FEMS Microbiol Lett, 1991 Mar 1, 62(2-3), 139 - 43 A novel eubacterial phylum: comparative nucleotide sequence analysis of a tuf-gene of Flexistipes sinusarabici; Ludwig W et al.; A tuf-gene of Flexistipes sinusarabici has been cloned and sequenced . The primary structure of the predicted elongation factor protein was compared with available sequences of homologous genes and elongation factors Tu or 1 alpha of eubacteria, archaebacteria and eukaryotes . Based on elongation factor Tu data Flexistipes sinusarabici belongs to the eubacterial kingdom but no specific relationship to any phylum was detected . The amino acid of the elongation factor Tu of F . sinusarabici exhibits no striking pecularities . Among the highly conserved positions only two are different . Sites of known or postulated functions are conserved. Microbiol Rev, 1991 Mar, 55(1), 143 - 90 Interaction of chlamydiae and host cells in vitro; Moulder JW; The obligately intracellular bacteria of the genus Chlamydia, which is only remotely related to other eubacterial genera, cause many diseases of humans, nonhuman mammals, and birds . Interaction of chlamydiae with host cells in vitro has been studied as a model of infection in natural hosts and as an example of the adaptation of an organism to an unusual environment, the inside of another living cell . Among the novel adaptations made by chlamydiae have been the substitution of disulfide-bond-cross-linked polypeptides for peptidoglycans and the use of host-generated nucleotide triphosphates as sources of metabolic energy . The effect of contact between chlamydiae and host cells in culture varies from no effect at all to rapid destruction of either chlamydiae or host cells . When successful infection occurs, it is usually followed by production of large numbers of progeny and destruction of host cells . However, host cells containing chlamydiae sometimes continue to divide, with or without overt signs of infection, and chlamydiae may persist indefinitely in cell cultures . Some of the many factors that influence the outcome of chlamydia-host cell interaction are kind of chlamydiae, kind of host cells, mode of chlamydial entry, nutritional adequacy of the culture medium, presence of antimicrobial agents, and presence of immune cells and soluble immune factors . General characteristics of chlamydial multiplication in cells of their natural hosts are reproduced in established cell lines, but reproduction in vitro of the subtle differences in chlamydial behavior responsible for the individuality of the different chlamydial diseases will require better in vitro models. J Bacteriol, 1991 Mar, 173(6), 2086 - 92 Characterization of enzymes of the branched-chain amino acid biosynthetic pathway in Methanococcus spp; Xing RY et al.; Methanococcus aeolicus, Methanococcus maripaludis, and Methanococcus voltae contain similar levels of four enzymes of branched-chain amino acid biosynthesis: acetohydroxy acid synthase, acetohydroxy acid isomeroreductase, dihydroxy acid dehydratase, and transaminase B . Following growth at low partial pressures of H2-CO2, the levels of these enzymes in extracts of M . voltae are reduced three- to fivefold, which suggests that their synthesis is regulated . The enzymes from M . aeolicus were found to be similar to the eubacterial and eucaryotic enzymes with respect to molecular weights, pH optima, kinetic properties, and sensitivities to O2 . The acetohydroxy acid isomeroreductase has a specific requirement for Mg2+, and other divalent cations were inhibitory . It was stimulated threefold by K+ and NH4+ ions and was able to utilize NADH as well as NADPH . The partially purified enzyme was not sensitive to O2 . The dihydroxy acid dehydratase is extremely sensitive to O2, and it has a half-life under 5% O2 of 6 min at 25 degrees C . Divalent cations were required for activity, and Mg2+, Mn2+, Ni2+, Co2+, and Fe2+ were nearly equally effective . In conclusion, the archaebacterial enzymes are functionally homologous to the eubacterial and eucaryotic enzymes, which implies that this pathway is very ancient. J Bacteriol, 1991 Mar, 173(5), 1835 - 7 Genes for 7S RNAs can replace the gene for 4.5S RNA in growth of Escherichia coli; Brown S; 4.5S RNAs of eubacteria and 7S RNAs of archaebacteria and eukaryotes exist in a hairpin conformation . The apex of this hairpin displays structural and sequence similarities among both 4.5S and 7S RNAs . Furthermore, a hyphenated sequence of 16 nucleotides is conserved in all eubacterial 4.5S RNAs examined . In this article I report that 7S RNAs that contain this 16-nucleotide sequence are able to replace 4.5S RNAs and permit growth of Escherichia coli. J Bacteriol, 1991 Mar, 173(6), 2035 - 44 Sequence and TnphoA analysis of a Mycoplasma hyorhinis protein with membrane export function; Yogev D et al.; Proteins translocated across the single plasma membrane of mycoplasmas (class Mollicutes) represent important components likely to affect several interactions of these wall-less microbes with their respective hosts . However, identification and functional analysis of such proteins is hampered by the lack of mutational systems in mycoplasmas and by a perceived limitation in translating recombinant mycoplasma genes containing UGA (Trp) codons in other eubacteria . Here we directly analyze a gene encoding a Mycoplasma hyorhinis protein capable of promoting its membrane translocation . It was initially detected by screening a recombinant phage genomic library with antibody from a host with M . hyorhinis-induced arthritis and was localized by Tn5 and deletion mutations affecting expression of antigenic translational products . Sequence analysis of the isolated gene predicted a hydrophilic protein, P101, containing three UGA codons and a putative signal peptide with an uncharacteristic cluster of positively charged amino acids near its C terminus . Nevertheless, lambda::TnphoA transposon mutagenesis of an Escherichia coli plasmid bearing the p101 gene resulted in p101::TnphoA fusions expressing products that could translocate as much as 48 kDa of the P101 sequence (up to the first UGA codon) across the E . coli plasma membrane . Fusion proteins containing mature P101 sequences expressed mycoplasma epitopes and were found by cell fractionation and detergent phase partitioning to be integral membrane proteins in E . coli, suggesting a lack of signal peptide cleavage in this system . Importantly, identification of P101 by direct analysis of its export function relied neither on prior identification of the mycoplasmal product nor on complete expression of the product from the cloned mycoplasma gene. Planta Med, 1991 Feb, 57(1), 15 - 9 Isolation of a human intestinal bacterium capable of transforming barbaloin to aloe-emodin anthrone; Che QM et al.; A strictly anaerobic bacterium, Eubacterium sp . BAR, was isolated from human feces as one of the intestinal bacteria capable of metabolizing barbaloin . The bacterium grew in PYF broth containing barbaloin and converted barbaloin to aloe-emodin anthrone . On the other hand, the bacterium had little metabolic activity in GAM broth. J Steroid Biochem Mol Biol, 1991 Feb, 38(2), 257 - 63 Characteristics of 16-dehydroprogesterone reductase in cell extracts of the intestinal anaerobe, Eubacterium sp . strain 144; Watkins WE et al.; 16-Dehydroprogesterone reductase (16-DHPR) activity was present in cell extracts of Eubacterium sp . strain 144 only when the organism was grown in the presence of steroids containing a delta 16-17 double bond and C-20-ketone . Cells grown with 16-dehydropregnenolone contained 16-DHPR activity but lacked delta 4-5-3-keto steroid reductase activity . Pyruvate or sodium dithionite served as electron donors for 16-DHPR and both reactions required methyl viologen as an electron carrier . Neither NADH nor NADPH, with or without flavin nucleotides, were used by 16-DHPR . Enzyme activity was detected in the cytoplasmic fraction (40%) and membrane fraction (20%) of crude cell extracts, but 40% of the activity was unaccounted for following ultracentrifugation . 16-DHPR activity was unaffected by pH in potassium phosphate buffer over the range 5.0 to 8.5, but was inhibited by Tris-HCl above pH 7.0 . 16-DHPR activity was inhibited by sulfhydryl reagents, but inhibitors of electron transport reactions or metal chelators did not affect the enzyme. Biochem J, 1991 Feb 1, 273 ( Pt 3), 627 - 34 Early steps of isoprenoid biosynthesis in Escherichia coli; Zhou D et al.; The incorporation of 2H- and 13C-labelled precursors into ubiquinone-8 (Uq-8) by strains of Escherichia coli was measured in order to define the pathway for the early steps in the biosynthesis of isoprenoids in these eubacteria . Cells grown with DL-{methyl-2H6}valine were found to label both the alpha-oxoisovaleric ('alpha-ketoisovaleric') acid alpha-oxoisohexanoic ('alpha-ketoisocaproic') acid, but not the Uq-8 . Since these acids are required for the biosynthesis of isoprenoids by the acetolactate pathway, the operation of this pathway in the biosynthesis of Uq-8 is excluded . Cells grown with {1,2-13C2}acetate and non-labelled glucose readily incorporated 13C2 units into fatty acids, but failed to incorporate any label into the Uq-8 . Cells grown with {U-13C6}glucose and non-labelled acetate, however, were found to label both the fatty acids and the Uq-8 . Oxidative cleavage with periodate/permanganate of the Uq-8 isolated from cells grown with U-13C6-labelled glucose produced laevulinic acid, which was shown to be derived from two C2 units and one C1 unit of the labelled glucose by mass-spectral analysis of the 4,5-dihydro-6-methyl-2-phenylpyridazin-3(2H)-one derivative . The results of this work indicate that the C-2 and C-3 carbon unit of pyruvate, not acetyl-CoA, is the precursor to isopentenyl pyrophosphate (IPP) in these cells; however, the labelling pattern observed is consistent with the established acetoacetate pathway of isoprenoid biosynthesis . These data, coupled with the observed lack of inhibition of the growth of E . coli by mevinolin, a specific inhibitor of 3-hydroxy-3-methylglutaryl-CoA, can be best rationalized by the biosynthesis of IPP occurring in E . coli through a series of bound intermediates. Proc Natl Acad Sci U S A, 1991 Feb 1, 88(3), 921 - 5 CGG: an unassigned or nonsense codon in Mycoplasma capricolum; Oba T et al.; CGG is an arginine codon in the universal genetic code . We previously reported that in Mycoplasma capricolum, a relative of Gram-positive eubacteria, codon CGG did not appear in coding frames, including termination sites, and tRNA(ArgCCG) pairing with codon CGG, was not detected . These facts suggest that CGG is a nonsense (unassigned and untranslatable) codon--i.e., not assigned to arginine or to any other amino acid . We have investigated whether CGG is really an unassigned codon by using a cell-free translation system prepared from M . capricolum . Translation of synthetic mRNA containing in-frame CGG codons does not result in "read-through" to codons beyond the CGG codons--i.e., translation ceases just before CGG . Sucrose-gradient centrifugation profiles of the reaction mixture have shown that the bulk of peptide that has been synthesized is attached to 70S ribosomes and is released upon further incubation with puromycin . The result suggests that the peptide is in the P site of ribosome in the form of peptidyl-tRNA, leaving the A site empty . When in-frame CGG codons are replaced by UAA codons in mRNA, no read-through occurs beyond UAA, just as in the case of CGG . However, the synthesized peptide is released from 70S ribosomes, presumably by release factor 1 . These data suggest strongly that CGG is an unassigned codon and differs from UAA in that CGG is not used for termination. FEMS Microbiol Lett, 1991 Feb, 62(1), 53 - 8 Propionigenium modestum: a separate line of descent within the eubacteria; Both B et al.; The complete nucleotide sequence of 16S rRNA from Propionigenium modestum was determined and compared with 380 16S rRNA sequences from representatives of all eu- and archaebacterial phyla known so far . The phylogenetic analysis of this data set indicated P . modestum to represent a new separated line of descent within the radiation of eubacterial phyla moderately related to cyanobacteria and Gram-positive bacteria with low DNA GC content. Zhonghua Yi Xue Za Zhi, 1991 Feb, 71(2), 72 - 5, 6 {Bacteriological study on juvenile periodontitis}; Han N; The predominant cultivable microflora of 23 pockets in 15 juvenile periodontitis (JP) patients was studied for the first time in China using the current anaerobic methodology . Samples were taken with sterile paper points and dispersed on a vortex mixer . Then the diluted samples were plated on the non-selective blood agar plates and selective MGB medium which favors the growth of Actinobacillus actimycetemcomitans (Aa) and incubated in anaerobic chamber for 5 days . From each sample 15 or more isolated colonies were picked in sequence without selection and subcultured . The isolates were identified mainly by Schrechenberger's 4 hour rapid methods for biochemical and fermentative tests and the chromatographic analysis of acid end products using ion-chromatography . The results were as follows: 1 . The microflora of healthy sulci of 7 healthy young subjects was significantly different from that in the pocket of JP patients . The predominant species in healthy sulci were Streptococcus spp and Capnocytophaga gingivalis . 