 nucleotides of {5' -32P}pCp-labeled wheat mitochondrial, wheat cytosol, and E . coli small sub-unit rRNAs . Sequence comparison demonstrates that within this region, there is a substantially greater degree of homology between wheat mitochondrial 18S and E . coli 16S rRNAs than between either of these and wheat cytosol 18S rRNA . Moreover, at a position occupied by 3-methyluridine in E . coli 16S rRNA, the same (or a very similar) modified nucleoside is present in wheat mitochondrial 18S rRNA but not in wheat cytosol 18S rRNA . Further, E . coli 16S and 23S rRNAs hybridize extensively to wheat mitochondrial 18S and 26S rRNA genes, respectively, but wheat cytosol 18S and 26S rRNAs do not . No other mitochondrial system studies to date has provided comparable evidence that a mitochondrial rRNA is more closely related to its eubacterial homolog than is its counterpart in the cytoplasmic compartment of the same cell . The results reported here provide additional support for the view that plant mitochondria are of endosymbiotic, specifically eubacterial, origin.

Ann Immunol (Paris), 1982 Jul-Aug, 133D(1), 29 - 39
{Relationship between the development of the intestinal IgA immune system and the establishment of microbial flora in the digestive tract of young holoxenic mice}; Moreau MC et al.; The intestinal villi of axenic mice contain ten-fold less IgA plasmocytes than that of conventional ones . The major stimulus for proliferation of plasma cells synthetizing IgA in the gut of axenic mice is the total microbial flora from adult conventional mice . In young mice, the intestinal IgA immune system (intestinal IgA IS) is fully developed at the age of six weeks . The purpose of this work was to determine the role of intestinal flora on the development of the intestinal IgA IS . To that end, the complete digestive microflora from 1-25 day-old mice was transferred into adult axenic mice . The adult recipient mice harboured the same proportion of the same bacteria as the 1-4 day-old donor mice, Lactobacillus excepted . Thus, development of Lactobacillus is inhibited in recipient mice, whereas we did not observe any inhibition in young donor mice . For the 7-25 day-old donor mice, we still observed some resemblance between the flora of the donors and that of the recipients . However, the number of bacteria belonging to the genera Bacteroides and Eubacterium was larger in recipient than in donor mice . The microflora obtained from 1-23 day-old donor mice did not fully stimulate the development of the intestinal IgA IS of the recipient mice . In contrast, the microflora obtained from a 25 day-old mouse induced a full stimulation of the intestinal IgA IS in the recipient mice . Attempt to isolate the bacteria responsible for this complete stimulation were unsuccessful . We only know that these bacteria are present in a large proportion (10 8/g of faeces), that they are heat-sensible (70 degrees C, 10 min) and bacitracin-sensible . These results showed the important role of the sequential implantation of intestinal microflora in the development of intestinal IgA IS.

J Clin Microbiol, 1982 Jul, 16(1), 107 - 10
Comparative evaluation of supplemented peptone broth with sodium polyanetholesulfonate and trypticase soy broth with sodium amylosulfate for detection of septicemia; Tenney JH et al.; We compared the yield and speed of detection of clinically important microorganisms from 10,156 paired 5-ml samples of blood cultured in supplemented peptone broth (SPB) with 0.03% sodium polyanetholesulfonate (SPS) or Trypticase soy broth (TSB) with 0.5% sodium amylosulfate (SAS) . The atmosphere of incubation (open venting units) and ratio of blood to broth (1:10) were the same for both samples . Only cultures with adequate blood samples (greater than or equal to 80% of stated volume) were compared statistically . Overall, SPB/SPS outperformed TSB/SAS . Bacteroidaceae and Eubacterium were found more often (P less than 0.05) and viridans streptococci were found sooner (P less than 10(-4)) in SPB/SPS than in TSB/SAS . Most importantly, staphylococci were found both more often (P less than 0.03) and sooner (P less than 10(-7)) in SPB/SPS than in TSB/SAS . In a separate experiment, SAS slowed the growth of a clinical strain of Staphylococcus aureus in TSB . Unless important advantages can be confirmed for SAS in controlled clinical trials, SAS cannot be recommended for routine use as an anticoagulant in blood culture media.

