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 sp