2 . The species increased significantly in JP patients in prevalence and proportions was Eubacterium . Other species in high proportions were Bacteroides oris, B . melaninogenicus, B . gingivalis, Capnocytophaga sputigena, and Actinomyces meyeri, etc . 3 . Actinobacillus actinomycetemcomitans was not detected in any of the samples. Eur J Biochem, 1991 Jan 30, 195(2), 321 - 7 Gene for the ADP-ribosylatable elongation factor 2 from the extreme thermoacidophilic archaebacterium Sulfolobus acidocaldarius . Cloning, sequencing, comparative analysis; Schroder J et al.; The gene coding for ADP-ribosylatable elongation factor 2 (EF-2) from the extreme thermoacidophilic archaebacterium Sulfolobus acidocaldarius has been cloned and its sequence is reported . Amino acid sequence comparisons showed that EF-2 from S . acidocaldarius is more closely related to eukaryotic EF-2 than to eubacterial EF-G . Consensus sequences are derived from comparison of a region around the unique amino acid diphthamide, which is the target for ADP-ribosylation by diphtheria toxin in archaebacteria and eukaryotes . The conserved positions are likely to constitute a recognition site for the toxin and the histidine-modifying enzymes . A single transcript of approximately the size of the EF-2 gene was observed in Northern blot experiments . Transcription initiation and termination signals were identified in the immediate vicinity of the respective translation start and stop codons of the gene . These results indicate that, in contrast to all prokaryotic EF-2 genes studied previously, the gene of S . acidocaldarius is not located within the streptomycin operon but is transcribed separately. FEMS Microbiol Lett, 1991 Jan 15, 61(2-3), 217 - 22 Expression in Caulobacter crescentus of the phosphate-starvation-inducible porin OprP of Pseudomonas aeruginosa; Walker SG et al.; The gene for the phosphate-starvation-inducible outer membrane protein OprP, of Pseudomonas aeruginosa was introduced into Caulobacter crescentus CB2A on a plasmid vector . As is the case in P . aeruginosa and Escherichia coli the oprP gene was inducible under conditions of limiting phosphate in C . crescentus . However, the maximal medium concentration of phosphate which still permitted induction of OprP was lower in C . crescentus (50 microM) than in P . aeruginosa (200 microM) . Induction of OprP was coincident with the process of stalk elongation, known to occur in C . crescentus under phosphate starvation conditions . When induced, OprP was localized to the cell envelope and became a major membrane protein, indicating that the Pseudomonas promoter was efficiently recognized in C . crescentus and that the gene product was targeted to the appropriate region of the cell . Our data provide support for the hypothesis that the mechanism for regulation of phosphate-starvation-inducible genes is highly conserved amongst the eubacteria. FEMS Microbiol Lett, 1991 Jan 15, 61(2-3), 151 - 6 A phylogenetic comparison of the 16S rRNA sequence of the fish pathogen, Renibacterium salmoninarum, to gram-positive bacteria; Gutenberger SK et al.; The 16S rRNA of Renibacterium salmoninarum, the causative agent of bacterial kidney disease in salmonids, was sequenced by reverse transcriptase to produce a nearly complete sequence (97%) of 1475 nucleotides . Phylogenetic comparisons to seventeen genera and signature sequence analysis indicated that R . salmoninarum was a member of the high G + C Gram-positive eubacterial subdivision although the reported G + C value is only 53% . A phylogenetic tree details the relationship of R . salmoninarum to ten actinomycetes from diverse environments. Free Radic Res Commun, 1991, 12-13 Pt 1, 443 - 9 Halobacterium halobium Mn-SOD gene: archaebacterial and eubacterial features; Salin ML et al.; A 1.8 kb PstI fragment from Halobacterium halobium DNA was found to hybridize to synthetic oligonucleotide probes constructed by using the sequence of the N-terminus of a Mn-containing superoxide dismutase purified from H . halobium . The entire insert containing a 600-bp coding sequence for Mn-SOD and its 5' and 3' flanking regions was sequenced . The derived amino acid sequence of the structural gene showed a similarity to other manganic and iron-containing superoxide dismutases in normally conserved regions . Primer extension analysis of the H . halobium Mn-SOD mRNA showed that gene transcription begins 14 bases upstream of the translational start . A Shine-Dalgarno sequence and archaebacterial consensus promoter sequences were observed . Several other promoter and terminator nucleotide sequences homologous to prokaryotic and eukaryotic organisms were found. Biochem Cell Biol, 1991 Jan, 69(1), 72 - 8 Structure of the glycan chain from the surface layer glycoprotein of Bacillus alvei CCM 2051; Altman E et al.; The cell surface of the mesophilic eubacterium Bacillus alvei CCM 2051 is covered by an oblique arranged surface layer glycoprotein . The subunits revealed by sodium dodecyl sulfate - polyacrylamide gel electrophoresis were distinct bands of molecular masses 140,000, 128,000, and 127,000 . Proteolytic degradation of the purified S-layer glycoprotein yielded a single glycopeptide fraction with an apparent molecular mass of ca . 25,000 . Methylation analysis in conjunction with two-dimensional nuclear magnetic resonance experiments at 500 MHz established the branched trisaccharide (formula; see text) as the repeating unit for this glycan chain. J Lipid Res, 1991 Jan, 32(1), 89 - 96 Mechanism of intestinal 7 alpha-dehydroxylation of cholic acid: evidence that allo-deoxycholic acid is an inducible side-product; Hylemon PB et al.; We previously reported that the 7 alpha-dehydroxylation of cholic acid appears to be carried out by a multi-step pathway in intestinal anaerobic bacteria both in vitro and in vivo . The pathway is hypothesized to involve an initial oxidation of the 3 alpha-hydroxy group and the introduction of a double bond at C4-C5 generating a 3-oxo-4-cholenoic bile acid intermediate . The loss of water generates a 3-oxo-4,6-choldienoic bile acid which is reduced (three steps) yielding deoxycholic acid . We synthesized, in radiolabel, the following putative bile acid intermediates of this pathway 7 alpha,12 alpha-dihydroxy-3-oxo-4-cholenoic acid, 7 alpha,12 alpha-dihydroxy-3-oxo-5 beta-cholanoic acid, 12 alpha-dihydroxy-3-oxo-4,6-choldienoic acid, and 12 alpha-hydroxy-3-oxo-4-cholenoic acid and showed that they could be converted to 3 alpha,12 alpha-dihydroxy-5 beta-cholanoic acid (deoxycholic acid) by whole cells or cell extracts of Eubacterium sp . VPI 12708 . During studies of this pathway, we discovered the accumulation of two unidentified bile acid intermediates formed from cholic acid . These bile acids were purified by thin-layer chromatography and identified by gas-liquid chromatography-mass spectrometry as 12 alpha-hydroxy-3-oxo-5 alpha-cholanoic acid and 3 alpha,12 alpha-dihydroxy-5 alpha-cholanoic (allo-deoxycholic acid) . Allo-deoxycholic acid was formed only in cell extracts prepared from bacteria induced by cholic acid, suggesting that their formation may be a branch of the cholic acid 7 alpha-dehydroxylation pathway in this bacterium. J Periodontol, 1991 Jan, 62(1), 74 - 81 Microbiological study of HIV-related periodontitis; Rams TE et al.; The subgingival microbiota in 14 persons with HIV-periodontitis was examined . Subgingival plaque samples were collected with paper points, transported in VMGA III, and plated on anaerobic enriched brucella blood agar and various selective media . HIV-periodontitis sites revealed Actinobacillus actinomycetemcomitans, Wolinella recta, Peptostreptococcus micros, and Bacteroides intermedius, each averaging 7% to 16% of the cultivable subgingival flora in positive patients . High levels of spirochetes also were detected in diseased sites with phase-contrast microscopy . Low levels of Candida albicans or enteric Gram-negative rods were recovered in the subgingival flora in 7 HIV-periodontitis patients or Bacteroides fragilis, Fusobacterium necrophorum, Fusobacterium varium, and Eubacterium aerofaciens were recovered in 8 patients . These findings suggest that the major components of the subgingival microbial flora in HIV-periodontitis are similar to those associated with adult periodontitis in systemically healthy persons . However, HIV-periodontitis lesions also may contain organisms which are rarely found in common types of periodontitis . The etiological significance of specific periodontal organisms in HIV-periodontitis awaits further longitudinal study. Biofactors, 1991 Jan, 3(1), 1 - 9 Organic osmolytes in methanogenic archaebacteria; Robertson DE et al.; Methanogenic archaebacteria have developed unique ways of dealing with osmotic stress . While several of them have transport systems capable of internalizing betaine, an osmolyte in many eubacteria, in general they have developed de novo synthesis of a novel series of beta-amino acids as compatible solutes . 13C-NMR spectroscopy has been the key tool in elucidating both the identity of these organic osmolytes and in investigating their dynamics. J Biochem (Tokyo), 1991 Jan, 109(1), 45 - 8 Kinetic studies on a novel sulfotransferase from Eubacterium A-44, a human intestinal bacterium; Kim DH et al.; A novel sulfotransferase purified from a human intestinal bacterium stoichiometrically catalyzed the transfer of a sulfate group of phenylsulfate esters to phenolic compounds . Vmax values of the enzyme reaction were measured with various concentrations of a sulfate donor substrate, p-nitrophenylsulfate, and of a sulfate acceptor substrate, tyramine . Double reciprocal plots of the acceptor concentration and Vmax showed a linear correlation . One of the reaction products, tyramine O-sulfate, competitively inhibited the enzyme as to a donor substrate, p-nitrophenylsulfate (PNS), but the other reaction product, p-nitrophenol (PNP), noncompetitively inhibited it as to PNS . These kinetic data suggest that the sulfate transfer reaction proceeds according to a ping pong bi bi mechanism . The enzyme was activated by Mg2+ and inhibited by EDTA, which suggests that it is a metalloenzyme. J Mol Evol, 1991 Jan, 32(1), 70 - 8 Evolution of RNA polymerases and branching patterns of the three major groups of Archaebacteria; Iwabe N et al.; The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses . It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree . The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage . This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases . It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints . In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited . In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method . It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues. Arch Biochem Biophys, 1991 Jan, 284(1), 22 - 5 Gene cluster rpoBC1C2 in cyanobacteria does not constitute an operon; Xie WQ et al.; The core enzyme of the cyanobacterial DNA-dependent RNA polymerase contains a unique component, gamma, which is absent from the corresponding enzymes of other eubacteria . In the heterocystous cyanobacterium Nostoc commune the gene encoding gamma, rpoC1, is immediately adjacent to, and downstream of, rpoB . The rpoC1 gene, and a 3' adjacent gene, rpoC2, correspond to the single rpoC gene found in Escherichia coli with respect to those domains conserved within their translational products . Northern analysis and primer extension assay show that in N . commune, rpoC1 and rpoC2 are transcribed separately from rpoB . The promoter of rpoC1C2 can direct the expression of a promotorless lacZ gene in E . coli . As a consequence, cyanobacterial rpo gene expression is distinct from the mode of cotranscription described for the equivalent sequences found in other eubacteria, archaebacteria, and plant chloroplasts . Also in this paper, a simple protocol for RNA isolation, which should be applicable for RNA isolation from plant cells, is presented. Virology, 1991 Jan, 180(1), 88 - 98 Identification, sequence, and expression of the gene encoding the second-largest subunit of the vaccinia virus DNA-dependent RNA polymerase; Amegadzie BY et al.; The gene, rpo 132, encoding the second-largest subunit of the vaccinia virus DNA-dependent RNA polymerase was identified and sequenced . Two complementary approaches, involving antiserum to purified vaccinia virus RNA polymerase, were used to locate the rpo 132 gene . One method involved the screening of a lambda gt11 library of vaccinia virus genome fragments and the other was based on the immunoprecipitation and polyacrylamide gel electrophoresis of the in vitro translation products of mRNA that hybridized to immobilized