Infect Immun, 1982 Jun, 36(3), 977 - 82
Predominant cultivable microflora of human dental fissure plaque; Theilade E et al.; Plaque developed in 10 occlusal fissures from unerupted third molars during implantation for 200 to 270 days in lower molars of dental students was studied . To characterize the predominant cultivable flora, 592 isolates (51 to 67 from each fissure) were subcultured from anaerobic roll tubes . Twenty-eight of the isolates were lost . Streptococci constituted 8 to 86% (median, 45%) of the isolates, Streptococcus mutans constituted 0 to 86% (median, 25%) and S . sanguis constituted 0 to 15% (median, 1%) . A few isolates of "S . mitior" and "S . milleri" were found, but no S . salivarius . Staphylococci made up 0 to 23% (median, 9%) . Gram-positive rods constituted 6 to 59% (median, 35%) . Of these, 0 to 46% (median, 18%) were Actinomyces naeslundii and A . viscosus, but no anaerobic actinomyces were isolated . Arachnia and propionibacteria made up small proportions, lactobacilli were isolated from two fissures, constituting 10 and 29%, and eubacteria were isolated from one fissure (27%) . Gram-negative cocci made up 0 to 46% (media, 4%) . Only two isolates of gram-negative rods were found, both facultative anaerobes . Although 8 of the 10 fissures had large proportions of S . mutans, lactobacilli, or both, no caries was found even with microradiography . The large individual variation probably reflects differences in initial colonization from saliva and in growth conditions in each fissure.

Biochimie, 1982 May, 64(5), 311 - 29
Conservation of secondary structure in 5 S ribosomal RNA: a uniform model for eukaryotic, eubacterial, archaebacterial and organelle sequences is energetically favourable; De Wachter R et al.; The most commonly accepted secondary structure models for 5S RNA differ for molecules of eubacterial origin, where the four-helix model of Fox and Woese is generally cited, and those of eukaryotic origin, where a fifth helix is assumed to exist . We have carefully aligned all available sequences from eukaryotes, eubacteria, chloroplasts, archaebacteria and plant mitochondria . We could thus derive a unified secondary structure model applicable to all 5S RNA sequences known to-date . It contains the five helices already present in the eukaryotic model, extended by additional segments that were not previously assumed to be universally present . One of the helices can be written in two equilibrium forms, which could reflect the existence of a flexible, dynamic structure . For the derivation of the model and the estimation of the free energies we followed a set of rules optimized to predict the tRNA cloverleaf . The stability of the unified model is higher than that of nearly all previously proposed sequence-specific and general models.

J Clin Microbiol, 1982 May, 15(5), 895 - 901
Nutritional and metabolic features of Eubacterium suis; Wegienek J et al.; We studied the nutritional and metabolic features of Eubacterium suis, an anaerobic animal pathogen that causes cystitis and pyelonephritis in pigs . Peptone-yeast extract-starch (PYS) medium, which contained Trypticase (BBL Microbiology Systems), yeast extract, starch, minerals, cysteine, and sodium carbonate, was shown to support excellent growth of this organism (absorbance at 600 nm = 1.8) . Growth was considerably less (absorbance at 600 nm = 0.6) when the starch in the medium was replaced by maltose . Formate, acetate, and ethanol were the major products of fermentation of starch or maltose . The organism appears to require a fermentable carbohydrate for growth since the deletion of starch from PYS resulted in a negligible amount of growth . Growth decreased by approximately 20% when CO2 was rigorously excluded from PYS minus Na2CO3 . The deletion of only yeast extract from PYS resulted in a decrease in growth of about 75%, and the simultaneous deletion of both yeast extract and Trypticase resulted in negligible growth . When the yeast extract in PYS was replaced by a defined mixture of purine and pyrimidine bases, vitamins, and amino acids, growth was greater than or equal to 80% that observed in PYS . The deletion of Trypticase from this medium resulted in no detectable growth, suggesting a possible peptide requirement for E . suis growth . Good growth (absorbance at 600 nm = 1.4) was obtained when adenine and uracil were substituted for the mixture of purine and pyrimidine bases in modified PYS; the substitution of pyridoxal, riboflavin, and nicotinic acid for the vitamin mixture gave comparable growth . The nutritional requirement of E . suis apparently reflect the fact that the organism adapts to its natural niche by doing away with certain biosynthetic capabilities which it does not seem to require.