vaccinia virus DNA . The deduced open reading frame of the rpo 132 gene predicted a polypeptide of 1164 amino acid residues with sequence similarities to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes as well as to other poxviruses . Transcriptional analyses indicated that rpo 132 has both early and late RNA start sites and is expressed throughout infection. Rheumatol Int, 1991, 11(4-5), 203 - 8 Histology of joint inflammation induced in rats by cell wall fragments of the anaerobic intestinal bacterium Eubacterium aerofaciens; Severijnen AJ et al.; To study the arthropathic properties of human intestinal bacteria, cell wall fragments (CWF) of the anaerobic bowel bacterium Eubacterium aerofaciens were injected intraperitoneally (i.p.) in arthritis-susceptible Lewis rats . Rat paw joints were subsequently studied for histopathological changes . A persisting synovitis accompanied by marginal erosions of cartilage and bone and a marked periosteal apposition of new bone tissue were the main features of the polyarthritis induced . These results are discussed in relation to streptococcal cell wall induced arthritis and compared with histopathological findings in rheumatoid arthritis (RA) in man. Rev Latinoam Microbiol, 1991 Jan-Mar, 33(1), 87 - 101 {Functional and evolutionary aspects of the aminoacyl-tRNA synthetases}; Silva Gonzalez E et al.; A main event in protein bioshynthesis is the esterification of the correct aminoacid to cognate tRNA catalized by the aminoacyl-tRNA synthetases . The central role of this family of enzymes in metabolism is an evidence of their ancient origin . As it is the case in many others molecules involved in protein synthesis, the emergence of the aminoacyl-tRNA synthetases appears to be a problem that is not yet solved in order to understand the origin of the genetic translation . To obtain a comprehensive view of the evolution of the relationship between each one of the twenty aminoacyl-tRNA synthetases from one organism as well as from different sources (eubacteria, archaebacteria and eukaryotes) we review the information collected from the structural and catalytic properties of these enzyme . The results allow us to establish the following relationship between aminoacyl-tRNA synthetases . On one side there is a monofiletic origin for glutamyl, glutamynil and argynil-tRNA synthetases from Escherichia coli and for valyl, leucyl, metionyl, isoleucyl and phenylalanil-tRNA synthetases from eubacterias, archaebacterias and eukaryotes . On the other side there is an evolutionary relationship between aminoacyl-tRNA synthetases of eubacteria and organelles (plastids and mitochondria) and among eukaryotes and archaebacteria. Comp Biochem Physiol A, 1991, 98(2), 351 - 4 Identification and properties of an alpha-amylase from a strain of Eubacterium sp . isolated from the rat intestinal tract; Delahaye EP et al.; 1 . A bacterial amylase was isolated from the intestinal content of monoxenic rats inoculated with Eubacterium sp . B86 . 2 . Affinity chromatography on cross-linked starch allowed its separation from rat endogenous amylases . 3 . The bacterial enzyme was characterized by its pI, molecular weight and action pattern . It behaves as a typical endo-amylase (alpha-amylase). Science, 1990 Dec 14, 250(4987), 1570 - 3 An ancient group I intron shared by eubacteria and chloroplasts; Kuhsel MG et al.; Introns have been found in the genomes of all major groups of organisms except eubacteria . The presence of introns in chloroplasts and mitochondria, both of which are of eubacterial origin, has been interpreted as evidence either for the recent acquisition of introns by organelles or for the loss of introns from their eubacterial progenitors . The gene for the leucine transfer RNA with a UAA anticodon {tRNALeu (UAA)} from five diverse cyanobacteria and several major groups of chloroplasts contains a single group I intron . The intron is conserved in secondary structure and primary sequence, and occupies the same position, within the UAA anticodon . The homology of the intron across chloroplasts and cyanobacteria implies that it was present in their common ancestor and that it has been maintained in their genomes for at least 1 billion years. Science, 1990 Dec 14, 250(4987), 1566 - 70 Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria; Xu MQ et al.; A self-splicing group I intron has been found in the gene for a leucine transfer RNA in two species of Anabaena, a filamentous nitrogen-fixing cyanobacterium . The intron is similar to one that is found at the identical position in the same transfer RNA gene of chloroplasts of land plants . Because cyanobacteria were the progenitors of chloroplasts, it is likely that group I introns predated the endosymbiotic association of these eubacteria with eukaryotic cells. Eur J Biochem, 1990 Dec 12, 194(2), 367 - 72 The molybdoenzyme formylmethanofuran dehydrogenase from Methanosarcina barkeri contains a pterin cofactor; Karrasch M et al.; Recently formylmethanofuran dehydrogenase from the archaebacterium Methanosarcina barkeri has been shown to be a novel molybdo-iron-sulfur protein . We report here that the enzyme contains one mol of a bound pterin cofactor/mol molybdenum, similar but not identical to the molybdopterin of milk xanthine oxidase . The two pterins, after oxidation with I2 at pH 2.5, showed identical fluorescence spectra and, after oxidation with permanganate at pH 13, yielded pterin 6-carboxylic acid . They differed, however, in their apparent molecular mass: the pterin of formylmethanofuran dehydrogenase was 400 Da larger than that of milk xanthine oxidase, a property also exhibited by the pterin cofactor of eubacterial molybdoenzymes . A homogeneous formylmethanofuran dehydrogenase preparation was used for these investigations . The enzyme, with a molecular mass of 220 kDa, contained 0.5-0.8 mol molybdenum, 0.6-0.9 mol pterin, 28 +/- 2 mol non-heme iron and 28 +/- 2 mol acid-labile sulfur/mol based on a protein determination with bicinchoninic acid . The specific activity was 175 mumol.min-1.mg-1 (kcat = 640 s-1) assayed with methylviologen (app . Km = 0.02 mM) as artificial electron acceptor . The apparent Km for formylmethanofuran was 0.02 mM. N Engl J Med, 1990 Dec 6, 323(23), 1573 - 80 The agent of bacillary angiomatosis . An approach to the identification of uncultured pathogens; Relman DA et al.; BACKGROUND . Bacillary angiomatosis is an infectious disease causing proliferation of small blood vessels in the skin and visceral organs of patients with human immunodeficiency virus infection and other immunocompromised hosts . The agent is often visualized in tissue sections of lesions with Warthin-Starry staining, but the bacillus has not been successfully cultured or identified . This bacillus may also cause cat scratch disease . METHODS . In attempting to identify this organism, we used the polymerase chain reaction . We used oligonucleotide primers complementary to the 16S ribosomal RNA genes of eubacteria to amplify 16S ribosomal gene fragments directly from tissue samples of bacillary angiomatosis . The DNA sequence of these fragments was determined and analyzed for phylogenetic relatedness to other known organisms . Normal tissues were studied in parallel . RESULTS . Tissue from three unrelated patients with bacillary angiomatosis yielded a unique 16S gene sequence . A sequence obtained from a fourth patient with bacillary angiomatosis differed from the sequence found in the other three patients at only 4 of 241 base positions . No related 16S gene fragment was detected in the normal tissues . These 16S sequences associated with bacillary angiomatosis belong to a previously uncharacterized microorganism, most closely related to Rochalimaea quintana . CONCLUSIONS . The cause of bacillary angiomatosis is a previously uncharacterized rickettsia-like organism, closely related to R . quintana . This method for the identification of an uncultured pathogen may be applicable to other infectious diseases of unknown cause. J Med Microbiol, 1990 Dec, 33(4), 239 - 42 Comparison of identification methods for oral asaccharolytic Eubacterium species; Wade WG et al.; Thirty one strains of oral, asaccharolytic Eubacterium spp . and the type strains of E . brachy, E . nodatum and E . timidum were subjected to three identification techniques--protein-profile analysis, determination of metabolic end-products, and the API ATB32A identification kit . Five clusters were obtained from numerical analysis of protein profiles and excellent correlations were seen with the other two methods . Protein profiles alone allowed unequivocal identification. J Bacteriol, 1990 Dec, 172(12), 7011 - 9 Cloning and sequencing of a bile acid-inducible operon from Eubacterium sp . strain VPI 12708; Mallonee DH et al.; Two bile acid-inducible polypeptides from Eubacterium sp . strain VPI 12708 with molecular weights of 27,000 and approximately 45,000 have previously been shown to be encoded by genes residing on a 2.9-kb EcoRI fragment . We now report the cloning and sequencing of three additional overlapping DNA fragments upstream from this EcoRI fragment . Together, these four fragments contain a large segment of a bile acid-inducible operon which encodes the 27,000- and 45,000-Mr (now shown to be 47,500-Mr) polypeptides and open reading frames potentially coding for four additional polypeptides with molecular weights of 59,500, 58,000, 19,500, and 9,000 to 11,500 . A bile acid-inducible polypeptide with an apparent Mr of 23,500, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was purified to homogeneity, and the N-terminal amino acid sequence that was obtained matched the sequence deduced from the open reading frame coding for the 19,500-Mr polypeptide . A short DNA segment containing the 3' downstream end of the gene coding for the 47,500-Mr polypeptide was not successfully cloned but was directly sequenced from DNA fragments synthesized by polymerase chain reaction . The mRNA initiation site for the bile acid-inducible operon was shown by primer extension to be immediately upstream from the gene encoding the 58,000-Mr polypeptide . A potential promoter region upstream from the mRNA initiation site displayed significant homology with the promoter regions of previously identified bile acid-inducible genes from Eubacterium sp . strain VPI 12708 . We hypothesize that this bile acid-inducible operon codes for most of the enzymes involved in the bile acid 7 alpha-dehydroxylation pathway in this bacterium. J Bacteriol, 1990 Dec, 172(12), 6789 - 96 Nitrogenase in the archaebacterium Methanosarcina barkeri 227; Lobo AL et al.; The discovery of nitrogen fixation in the archaebacterium Methanosarcina barkeri 227 raises questions concerning the similarity of archaebacterial nitrogenases to Mo and alternative nitrogenases in eubacteria . A scheme for achieving a 20- to 40-fold partial purification of nitrogenase components from strain 227 was developed by using protamine sulfate precipitation, followed by using a fast protein liquid chromatography apparatus operated inside an anaerobic glove box . As in eubacteria, the nitrogenase activity was resolved into two components . The component 1 analog had a molecular size of approximately 250 kDa, as estimated by gel filtration, and sodium dodecyl sulfate-polyacrylamide gels revealed two predominant bands with molecular sizes near 57 and 62 kDa, consistent with an alpha 2 beta 2 tetramer as in eubacterial component 1 proteins . For the component 2 analog, a molecular size of approximately 120 kDa was estimated by gel filtration, with a subunit molecular size near 31 kDa, indicating that the component 2 protein is a tetramer, in contrast to eubacterial component 2 proteins, which are dimers . Rates of C2H2 reduction by the nearly pure subunits were 1,000 nmol h-1 mg of protein-1, considerably lower than those for conventional Mo nitrogenases but similar to that of the non-Mo non-V nitrogenase from Azotobacter vinelandii . Strain 227 nitrogenase reduced N2 at a higher rate per electron than it reduced C2H2, also resembling the non-Mo non-V nitrogenase of A . vinelandii . Ethane was not produced from C2H2 . NH4+ concentrations as low as 10 microM caused a transient inhibition of C2H2 reduction by strain 227 cells . Antiserum against component 2 Rhodospirillum rubrum nitrogenase was found to cross-react with component 2 from strain 227, and Western immunoblots using this antiserum showed no evidence for covalent modification of component 2 . Also, extracts of strain 227 cells prepared before and after switch-off had virtually the same level of nitrogenase activity . In conclusion, the nitrogenase from strain 227 is similar in overall structure to the eubacterial nitrogenases and shows greatest similarity to alternative nitrogenases. J Bacteriol, 1990 Dec, 172(12), 6809 - 17 Characterization of the H(+)-pumping F1F0 ATPase of Vibrio alginolyticus; Krumholz LR et al.; The F1F0 ATPase of Vibrio alginolyticus was cloned from a chromosomal lambda library . The unc operon, which contains the structural genes for the ATPase, was sequenced and shown to have a gene organization of uncIBEFHAGDC . The sequence of each subunit was compared with those of other eubacterial ATPases . The V . alginolyticus unc genes exhibited greater similarity to the Escherichia coli unc genes than to any of the other bacterial unc genes for which the sequence is available . The ATPase was expressed in an E . coli unc deletion strain, and the ATP hydrolytic activity was characterized . It has a pH optimum of 7.6 and is stimulated by the addition of Triton X-100 or any of a variety of salts . The recombinant F1F0 was purified 30.4-fold and reconstituted into proteoliposomes . This enzyme catalyzed the pumping of protons coupled to ATP hydrolysis as measured in fluorescence quenching experiments but would not pump Na+ ions under similar conditions. Proc Natl Acad Sci U S A, 1990 Dec, 87(24), 9509 - 13 Mutational analysis of an archaebacterial promoter: essential role of a TATA box for transcription efficiency and start-site selection in vitro; Reiter WD et al.; By using a recently developed in vitro transcription assay, the 16S/23S rRNA-encoding DNA promoter from the archaebacterium Sulfolobus sp . B12 was dissected by deletion and linker substitution mutagenesis . The analysis of 5' and 3' deletion mutants defined a core promoter region between positions -38 and -2 containing all information for efficient and specific transcription . Further characterization of this region by linker substitution mutagenesis indicated two sequence elements important for promoter function--one located between positions -38 and -25 (distal promoter element) and the other one located between positions -11 and -2 (proximal promoter element) . The distal promoter element encompassed the TATA-like "box A" element located approximately 26 nucleotides upstream of the majority of transcription start sites in archaebacteria (Archaeobacteria) . All mutations within this box A motif virtually abolished promoter function . Complete inactivation of the proximal promoter element was dependent on extensive mutagenesis; this element is not conserved between archaebacterial promoters except for a high A + T content in stable RNA gene promoters from Sulfolobus . Mutants containing insertions or deletions between the distal and proximal promoter elements were only slightly affected in their transcription efficiency but displayed a shift in their major initiation site, retaining an essentially fixed distance between the distal promoter element and the transcription start site . Thus, efficient transcription and start-site selection were dependent on a conserved TATA-like sequence centered approximately 26 nucleotides upstream of the initiation site, a situation unlike that of eubacterial promoters but resembling the core structure of most eukaryotic RNA polymerase II (and some RNA polymerase III) promoters . This finding suggests a common evolutionary origin of these promoters consistent with the known similarities between archaebacterial and eukaryotic RNA polymerases. Oral Microbiol Immunol, 1990 Dec, 5(6), 340 - 5 Antimicrobial activities of thiolactomycin against gram-negative anaerobes associated with periodontal disease . f1; Hamada S et al.; Thiolactomycin (TLM), (4R)-(2E,5E)-2,4,6-trimethyl-3-hydroxy-2,5, 7-octatriene-4-thiolide, purified from a culture filtrate of a strain of the Nocardia species, was examined for antimicrobial activities against more than 100 strains of oral and periodontally associated bacteria . Nine other commonly used antibiotics were also included for the test . We found that TLM exhibited strong and selective antimicrobial activities against Bacteroides gingivalis and other oral black-pigmented Bacteroides species that may be etiologically associated with adult periodontitis . TLM also inhibited the growth of Actinobacillus actinomycetemcomitans, but did not affect the growth of oral streptococcal species and Eubacterium species . Strains of Eikenella corrodens were moderately susceptible to TLM, while Actinomyces viscosus strains were only slightly susceptible to it . Other antibiotics used for comparison showed a broad spectrum of antimicrobial activities in general . In conclusion, TLM exhibited highly selective antimicrobial activities to black-pigmented Bacteroides species and A . actinomycetemcomitans, both of which are implicated in the pathogenesis of human periodontal disease. FEMS Microbiol Rev, 1990 Dec, 7(3-4), 377 - 82 Formate dehydrogenase; Ferry JG; Formate is a substrate, or product, of diverse reactions catalyzed by eukaryotic organisms, eubacteria, and archaebacteria . A survey of metabolic groups reveals that formate is a common growth substrate, especially among the anaerobic eubacteria and archaebacteria . Formate also functions as an accessory reductant for the utilization of more complex substrates, and an intermediate in energy-conserving pathways . The diversity of reactions involving formate dehydrogenases is apparent in the structures of electron acceptors which include pyridine nucleotides, 5-deazaflavin, quinones, and ferredoxin . This diversity of electron acceptors is reflected in the composition of formate dehydrogenase . Studies on these enzymes have contributed to the biochemical and genetic understanding of selenium, molybdenum, tungsten, and iron in biology . The regulation of formate dehydrogenase synthesis serves as a model for understanding general principles of regulation in anaerobic organisms. Scand J Dent Res, 1990 Dec, 98(6), 472 - 81 Hydrophobicities of human polymorphonuclear leukocytes and oral Bacteroides and Porphyromonas spp., Wolinella recta, and Eubacterium yurii with special reference to bacterial surface structures; Haapasalo M et al.; The hydrophobicities of human polymorphonuclear leukocytes (PMNLs) and Bacteroides buccae, B . oris, B . oralis, B . veroralis, B . buccalis, B . heparinolyticus, B . intermedius, B . denticola, B . loescheii, B . melaninogenicus, Porphyromonas gingivalis, P . endodontalis, Wolinella recta, and Eubacterium yurii were studied by the hexadecane method . The majority of the strains were equally or less hydrophobic than the PMNLs . Only in the case of E . yurii and the only strain of B . buccalis were all strains more hydrophobic than the PMNLs . However, some strains of B . intermedius, B . oris, B . denticola, and P . gingivalis were also more hydrophobic than the PMNLs . With the exception of B . intermedius and species with a crystalline surface protein layer (S-layer), the strains of all other species with a thick capsule were more hydrophilic than the strains with little or no extracellular polymeric material . All strains of the S-layer species were either quite hydrophilic or hydrophobic depending on the species, totally irrespective of the presence of the capsule . The results suggest that the S-layers of oral anaerobic bacteria may be important determinants of cell surface hydrophobicity. Curr Genet, 1990 Dec, 18(6), 547 - 51 Phylogenetic analysis of the RNA polymerases of Trypanosoma brucei, with special reference to class-specific transcription; Jess W et al.; We have sequenced the genes encoding to largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei . The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes . Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method . These independent calculations resulted in trees with very similar topologies . The analyses show that all the largest subunits of T . brucei are evolutionarily distant members within each of the three RNA polymerase classes . An early separation of the trypanosomal subunits from the eukaryotic lineage might form the fundamental basis for the unusual transcription process of this species . Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III . RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage, RNA polymerase I, however, arises separately from the eubacterial beta' lineage . This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation. Proc Natl Acad Sci U S A, 1990 Nov, 87(22), 8918 - 22 Differential intron loss and endosymbiotic transfer of chloroplast glyceraldehyde-3-phosphate dehydrogenase genes to the nucleus; Liaud MF et al.; Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is composed of two different subunits, GAPA and GAPB, which are encoded in the nucleus by two related genes of eubacterial origin . In the present work the genes encoding chloroplast GAPA and GAPB from pea have been cloned and sequenced . The gene for GAPB is split by eight introns . Two introns interrupt the region encoding the transit peptide and six are found within the region encoding the mature subunit, four of which are in identical or similar positions relative to genes for cytosolic GAPDH of eukaryotic organisms . As opposed to this, the gene encoding pea GAPA has only two introns in the region encoding the mature subunit . These findings strongly support the "intron early" hypothesis and suggest that the low number of introns in the gene for chloroplast GAPA is due to differential loss of introns during the streamlining period of the chloroplast genome following the GAPB/GAPA separation . We deduce from this that eubacteria and chloroplasts contained GT-AG introns until relatively recently and that the duplication event leading to the genes encoding GAPB and GAPA and their respective transit peptides occurred in the chloroplast progenitor prior to the successive transfer and functional reintegration of these genes into the nuclear environment . These conclusions imply that GAPA/GAPB transit peptides are of eubacterial origin. J Bacteriol, 1990 Nov, 172(11), 6568 - 72 Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria; de Lorenzo V et al.; A collection of Tn5-derived minitransposons has been constructed that simplifies substantially the generation of insertion mutants, in vivo fusions with reporter genes, and the introduction of foreign DNA fragments into the chromosome of a variety of gram-negative bacteria, including the enteric bacteria and typical soil bacteria like Pseudomonas species . The minitransposons consist of genes specifying resistance to kanamycin, chloramphenicol, streptomycin-spectinomycin, and tetracycline as selection markers and a unique NotI cloning site flanked by 19-base-pair terminal repeat sequences of Tn5 . Further derivatives also contain lacZ, phoA, luxAB, or xylE genes devoid of their native promoters located next to the terminal repeats in an orientation that affords the generation of gene-operon fusions . The transposons are located on a R6K-based suicide delivery plasmid that provides the IS50R transposase tnp gene in cis but external to the mobile element and whose conjugal transfer to recipients is mediated by RP4 mobilization functions in the donor. J Bacteriol, 1990 Nov, 172(11), 6557 - 67 Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria; Herrero M et al.; A simple procedure for cloning and stable insertion of foreign genes into the chromosomes of gram-negative eubacteria was developed by combining in two sets of plasmids (i) the transposition features of Tn10 and Tn5; (ii) the resistances to the herbicide bialaphos, to mercuric salts and organomercurial compounds, and to arsenite, and (iii) the suicide delivery properties of the R6K-based plasmid pGP704 . The resulting constructions contained unique NotI or SfiI sites internal to either the Tn10 or the Tn5 inverted repeats . These sites were readily used for cloning DNA fragments with the help of two additional specialized cloning plasmids, pUC18Not and pUC18Sfi . The newly derived constructions could be maintained only in donor host strains that produce the R6K-specified pi protein, which is an essential replication protein for R6K and plasmids derived therefrom . Donor plasmids containing hybrid transposons were transformed into a specialized lambda pir lysogenic Escherichia coli strain with a chromosomally integrated RP4 that provided broad-host-range conjugal transfer functions . Delivery of the donor plasmids into selected host bacteria was accomplished through mating with the target strain . Transposition of the hybrid transposon from the delivered suicide plasmid to a replicon in the target cell was mediated by the cognate transposase encoded on the plasmid at a site external to the transposon . Since the transposase function was not maintained in target cells, such cells were not immune to further transposition rounds . Multiple insertions in the same strain are therefore only limited by the availability of distinct selection markers . The utility of the system was demonstrated with a kanamycin resistance gene as a model foreign insert into Pseudomonas putida and a melanin gene from Streptomyces antibioticus into Klebsiella pneumoniae . Because of the modular nature of the functional parts of the cloning vectors, they can be easily modified and further selection markers can be incorporated . The cloning system described here will be particularly useful for the construction of hybrid bacteria that stably maintain inserted genes, perhaps in competitive situations (e.g., in open systems and