Can J Biochem, 1982 Apr, 60(4), 480 - 9
Comparative sequence analysis as an approach to evaluating structure, function, and evolution of 5S and 5.8S ribosomal RNAs; MacKay RM et al.; Nucleotide sequences of nine eukaryotic and nine eubacterial 5S rRNAs have been selected for their diversity and subjected to analysis of primary and potential secondary structure . This analysis has allowed the quantitative confirmation of several previously made observations concerning 5S rRNA structure: (i) these two 5S rRNAs are derived from a common ancestor and probably perform essentially the same function in protein synthesis; (ii) one domain of 5S rRNA has undergone considerable divergence of structure (and presumably function) since the separation of the eukaryotic and eubacterial lineages; and (iii) single-stranded regions are more highly conserved than double-stranded regions . In addition, this analysis leads us to propose that (i) some of the highly conserved nucleotide residues in single-stranded regions interact in a specific manner with protein components of the translational apparatus, and (ii) repetitive folding and unfolding of helical regions occurs in two regions of eukaryotic 5S rRNA and one region of eubacterial 5S rRNA . In the context of these observations and propositions we also consider the potential secondary structure of plant mitochondrial 5S rRNA . Nucleotide sequences of 5.85 rRNAs have yielded less information about secondary structure and possible functional interactions . However, we have identified highly conserved and variable regions within this molecule and we show (in contrast to the situation with 5S rRNA) that these do not correlate well with proposed single-stranded and helical regions in a current model of 5.8S secondary structure.

Eur J Biochem, 1982 Mar 1, 122(3), 569 - 71
Biosynthesis of vitamin B12 in anaerobic bacteria . Mode of incorporation of glycine into the 5,6-dimethylbenzimidazole moiety in Eubacterium limosum; Lamm L et al.; {1-13C}Glycine, {2-13C}glycine, and {15N}glycine were added to fermentations with the strictly anaerobic vitamin B12 producer Eubacterium limosum . The vitamin B12 isolated was almost exclusively labeled in its 5,6-dimethylbenzimidazole moiety . It was methylated and degraded to 1,5,6-trimethylbenzimidazole . The position of the 13C label was determined from the 13 C NMR spectrum using the natural-abundance 13C NMR spectrum of 1,5,6-trimethylbenzimidazole as reference . Thus it was found that C-1 of glycine is incorporated into position 7a, C-2 of glycine into position 3a of the 5,6-dimethylbenzimidazole moiety of vitamin B12 . In order to show whether the nitrogen atom of glycine is also incorporated, the vitamin B12 from the experiment with {15N}glycine was degraded to 5,6-dimethylbenzimidazole . The 1H NMR spectrum of this compound exhibited in the region of the C-2 proton a doublet from the 15N-labeled part of the molecules (35%) and a singlet from the unlabeled molecules . This doublet indicates that only one of the two nitrogen atoms of 5,6-dimethylbenzimidazole is labeled . From the incorporation pattern of 13C-labeled glycine it must be deduced that this is N-3 of the 5,6-dimethylbenzimidazole moiety of vitamin B12 . These experiments reveal that one molecule of glycine is incorporated into 5,6-dimethylbenzimidazole moiety of vitamin B12 in a regiospecific manner.

J Lipid Res, 1982 Feb, 23(2), 352 - 6
Biotransformation of 16 alpha-hydroxyprogesterone by Eubacterium sp . 144: non-enzymatic addition of L-cysteine to delta 16-progesterone; Glass TL et al.; Eubacterium sp . 144 dehydroxylated 16 alpha-hydroxy-progesterone; however, the expected intermediate, delta 16-progesterone, did not accumulate to significant concentrations in the culture medium . Moreover, the final end product of this biotransformation, 17 alpha-progesterone, was produced at a very slow rate . It was discovered that, under our culture conditions, delta 16-progesterone reacted chemically with L-cysteine to form a highly water-soluble derivative . The ability of delta 16-progesterone to react with L-cysteine in culture media was considerably reduced when L-cysteine was autoclaved in the presence of complex medium components . delta 16-Progesterone also reacted chemically with D-cysteine, L-homocysteine, glutathione, and 2-mercaptoethylamine . The reaction was favored by alkaline pH (greater than or equal to pH 8.0) and required both an unhindered thiol group and a proximal amino group on the mercapto compound . Chromatography of the putative delta 16-progesterone L-{U-14C}-cysteine reaction product by HPLC showed a single UV-absorbing, radioactive peak (RT 4.31 min).

Digestion, 1982, 23(2), 104 - 9
Factors determining the occurrence of serum agglutinins to eubacterium and peptostreptococcus species in patients with Crohn's disease and ulcerative colitis; van de Merwe JP et al.; Recently, the demonstration of serum agglutinins to Eubacterium and Peptostreptococcus strains has been found to be useful as a diagnostic test for Crohn's disease . Therefore, conditions determining the occurrence of these antibodies were studied in patients with Crohn's disease and ulcerative colitis . Localization of Crohn's disease in the colon, the presence of fistulae and serum levels of immunoglobulins were found to be contributory determinants for the occurrence of the agglutinins.