natural environments), and that do not carry antibiotic resistance markers characteristic of most available cloning vectors (as is currently required of live bacterial vaccines). Cell, 1990 Oct 19, 63(2), 417 - 24 A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1; Goodrich-Blair H et al.; We report a self-splicing intron in bacteriophage SPO1, whose host is the gram-positive Bacillus subtilis . The intron contains all the conserved features of primary sequence and secondary structure previously described for the group IA introns of eukaryotic organelles and the gram-negative bacteriophage T4 . The SPO1 intron contains an open reading frame of 522 nucleotides . As in the T4 introns, this open reading frame begins in a region that is looped out of the secondary structure, but ends in a highly conserved region of the intron core . The exons encode SPO1 DNA polymerase, which is highly similar to E . coli DNA polymerase I . The demonstration of self-splicing introns in viruses of both gram-positive and gram-negative eubacteria lends further evidence for their early origin in evolution. Biochemistry, 1990 Oct 16, 29(41), 9733 - 6 Ribosomal protein L35: identification in spinach chloroplasts and isolation of a cDNA clone encoding its cytoplasmic precursor; Smooker PM et al.; We describe the isolation of spinach chloroplast ribosomal protein L35 and characterization of a cDNA clone encoding its cytoplasmic precursor . This protein was only recently identified in ribosomes, but the sequences of four L35 genes have now been reported and confirm its presence in eubacteria, chloroplasts, and cyanelles . Using N-terminal sequence data, oligonucleotides were designed and a cDNA library was screened . The nucleotide sequence of the cDNA clones shows that the spinach L35 protein is encoded as a precursor of 159 residues, comprising a mature protein of 73 residues and a transit peptide of 86 residues . The cleavage site for forming the mature protein is deduced to be Thr-Val-Phe-Ala decreases Ala-Lys-Gly-Tyr . The L35 protein in the photosynthetic organelle of the protozoan Cyanophora paradoxa is encoded in the organelle DNA {Bryant & Stirewalt (1990) FEBS Lett . 259, 273-280} . The corresponding gene has not been found in the chloroplast DNA of a lower plant (liverwort) and two higher plants . Our results demonstrate that the L35 protein in a higher plant (spinach) is encoded in the nucleus . This finding, in light of the endosymbiont hypothesis, suggests an organelle to nucleus transfer of the L35 gene at the evolutionary beginnings of land plants. J Clin Microbiol, 1990 Oct, 28(10), 2375 - 6 Eubacterium lentum ATCC 43055, a new reference strain for quality control of anaerobic susceptibility tests; Barry AL et al.; A strain of Eubacterium lentum (ATCC 43055) was selected for quality control of anaerobic susceptibility tests . Multilaboratory collaborative studies with 13 different antimicrobial agents were reviewed, and MIC control limits were proposed for agar dilution tests with the new control strain. J Bacteriol, 1990 Oct, 172(10), 6165 - 8 Nucleotide sequence analysis of the Leptospira biflexa serovar patoc rpsL and rpsG genes; Zuerner RL et al.; The Leptospira biflexa rpsL and rpsG genes were sequenced . Although similar in many respects, proteins encoded by these L . biflexa genes had several unusual features when compared with homologous proteins of other organisms . Unlike the rpsL genes of other eubacteria, the L . biflexa rpsL gene is adjacent to a rpoC-like gene. Antimicrob Agents Chemother, 1990 Oct, 34(10), 1908 - 14 Synthesis of active nitroguaiacol ether derivatives of streptomycin; Abad JP et al.; The synthesis, purification, and biological properties of nitroguaiacol ether derivatives of streptomycin and their corresponding radioactive reduced products were examined . These derivatives are biologically active against gram-positive and gram-negative eubacteria and they are also photoreactive because of the presence of the nitroguaiacol group in the molecule . We demonstrated that these derivatives can be used as streptomycin analogs in photoaffinity labeling of the macromolecular structures related to the mode of action of the antibiotic. Naturwissenschaften, 1990 Oct, 77(10), 472 - 5 Comparison of the biosynthesis of the methanobacterial pseudomurein and the eubacterial murein; Hartmann E et al.; From cell extracts of the archaebacterium Methanobacterium thermoautotrophicum 11 putative precursors of the pseudomurein were isolated and characterized . On the basis of the isolated intermediates, a biosynthetic pathway of the pseudomurein is proposed . Compared to the eubacterial murein the biosynthetic stages follow different pathways as indicated by the occurrence of a nucleotide-activated disaccharide and nucleotide-activated peptides. Int J Syst Bacteriol, 1990 Oct, 40(4), 399 - 404 5S rRNA sequences of myxobacteria and radioresistant bacteria and implications for eubacterial evolution; Van den Eynde H et al.; 5S rRNA sequences were determined for the myxobacteria Cystobacter fuscus, Myxococcus coralloides, Sorangium cellulosum, and Nannocystis exedens and for the radioresistant bacteria Deinococcus radiodurans and Deinococcus radiophilus . A dendrogram was constructed by using weighted pairwise grouping based on these and all other previously known eubacterial 5S rRNA sequences, and this dendrogram showed differences as well as similarities compared with results derived from 16S rRNA analyses . In the dendrogram, Deinococcus 5S rRNA sequences clustered with 5S rRNA sequences of the genus Thermus, as suggested by the results of 16S rRNA analyses . However, in contrast to the 16S rRNA results, the Deinococcus-Thermus cluster divided the 5S rRNA sequences of the alpha subdivision of the class Proteobacteria from the 5S rRNA sequences of the beta and gamma subgroups of the Proteobacteria . The myxobacterial 5S rRNA sequence data failed to confirm the existence of a delta subgroup of the class Proteobacteria, which was suggested by the results of 16S rRNA analyses. J Bacteriol, 1990 Oct, 172(10), 5624 - 30 Purification and partial characterization of the DNA-dependent RNA polymerase from Rickettsia prowazekii; Ding HF et al.; The DNA-dependent RNA polymerase was purified from Rickettsia prowazekii, an obligate intracellular bacterial parasite . Because of limitation of available rickettsiae, the classical methods for isolation of the enzyme from other procaryotes were modified to purify RNA polymerase from small quantities of cells (25 mg of protein) . The subunit composition of the rickettsial RNA polymerase was typical of a eubacterial RNA polymerase . R . prowazekii had beta' (148,000 daltons), beta (142,000 daltons), sigma (85,000 daltons), and alpha (34,500 daltons) subunits as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis . The appropriate subunits of the rickettsial RNA polymerase bound to polyclonal antisera against Escherichia coli core polymerase and E . coli sigma 70 subunit in Western blots (immunoblots) . The enzyme activity was dependent on all four ribonucleoside triphosphates, Mg2+, and a DNA template . Optimal activity occurred in the presence of 10 mM MgCl2 and 50 mM NaCl . Interestingly, in striking contrast to E . coli, approximately 74% of the rickettsial RNA polymerase activity was associated with the rickettsial cell membrane at a low salt concentration (50 mM NaCl) and dissociated from the membrane at a high salt concentration (600 mM NaCl). J Vet Diagn Invest, 1990 Oct, 2(4), 318 - 22 Evaluation of four commercial anaerobic systems for identification of Eubacterium suis; Walker RL et al.; Four commercial anaerobic systems (CASs) were evaluated for usefulness in identification of Eubacterium suis . Twelve strains were evaluated in each system in triplicate, and results were interpreted independently by 5 individuals . Statistically significant differences (P less than 0.01) due to strain variation and reader interpretation accounted for discrepancies encountered . The reactivity, repeatability, and unique profiles generated made both CAS-1 and CAS-2 suitable adjuncts for identification of E . suis when colony morphology and Gram reaction were considered . Limited reactivity in CAS-3 limited its use as an aid in identification . Variability in test observations and the large number of numerical profiles generated precluded use of CAS-4. FEMS Microbiol Lett, 1990 Sep 15, 59(3), 241 - 6 In vivo and in vitro methylation of the elongation factor EF-Tu from Euglena gracilis chloroplast; Toledo H et al.; Based on amino acid sequence similarities between the methylated elongation factor EF-Tu from Escherichia coli and the EF-Tu from Euglena gracilis chloroplast, we predicted that the latter could also be methylated in the presence of an appropriate methyltransferase . We found that, as reported for the eubacterial homologous protein, the organellar factor could be methylated in vivo and in vitro to yield monomethyllysine. Nucleic Acids Res, 1990 Sep 11, 18(17), 5037 - 43 The organization and evolution of transfer RNA genes in Mycoplasma capricolum; Muto A et al.; The genes for presumably all the tRNA species in Mycoplasma capricolum, a derivative of Gram-positive eubacteria, have been cloned and sequenced . There are 30 genes encoding 29 tRNA species . This number is the smallest in all the known genetic systems except for mitochondria . The sequences of 9 tRNA genes of them have been previously reported (1-3) . Twenty-two genes are organized in 5 clusters consisting of nine, five, four and two genes (2 sets), respectively . The other eight genes exist as a single transcription unit . All the tRNAs are encoded each by a single gene, except for the occurrence of two tRNA(Lys)(TTT) genes . The arrangement of tRNA genes in the 9-gene cluster, the 5-gene cluster, the 4-gene cluster and one of the 2-gene clusters reveals extensive similarity with a part of the 21-tRNA gene cluster and/or the 16-tRNA gene cluster in Bacillus subtilis, respectively . The results suggest that the present M . capricolum tRNA genes have evolved from large tRNA gene clusters in the ancestral Gram-positive bacterial genome common to M . capricolum and B . subtilis, by discarding genes for redundant as well as non-obligate tRNAs, so that all the codons may be translated by as small a number of tRNAs as possible. Gene, 1990 Sep 1, 93(1), 73 - 8 Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria; Fujita MQ et al.; A phylogenetic tree constructed by 5S rRNA analysis is composed of three major branches in eubacteria: high G + C Gram+, low G + C Gram+ and Gram- {Hori and Osawa, Mol . Biol . Evol . 4 (1987) 445-472} . We have shown that the characteristic dnaA region is common among Escherichia coli (Gram-), Pseudomonas putida (Gram-), and Bacillus subtilis (low G + C Gram+) . We have now determined the structure of the dnaA region of Micrococcus luteus, as a representative of the last branch, high G + C Gram+ . The dnaA gene and at least three other genes, rnpA, rpmH and dnaN were found to be conserved in M . luteus . Large nontranslatable regions were found flanking the dnaA gene . The upstream region is conserved in the four bacteria so far examined . On the other hand, the downstream region is conserved only in Gram+ bacteria, M . luteus and B . subtilis . The consensus sequence of the DnaA box in M . luteus seems to be TTGTCCACA, in contrast to TTATCCACA of other bacteria . These results confirm our hypothesis that the dnaA region is the replication origin of the ancestral bacteria and that the essential feature of the DnaA protein and DnaA-box combination is conserved in eubacteria. J Mol Evol, 1990 Sep, 31(3), 205 - 10 Compartmentalized isozyme genes and the origin of introns; Iwabe N et al.; Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes . The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (= 1.3 x 10(-3), suggesting that the conservation of the intron positions has a biological significance . On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes . In the aspartate aminotransferase isozyme genes, five of the introns are at identical places . The origins of the five conserved introns, however, are not obvious at present . It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes. J Bacteriol, 1990 Sep, 172(9), 5343 - 51 Streptomyces hygroscopicus has two glutamine synthetase genes; Kumada Y et al.; Streptomyces hygroscopicus, which produces the glutamine synthetase inhibitor phosphinothricin, possesses at least two genes (glnA and glnB) encoding distinct glutamine synthetase isoforms (GSI and GSII) . The glnB gene was cloned from S . hygroscopicus DNA by complementation in an Escherichia coli glutamine auxotrophic mutant (glnA) . glnB was subcloned in Streptomyces plasmids by insertion into pIJ486 (pMSG3) and pIJ702 (pMSG5) . Both constructions conferred resistance to the tripeptide form of phosphinothricin (bialaphos) and were able to complement a glutamine auxotrophic marker in S . coelicolor . Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of S . lividans(pMSG5) revealed a highly overexpressed 40-kilodalton protein . When GS was purified from this strain, it was indistinguishable in apparent molecular mass from the 40-kilodalton protein . The nucleic acid sequence of the cloned region contained an open reading frame which encoded a protein whose size, amino acid composition, and N-terminal sequence corresponded to those of the purified GS . glnB had a high G + C content and codon usage typical of streptomycete genes . A comparison of its predicted amino acid sequence with the protein data bases revealed that it encoded a GSII-type enzyme which had previously been found only in various eucaryotes (47 to 50% identity) and nodulating bacteria such as Bradyrhizobium spp . (42% identity) . glnB had only 13 to 18% identity with eubacterial GSI enzymes . Southern blot hybridization experiments showed that sequences similar to glnB were present in all of the five other Streptomyces species tested, as well as Frankia species . These results do not support the previous suggestion that GSII-type enzymes found in members of the family Rhizobiaceae represent a unique example of interkingdom gene transfer associated with symbiosis in the nodule . Instead they imply that the presence of more than one gene encoding GS may be more common among soil microorganisms than previously appreciated. Appl Environ Microbiol, 1990 Sep, 56(9), 2858 - 65 Use of oligodeoxynucleotide signature probes for identification of physiological groups of methylotrophic bacteria; Tsien HC et al.; Oligodeoxynucleotide sequences that uniquely complemented 16S rRNAs of each group of methylotrophs were synthesized and used as hybridization probes for the identification of methylotrophic bacteria possessing the serine and ribulose monophosphate (RuMP) pathways for formaldehyde fixation . The specificity of the probes was determined by hybridizing radiolabeled probes with slot-blotted RNAs of methylotrophs and other eubacteria followed by autoradiography . The washing temperature was determined experimentally to be 50 and 52 degrees C for 9-alpha (serine pathway) and 10-gamma (RuMP pathway) probes, respectively . RNAs isolated from serine pathway methylotrophs bound to probe 9-alpha, and RNAs from RuMP pathway methylotrophs bound to probe 10-gamma . Nonmethylotrophic eubacterial RNAs did not bind to either probe . The probes were also labeled with fluorescent dyes . Cells fixed to microscope slides were hybridized with these probes, washed, and examined in a fluorescence microscope equipped with appropriate filter sets . Cells of methylotrophic bacteria possessing the serine or RuMP pathway specifically bind probes designed for each group . Samples with a mixture of cells of type I and II methanotrophs were detected and differentiated with single probes or mixed probes labeled with different fluorescent dyes, which enabled the detection of both types of cells in the same microscopic field. FEMS Microbiol Lett, 1990 Sep 1, 59(1-2), 139 - 43 The phylogenetic position of Peptococcus niger based on 16S rRNA sequence studies; Ludwig W et al.; A 1330 base-pair fragment of a 16S rRNA gene has been amplified, cloned and sequenced . Comparison to other 16S rRNA sequences of eubacteria showed that P . niger represents a deep branch within the subdivision "Gram-positive with Gram-negative cell walls" . It is not related to peptostreptococci, representatives of this genus studied so far are more closely related to clostridia. Biochim Biophys Acta, 1990 Aug 27, 1050(1-3), 56 - 60 Evidence for an additional archaebacterial gene cluster in Halobacterium marismortui encoding ribosomal proteins HL46e and HL30; Bergmann U et al.; A small and extremely basic ribosomal protein (HL46e) has been purified from Halobacterium marismortui using reversed-phase high-performance liquid chromatography (HPLC) . The amino acid sequence of the protein was determined by automated N-terminal and internal sequence analysis . Comparison of this sequence with other ribosomal protein sequences from eubacteria, archaebacteria and eukaryotes revealed a strong homology to SL46e from Sulfolobus solfataricus, YeaL46 from yeast and RL39 from rat . No significant sequence similarly was found to any eubacterial ribosomal protein so far known . Using a specific oligonucleotide probe the HL46e gene was identified, cloned and the nucleotide sequence including the 5'- and 3'-flanking regions were analysed . The HL46e gene is followed by the gene coding for HL30 . A putative halobacterial promoter sequence with the motive 'TTTAAA' has been localized 32 bp upstream of the HL46e gene and a putative terminator sequence localized downstream from the HL30 gene . An equivalent to this HL46e/HL30 operon is apparently not present in Escherichia coli. Biochim Biophys Acta, 1990 Aug 27, 1050(1-3), 61 - 8 Cloning and characterization of the genes for ribosomal proteins L10 and L12 from Synechocystis Sp . PCC 6803: comparison of gene clustering pattern and protein sequence homology between cyanobacteria and chloroplasts; Sibold C et al.; The endosymbiont theory proposes that chloroplasts have originated from ancestral cyanobacteria through a process of engulfment and subsequent symbiotic adaptation . The molecular data for testing this theory have mainly been the nucleotide sequence of rRNAs and of photosystem component genes . In order to provide additional data in this area, we have isolated genomic clones of Synechocystis DNA containing the ribosomal protein gene cluster rplJL . The nucleotide sequence of this cluster and flanking regions was determined and the derived amino acid sequences were compared to the available homologous sequences from other eubacteria and chloroplasts . In Escherichia coli these two genes are part of a larger cluster, i.e., rplKAJL-rpoBC . In Synechocystis, the genes for the RNA polymerase subunit (rpoBC) are shown to be widely separated from the r-protein genes . The Synechocystis gene arrangement is similar to that in the chloroplast system, where the rpoBC1C2 and rplKAJL clusters are separated and located in two cell compartments, the chloroplast and the nucleus, respectively. J Mol Biol, 1990 Aug 5, 214(3), 737 - 49 Three-dimensional structure of the mammalian cytoplasmic ribosome; Verschoor A et al.; A three-dimensional reconstruction of the 80 S ribosome from rabbit reticulocytes has been calculated from low-dose electron micrographs of a negatively stained single-particle specimen . At 37 A resolution, the precise orientations of the 40 S and 60 S subunits within the monosome can be discerned . The translational domain centered on the upper portion of the subunit/subunit interface is quite open, allowing considerable space between the subunits for interactions with the non-ribosomal macromolecules involved in protein synthesis . Further, the cytosolic side of the monosome is strikingly more open than the membrane-attachment side, suggesting a greater ease of communication with the cytoplasm, which would facilitate the inwards and outwards diffusion of a number of ligands . Although the 60 S subunit portion of the 80 S structure shows essentially all of the major morphological features identified for the eubacterial 50 S large subunit, it appears to possess a region of additional mass that evidently accounts for the more ellipsoidal form of the eukaryotic subunit. Appl Environ Microbiol, 1990 Aug, 56(8), 2572 - 5 Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton; Giovannoni SJ et al.; A procedure was developed for harvesting gram quantities of microbial biomass from oligotrophic waters, when mixed populations are present in low abundance . Picoplankton from Atlantic Ocean (Hydrostation S, Sargasso Sea) and Pacific Ocean (Aloha Station) sites were collected in a three-stage process: (i) collection of seawater through an intake covered with 10-microns-pore Nytex; (ii) concentration by a tangential flow filtration device equipped with 10 ft2 (0.929 m2) of 0.1-micron-pore fluorocarbon membrane; (iii) collection of cells from concentrate by centrifugation . The overall efficiency of picoplankton recovery was at least 37% . The cellular morphotypes recovered matched those of the original population . DNA was prepared from frozen cell pellets by enzymatic digestion, solvent extraction, and isopycnic centrifugation . As indicated by the binding of kingdom-specific hybridization probes to the purified DNA, the Sargasso Sea picoplankton in this collection were largely eubacteria. Carcinogenesis, 1990 Aug, 11(8), 1381 - 7 Biliary excretion of glutathione conjugates of 4,5-epoxy-4,5-dihydro-1- nitropyrene and 9,10-epoxy-9,10-dihydro-1-nitropyrene in rats administered 1-nitropyrene orally and their further metabolism in the intestinal tract; Kinouchi T et al.; 1-Nitropyrene (1-NP), a mutagenic and carcinogenic substance that occurs in the environment, is metabolized by reductive and oxidative pathways . 4,5-Epoxy,4,5-dihydro-1-NP (1-NP 4,5-oxide) and 9,10-epoxy-9,10-dihydro-1-NP (1-NP 9,10-oxide) are oxidatively activated metabolites of 1-NP, and react with glutathione . HPLC analysis of biliary metabolites from rats administered {3H}1-NP orally showed the presence of glutathione conjugates of 1-NP 4,5-oxide and 1-NP 9,10-oxide and their metabolites, cysteinylglycine and cysteine conjugates . During the 48 h following {3H}1-NP administration, 21.4% of the biliary metabolites were excreted as glutathione, cysteinylglycine and cysteine conjugates of 1-NP oxides . The proportions of glutathione conjugates of 1-NP 4,5-oxide and 1-NP 9,10-oxide were 2.6 and 10.4% respectively . Bile and pancreatic juice collected from normal rats metabolized glutathione conjugates of 1-NP oxides and produced the corresponding cysteinylglycine and cysteine conjugates . In particular, the gamma-glutamyltransferase activity of pancreatic juice was markedly high . When glutathione conjugates of 1-NP oxides were incubated with a cell-free extract of small intestinal contents, they decreased rapidly and cysteine conjugates increased via cysteinylglycine conjugates, indicating that pancreatic juice plays an important role in the small intestine for the metabolism of glutathione conjugates to corresponding cysteine conjugates . Although degradation activity of small intestinal contents for cysteine conjugates was very low, degradation activity of the contents of the cecum and large intestine was high and was inhibited by an inhibitor of cysteine conjugate beta-lyase (beta-lyase) activity, aminooxyacetic acid . Furthermore, the intestinal anaerobic bacteria Peptostreptococcus magnus and Eubacterium limosum showed high beta-lyase activity, suggesting that the cysteine conjugates might be further metabolized by beta-lyase of the normal bacterial flora in the lower intestine to the reactivated metabolites and reabsorbed. J Bacteriol, 1990 Aug, 172(8), 4420 - 6 Multiple copies of a bile acid-inducible gene in Eubacterium sp . strain VPI 12708; Gopal-Srivastava R et al.; Eubacterium sp . strain VPI 12708 is an anaerobic intestinal bacterium which possesses inducible bile acid 7-dehydroxylation activity . Several new polypeptides are produced in this strain following induction with cholic acid . Genes coding for two copies of a bile acid-inducible 27,000-dalton polypeptide (baiA1 and baiA2) have been previously cloned and sequenced . We now report on a gene coding for a third copy of this 27,000-dalton polypeptide (baiA3) . The baiA3 gene has been cloned in lambda DASH on an 11.2-kilobase DNA fragment from a partial Sau3A digest of the Eubacterium DNA . DNA sequence analysis of the baiA3 gene revealed 100% homology with the baiA1 gene within the coding region of the 27,000-dalton polypeptides . The baiA2 gene shares 81% sequence identity with the other two genes at the nucleotide level . The flanking nucleotide sequences associated with the baiA1 and baiA3 genes are identical for 930 bases in the 5' direction from the initiation codon and for at least 325 bases in the 3' direction from the stop codon, including the putative promoter regions for the genes . An additional open reading frame (occupying from 621 to 648 bases, depending on the correct start codon) was found in the identical 5' regions associated with the baiA1 and baiA3 clones . The 5' sequence 930 bases upstream from the baiA1 and baiA3 genes was totally divergent . The baiA2 gene, which is part of a large bile acid-inducible operon, showed no homology with the other two genes either in the 5' or 3' direction from the polypeptide coding region, except for a 15-base-pair presumed ribosome-binding site in the 5' region . These studies strongly suggest that a gene duplication (baiA1 and baiA3) has occurred and is stably maintained in this bacterium. FEMS Microbiol Rev, 1990 Aug, 6(4), 351 - 81 Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world; Le Faou A et al.; Among sulfur compounds, thiosulfate and polythionates are present at least transiently in many environments . These compounds have a similar chemical structure and their metabolism appears closely related . They are commonly used as energy sources for photoautotrophic