J Am Acad Dermatol, 1982 Jan, 6(1), 107 - 11
Diagnosis and treatment of mycetoma; Palestine RF et al.; A mycetoma is a chronic granulomatous infection of the skin and subcutaneous tissue from which grains of the causative organism are eliminated through sinus tracts . In a patient with a suspected mycetoma, evaluation should include (1) elicitation of a history of trauma, (2) determination of the presence of the clinical triad of swelling, sinus tracts, and extrusion of grains, (3) roentgenographic examination, (4) examination of the grains, (5) histopathologic study, and (6) culture . Identification of the causative organism is important for guiding therapy; etiologic agents include actinomycetes, eumycetes, eubacteria, and dermatophytes . Whereas surgical treatment is still usually required for eumycetomas, various chemotherapeutic agents have shown promising results in the other types of mycetoma.

Chemotherapy, 1982, 28(2), 129 - 34
Chemoprophylaxis of anaerobic pulmonary infections . An experimental study in rabbits; Dhawan VK et al.; Chemoprophylaxis of anaerobic pulmonary infection due to aspiration was studied in a rabbit model with the view of comparing the efficacy of procaine penicillin, clindamycin, chloramphenicol, doxycycline and cefoxitin . The antibiotic treatment was commenced immediately following transtracheal inoculation of a mixture of Bacteroides fragilis, Streptococcus morbillorum, Fusobacterium nucleatum and Eubacterium lentum . Treatment was stopped after 48 h and lungs were examined for evidence of infection on the 10th day . Only clindamycin and carbencillin were highly efficacious in chemoprophylaxis and both drugs prevented pulmonary infection in 7 of 8 (87%) of the animals tested.

J Lipid Res, 1982 Jan, 23(1), 145 - 53
7 beta-Dehydroxylation of ursodeoxycholic acid by whole cells and cell extracts of the intestinal anaerobic bacterium, Eubacterium species V.P.I . 12708; White BA et al.; Whole cells and cell extracts of Eubacterium species V . P . I . 12708 7-dehydroxylated {3H}ursodeoxycholic acid or {14C}chenodeoxycholic forming lithocholic acid . 7 beta-Dehydroxylation specific activity was 146 and 386 nmol hr-1 mg protein-1 for cell extracts and whole cells, respectively . 7 alpha- or 7 beta-Dehydroxylation activity was detected only in whole cells or cell extracts prepared from cultures grown in the presence of cholic acid . The addition of NAD+ (0.5 mM) to anaerobically dialyzed cell extracts stimulated 7 beta- and 7 alpha-dehydroxylation activity by 5- and 40-fold, respectively . The level of 7 beta-dehydroxylation specific activity was approximately 3- to 5-fold lower than 7 alpha-dehydroxylation in whole cells and 3-fold lower in cell extracts . Substrate saturation kinetics for ursodeoxycholic acid and chenodeoxycholic acid were hyperbolic and showed substrate inhibition at concentrations above 200 microM . The apparent Km values for ursodeoxycholic and chenodeoxycholic acid were 14.5 microM and 49 microM, respectively . Both 7 alpha- and 7 beta-dehydroxylase activities were inactivated (60% to 70%) by heating for 6 min at 45 degrees C . Moreover, both activities co-eluted from a anaerobic Bio-Gel A 1.5-M column as a single peak at approximately 114,000 (Mr) . These data show that this intestinal anaerobic bacterium has both 7 alpha- and 7 beta-dehydroxylase activities which may be catalyzed by the same enzyme.U

Mol Gen Genet, 1982, 188(1), 7 - 11
The protein composition of Mycoplasma capricolum; Kawauchi Y et al.; The whole cell proteins and the ribosomal proteins of Mycoplasma capricolum ATCC 27343 have been analyzed by two-dimensional polyacrylamide gel electrophoresis . The M . capricolum cell is relatively rich in basic proteins . The number of total protein spots detected was approximately 355, which is less than one-third of that of Escherichia coli or Bacillus subtilis . In contrast, the number (30 and 20 protein species have been found to be present in the 50S and 30S ribosomal subunits, respectively) and the size of the ribosomal proteins in the M . capricolum do not seem to be significantly different from those of typical eubacteria.

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