or chemolithotrophic microorganisms, but their assimilation has been seldom studied and their importance in bacterial physiology is not well understood . Almost all bacterial strains are able to cleave these compounds since they possess thiosulfate sulfur transferase, thiosulfate reductase or S-sulfocysteine synthase activities . However, the role of these enzymes in the assimilation of thiosulfate or polythionates has not always been clearly established . Elemental sulfur is, on the contrary, very common in the environment . It is an energy source for sulfur-reducing eubacteria and archaebacteria and many sulfur-oxidizing archaebacteria . A phenomenon still not well understood is the 'excessive assimilatory sulfur metabolism' as observed in methanogens which perform a sulfur reduction which exceeds their anabolic needs without any apparent benefit . In heterotrophs, assimilation of elemental sulfur is seldom described and it is uncertain whether this process actually has a physiological significance . Thus, reduction of thiosulfate and elemental sulfur is a common but incompletely understood feature among bacteria . These activities could give bacteria a selective advantage, but further investigations are needed to clarify this possibility . Presence of thiosulfate, polythionates and sulfur reductase activities does not imply obligatorily that these activities play a role in thiosulfate, polythionates or sulfur assimilation as these compounds could be merely intermediates in bacterial metabolism . The possibility also exists that the assimilation of these sulfur compounds is just a side effect of an enzymatic activity with a completely different function . As long as these questions remain unanswered, our understanding of sulfur and thiosulfate metabolism will remain incomplete. Plant Mol Biol, 1990 Aug, 15(2), 307 - 15 Evidence for a composite phylogenetic origin of the plastid genome of the brown alga Pylaiella littoralis (L.) Kjellm; Assali NE et al.; The nucleotide sequence and the 5' flanking region of the rbcL gene coding for the large subunit of ribulose bisphosphate-1,5-carboxylase/oxygenase of Pylaiella littoralis, a brown alga, has been determined and the deduced amino-acid sequence has been compared to those of various photosynthetic and chemoautotrophic Eubacteria, of a red alga and of green plastids (Euglena gracilis, green algae and higher plants) . Unlike the rbcL genes of green plastids which are more closely related to those of cyanobacteria, the P . littoralis rbcL gene is more closely related to that of a beta-purple bacterium, as was found for the rbcS gene of another chromophytic alga {Boczar et al., Proc Natl Acad Sci USA 86: 4996-4999, 1989} . Matrix data of homology between the rbcL gene of P . littoralis and the same gene of other organisms are presented . Based on our previous report, the gene coding for the 16S rRNA from P . littoralis is closely related to that of E . gracilis (Markowicz et al., Curr Genet 14: 599-608, 1988) . We suggest that the large plastid DNA molecule of P . littoralis is a phylogenetically composite genome which probably resulted from mixed endosymbiosis events, or from a horizontal transfer of DNA. Oral Microbiol Immunol, 1990 Aug, 5(4), 195 - 201 The formation of hydrogen sulfide and methyl mercaptan by oral bacteria; Persson S et al.; The capacity to form volatile sulfur compounds was tested in bacteria isolated from subgingival microbiotas and in a representative number of reference strains . A majority of the 75 tested oral bacterial species and 7 unnamed bacterial taxa formed significant amounts of hydrogen sulfide from L-cysteine . The most active bacteria were found in the genera Peptostreptococcus, Eubacterium, Selenomonas, Centipeda, Bacteroides and Fusobacterium . Methyl mercaptan from L-methionine was formed by some members of the genera Fusobacterium, Bacteroides, Porphyromonas and Eubacterium . When incubated in serum for 7 d, the most potent producers of hydrogen sulfide were Treponema denticola and the black-pigmented species, Bacteroides intermedius, Bacteroides loescheii, Porphyromonas endodontalis and Porphyromonas gingivalis . P . endodontalis and P . gingivalis also produced significant amounts of methyl mercaptan in serum . No other volatile sulfur compound was detected in serum or in the presence of L-cysteine and L-methionine . These findings significantly increase the list of oral bacteria known to produce volatile sulfur compounds. Biochim Biophys Acta, 1990 Jul 6, 1039(3), 343 - 7 Amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui; Hatakeyama T et al.; The complete amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui were determined . Protein HL30 was found to be acetylated at its N-terminal amino acid and shows homology to the eukaryotic ribosomal proteins YL34 from yeast and RL31 from rat . Protein HmaL5 was homologous to the protein L5 from Escherichia coli and Bacillus stearothermophilus as well as to YL16 from yeast . HmaL5 shows more similarities to its eukaryotic counterpart than to eubacterial ones. J Biol Chem, 1990 Jul 5, 265(19), 10925 - 8 Side chain conjugation prevents bacterial 7-dehydroxylation of bile acids; Batta AK et al.; The effect of side chain conjugation on 7-dehydroxylation of bile acids has been investigated . C24-bile acids and their glycine and taurine conjugates and keto bile acids were incubated with pure strains of Eubacterium sp . VPI 12708 . Bile acids of the 5 alpha- or 5 beta-series with a free terminal carboxyl group and a 3 alpha, 7 alpha-dihydroxy system were very effectively 7 alpha-dehydroxylated, whereas 7 beta-hydroxy bile acids resisted 7-dehydroxylation . Oxo bile acids were metabolized at the oxygen function also . Glycine- and taurine-conjugated bile acids were neither deamidated nor 7-dehydroxylated by the bacteria . Thus, side chain conjugation prevents 7-dehydroxylation of bile acids by Eubacterium sp . VPI 12708. Appl Environ Microbiol, 1990 Jul, 56(7), 2012 - 20 Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria; Coffin RB et al.; The natural abundance of stable carbon isotopes measured in bacterial nucleic acids extracted from estuarine bacterial concentrates was used to trace sources of organic matter for bacteria in aquatic environments . The stable carbon isotope ratios of Pseudomonas aeruginosa and nucleic acids extracted from cultures resembled those of the carbon source on which bacteria were grown . The carbon isotope discrimination between the substrate and total cell carbon from bacterial cultures averaged 2.3% +/- 0.6% (n = 13) . Furthermore, the isotope discrimination between the substrate and nucleic acids extracted from bacterial cultures was 2.4% +/- 0.4% (n = 10), not significantly different from the discrimination between bacteria and the substrate . Estuarine water samples were prefiltered through 1-micron-pore-size cartridge filters . Bacterium-sized particles in the filtrates were concentrated with tangential-flow filtration and centrifugation, and nucleic acids were then extracted from these concentrates . Hybridization with 16S rRNA probes showed that approximately 90% of the nucleic acids extracted on two sample dates were of eubacterial origin . Bacteria and nucleic acids from incubation experiments using estuarine water samples enriched with dissolved organic matter from Spartina alterniflora and Cyclotella caspia had stable carbon isotope values similar to those of the substrate sources . In a survey that compared diverse estuarine environments, stable carbon isotopes of bacteria grown in incubation experiments ranged from -31.9 to -20.5% . The range in isotope values of nucleic acids extracted from indigenous bacteria from the same waters was similar, -27.9 to -20.2% . Generally, the lack of isotope discrimination between bacteria and nucleic acids that was noted in the laboratory was observed in the field.(ABSTRACT TRUNCATED AT 250 WORDS) J Biochem Biophys Methods, 1990 Jul-Aug, 21(2), 155 - 64 Identification of bacterial periplasmic glycine betaine-binding protein after electrophoresis and affinity labeling; Talibart R et al.; Antibodies were elicited in rabbits against periplasmic proteins obtained by cold osmotic shock from the Gram-negative eubacterium Rhizobium meliloti . When analyzed by crossed immunoelectrophoresis (CIE), the periplasmic proteins gave rise to 20 distinct immunoprecipitates corresponding to the same number of bands in polyacrylamide gel electrophoresis (PAGE) under non-denaturing conditions and in SDS-PAGE . The periplasmic glycine betaine-binding protein (GB-BP) was identified by autoradiography after affinity labeling with {14C}glycine betaine in PAGE and in CIE gels . The binding proved to be quite specific to glycine betaine, since the GB-BP was not labeled by choline (a metabolic precursor of glycine betaine in Escherichia coli and Rhizobium meliloti) and 15 distinct L-amino acids, including L-proline which, like glycine betaine is also an osmoprotectant . Affinity labeling of the GB-BP with {14C}glycine betaine after protein separation by PAGE or CIE is a simple and sensitive technique permitting the GB-BP to the unambiguously detected and identified in samples of complex protein mixtures containing down to 2 micrograms of GB-BP in PAGE and only 0.2 micrograms in CIE. J Periodontol, 1990 Jul, 61(7), 405 - 11 Effects of subgingival irrigation on bacteremia following scaling and root planing; Waki MY et al.; The purpose of this study was to determine the effects of professional subgingival irrigation, together with subsequent patient administered home marginal irrigation, on the incidence of bacteremia after scaling and root planing (Sc/RP) . A total of 60 periodontal maintenance patients were assigned to either Group 1: subgingival irrigation, with 0.12% CHX and daily marginal irrigation with 0.04% CHX; Group 2: subgingival irrigation with 0.12% CHX and daily marginal irrigation with water; Group 3: subgingival and daily marginal irrigation with water; Group 4: Non-irrigation (control) . Patients entered the study after receiving a thorough periodontal maintenance appointment including a complete examination, Sc/RP, and standard oral hygiene instruction . Blood samples were taken at the 3-month visit before and after Sc/RP . Microbiological culturing was done using the Septi-Chek system, selective and non-selective media . Results from 54 patients showed that bacteremia was detected prior to Sc/RP in 2 patients and after Sc/RP in 10 patients . No significant effect by treatment regimens on post Sc/RP bacteremia could be detected . The organisms isolated included Eubacterium lentum, Propionibacterium acnes, Streptococcus species, Neisseria species, Candida albicans, Staphylococcus species, and un-identified Gram-negative rods. J Periodontol, 1990 Jul, 61(7), 412 - 9 Serum antibodies to periodontal bacteria; Gunsolley JC et al.; The purpose of this study was to determine how serum antibodies reactive with periodontitis-associated bacteria with relates to the diagnosis of periodontitis subjects . Study groups included localized juvenile periodontitis (LJP) subjects, severe periodontitis (SP) subjects, chronic adult periodontitis (AP) subjects, and age matched controls . Twenty-two bacterial strains, representing 18 different species most commonly found in early onset periodontitis were evaluated using serum from LJP, SP, and age matched controls . Serum IgG reactive with these organisms was determined using a radioimmunoassay (RIA) . Serum antibody reactive with 13 bacterial strains differed significantly (P less than 0.01) between the three clinical groups . Discriminate analysis revealed that antibodies reactive with 5 bacterial strains of the 13 were able to identify the clinical group to which subjects belonged 79% of the time with control subjects being correctly identified 100% of the time, LJP subjects 78% of the time, and SP subjects 60% of the time . These strains included two strains of Actinobacillus actinomycetemcomitans (Y4 and N27), Fusobacterium nucleatum (E1D1), Eubacterium brachy, and Bacteroides gingivalis . The low classification rate of SP subjects suggested heterogeneity . The SP group could be divided into three subgroups using the serological data . One subgroup, with "super" severe attachment loss, generally lacked antibody reactive with these five organisms, another subgroup was serologically similar to LJP subjects, while the third subgroup had antibodies to additional organisms . This suggests that some SP subjects may represent a more advanced form of LJP . Comparison of antibody reactivity of AP subjects with age matched controls to 23 bacterial types revealed that mean serum antibody reactivity to only Bacteroides gingivalis was higher in AP subjects.(ABSTRACT TRUNCATED AT 250 WORDS) J Mol Evol, 1990 Jul, 31(1), 51 - 68 Compositional statistics: an improvement of evolutionary parsimony and its application to deep branches in the tree of life; Sidow A et al.; We present compositional statistics, a new method of phylogenetic inference, which is an extension of evolutionary parsimony . Compositional statistics takes account of the base composition of the compared sequences by using nucleotide positions that evolutionary parsimony ignores . It shares with evolutionary parsimony the features of rate invariance and the fundamental distinction between transitions and transversions . Of the presently available methods of phylogenetic inference, compositional statistics is based on the fewest and mildest assumptions about the mode of DNA sequence evolution . It is therefore applicable to phylogenetic studies of the most distantly related organisms or molecules . This was illustrated by analyzing conservative positions in the DNA sequences of the large subunit of RNA polymerase from three archaebacterial groups, a eubacterium, a chloroplast, and the three eukaryotic polymerases . Internally consistent results, which are in accord with our knowledge of organelle origin and archaebacterial physiology, were achieved. J Biol Chem, 1990 Jun 25, 265(18), 10403 - 9 Site-directed mutagenesis of the conserved beta subunit tyrosine 331 of Escherichia coli ATP synthase yields catalytically active enzymes; Wise JG; The ATP synthases of eubacteria and eukaryotes possess a conserved tyrosine (beta 331) that is labeled by ATP analogs and is believed to be at the catalytic site . In this report, this tyrosine was replaced by Phe, Ser, Cys, Gly, and Ala in an attempt to determine its role in catalysis . Each of the beta 331 mutant strains assembled an ATP synthase . Membranes from the beta 331-Ser, -Cys, -Ala, or -Gly strains showed strongly attenuated ATP hydrolysis and ATP-driven proton-pumping activities . The beta 331-Phe membranes showed nearly normal ATPase and functional proton pumping . A new purification procedure yielding highly active unc+ F1 (ATPase rates greater than 1000 s-1) allowed rapid isolation of soluble F1-ATPases . Kinetic analyses of purified enzymes confirmed that the structural and functional properties of beta 331-Tyr can be substituted by Phe but not effectively by Ser, Cys, Ala, or Gly . Since all of the beta 331 mutant enzymes catalyzed measurable ATP hydrolysis, it is clear that beta 331-Tyr is not directly involved in the bond making-breaking steps of catalysis . The ability of the beta 331-Phe enzyme to rapidly bind and hydrolyze ATP, and the results with other beta 331 mutant enzymes, suggests that a residue with an aromatic character is required at this position. J Mol Biol, 1990 Jun 20, 213(4), 811 - 8 Scanning model for translational reinitiation in eubacteria; Adhin MR et al.; Premature termination of translation in eubacteria, like Escherichia coli, often leads to reinitiation at nearby start codons . Restarts also occur in response to termination at the end of natural coding regions, where they serve to enforce translational coupling between adjacent cistrons . Here, we present a model in which the terminated but not released ribosome reaches neighboring initiation codons by lateral diffusion along the mRNA . The model is based on the finding that introduction of an additional start codon between the termination and the reinitiation site consistently obstructs ribosomes to reach the authentic restart site . Instead, the ribosome now begins protein synthesis at this newly introduced AUG codon . This ribosomal scanning-like movement is bidirectional, has a radius of action of more than 40 nucleotides in the model system used, and activates the first encountered restart site . The ribosomal reach in the upstream direction is less than in the downstream one, probably due to dislodging by elongating ribosomes . The proposed model has parallels with the scanning mechanism postulated for eukaryotic translational initiation and reinitiation. J Bacteriol, 1990 Jun, 172(6), 3264 - 8 Isolation and characterization of the 5S rRNA gene of Leptospira interrogans; Fukunaga M et al.; The gene encoding the 5S rRNA for Leptospira interrogans serovar canicola strain Moulton was isolated and sequenced . The 5S rRNA gene occurs as a single copy within the genome and encodes a 117-nucleotide-long RNA molecule . The 5S rRNA gene is flanked at both the 5' and 3' ends by regions of A + T-rich sequences, and the 5'-flanking region contains a promoter sequence . L . interrogans has a unique and remarkable organization of the 5S rRNA gene . The 5S rRNA molecule exhibits a strong similarity to typical eubacterial 5S rRNA in terms of overall secondary structure, while the primary sequence is conserved to a lesser degree . Restriction analysis of the 5S rRNA gene indicated that the DNA sequence including the 5S rRNA gene is highly conserved in the genomes of parasitic leptospires. J Clin Microbiol, 1990 Jun, 28(6), 1089 - 93 Detection of Borrelia burgdorferi using the polymerase chain reaction; Malloy DC et al.; Segments of the ospA gene of Borrelia burgdorferi were amplified by the polymerase chain reaction (PCR) . Oligonucleotide primers used in the reaction flank a 309-base-pair segment within the ospA gene . After 35 cycles of amplification, the product could be detected by agarose gel electrophoresis or dot hybridization with a 32P-labeled probe . This segment was amplified in all strains of B . burgdorferi tested, but it was not detected in other bacterial species . An additional primer pair which has a broad specificity for conserved 16S rRNA sequences that are present in eubacteria amplified a 215-base-pair fragment in all organisms tested . The sensitivity of PCR for the detection of B . burgdorferi in clinical samples was evaluated by seeding blood and urine specimens with B . burgdorferi and subjecting them to amplification . We were able to detect 10 organisms per ml of blood or urine, using PCR with dot hybridization detection . DNA extraction is not required for sample preparation . Blood and urine specimens were obtained from canines with clinical and serologic evidence of Lyme disease and subjected to PCR analysis . Of 17 clinical specimens from 15 animals, one blood specimen showed reactivity in the PCR. J Bacteriol, 1990 Jun, 172(6), 2986 - 95 Multiple translational products from a Mycoplasma hyorhinis gene expressed in Escherichia coli; Notarnicola SM et al.; We analyzed protein expression from a cloned Mycoplasma hyorhinis genomic fragment that produces in Escherichia coli a set of related polypeptides of 110, 100, 65, and 55 kilodaltons from a coding region of just over 3.0 kilobases . Expression of these multiple products resulted from a mechanism operating at the translational level but not from truncation at UGA termination codons, which are known to encode tryptophan in several mycoplasma species . The structural relatedness of the proteins was demonstrated by two-dimensional tryptic peptic mapping, but their generation by posttranslational processing was ruled out by pulse-chase labeling analysis . Examination of proteins expressed from plasmid constructs and tryptic peptide analysis of these polypeptides and the original set of proteins revealed that they share carboxy-terminal regions, an observation inconsistent with truncation at UGA codons . Expression of proteins from this cloned fragment was not dependent on vector sequences and was observed when the coding region was placed under control of a T7 promoter, suggesting that all products were translated from a single message . Expression of related products in mycoplasmas was examined by immunoblot analysis of M . hyorhinis proteins with antiserum against overexpressed recombinant proteins . A single 115-kilodalton mycoplasma protein was detected, which is larger than any of the related proteins expressed in E . coli . Our analysis indicated that translation initiation sites are used in E . coli that are not active in mycoplasmas, thereby defining differences between the translational regulatory signals of mycoplasmas and eubacteria. J Bacteriol, 1990 Jun, 172(6), 2955 - 61 Gene fusions with lacZ by duplication insertion in the radioresistant bacterium Deinococcus radiodurans; Lennon E et al.; Deinococcus radiodurans is the most-studied species of a eubacterial family characterized by extreme resistance to DNA damage . We have focused on developing molecular biological techniques to investigate the genetics of this organism . We report construction of lacZ gene fusions by a method involving both in vitro splicing and the natural transformation of D . radiodurans . Numerous fusion strains were identified by expression of beta-galactosidase . Among these fusion strains, several were inducible by exposure to the DNA-damaging agent mitomycin C, and four of the inducible fusion constructs were cloned in Escherichia coli . Hybridization studies indicate that one of the damage-inducible genes contains a sequence reiterated throughout the D . radiodurans chromosome . Survival measurements show that two of the fusion strains have increased sensitivity to mitomycin C, suggesting that the fusions within these strains inactivate repair functions. Mol Gen Genet, 1990 Jun, 222(1), 129 - 34 Five transfer RNA genes lacking CCA termini are clustered in the chromosome of Streptomyces rimosus; Plohl M et al.; The nucleotide sequence of a 1105 bp Streptomyces rimosus DNA fragment containing five transfer RNA genes was determined . Two tRNA(Gln) (CUG) genes, differing by 1 bp in the aminoacyl stem, and three identical tRNA(Glu) (CUC) genes were identified . The five tRNA genes, arranged in the order: Gln1-Glu1-Glu2-Gln2-Glu3, were separated by short, nonhomologous intergenic regions . Surprisingly, none of these tRNA genes encoded the CCA 3' terminus of mature tRNAs . All five encoded tRNAs for the translation of GC rich codons, which are preferentially used in Streptomyces genes (CAG and GAG, respectively) . We recently reported nucleotide sequences of two initiator tRNA genes from S . rimosus, which also do not encode the CCA end of mature tRNAs . It is therefore very likely that S . rimosus represents an example of those eubacteria in which the majority of tRNA genes do not encode the 3' terminal CCA end of mature tRNAs . Evolutionary implications of this finding remain to be elucidated. FEBS Lett, 1990 May 21, 264(2), 218 - 22 McrI: a novel class-II restriction endonuclease from Micrococcus cryophilus recognizing 5'-CGRY/CG-3'; Brensing-Kuppers J et al.; A new class-II restriction endonuclease, McrI, with a novel sequence specificity as isolated from the Gram-positive eubacterium Micrococcus cryophilus . McrI recognizes the palindromic hexanucleotide sequence . {sequence: see text} The novel enzyme in the presence of Mg2(+)-ions cleaves specifically both strands as indicated by the arrows . The staggered cuts generate 3'-protruding ends with single-stranded 5'-RY-3' dinucleotide extensions . The McrI recognition sequence was deduced from mapping data on DNAs of bacteriophages theta X174RF and M13mp18RF characterized by one and four cleavage sites, respectively . The cut positions within both strands of the recognition sequence were determined in sequencing experiments by analyzing hydrolysis of phosphodiester bonds within a polylinker region of M13mp18RF DNA containing an additional McrI recognition site including treatment with T4 DNA polymerase . The novel enzyme may be a useful tool for cloning experiments by completion of the enzymes EclXI (5'-C/GGCCG-3'), NotI (5'-GC/GGCCGC-3'), PvuI (5'-CGAT/CG-3') as well as EaeI (5'-Y/GGCCR-3') and XhoII (5'-Y/GATCR-3') characterized by partly identical sequence specificities. Nature, 1990 May 17, 345(6272), 268 - 70 The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants; Manhart JR et al.; The relationship of green algae to land plants has greatly interested botanists for more than a century . In recent years, several characters, particularly ultrastructural ones, have been used to define a green algal group (Charophyceae) from which land plants are thought to have arisen . Here we provide the first molecular genetic evidence in support of the charophycean origin of land plants . Group II introns have previously been found in both the tRNAAla and tRNAIle genes of all land plant chloroplast DNAs examined, whereas all algae and eubacteria examined have uninterrupted genes . The distribution of these introns in Coleochaete, Nitella and Spirogyra, members of the Charophyceae, confirms that these taxa are part of the lineage that gave rise to land plants . Furthermore, the intron data place Coleochaete and Nitella closer to land plants than Spirogyra . These introns were most probably acquired by the chloroplast genome more than 400-500 million years ago, the time of land plant origin. Biochim Biophys Acta, 1990 May 8, 1038(3), 346 - 54 Conformational study of the chromosomal protein MC1 from the archaebacterium Methanosarcina barkeri; Imbert M et al.; Methanogen chromosomal protein MC1 is a polypeptide of 93 amino acid residues (Mr 10,757) which represents the major protein associated with the DNA of the archaebacterium Methanosarcina barkeri and can protect DNA against thermal denaturation . The conformation of protein MC1 has been investigated by means of predictive methods, infrared spectroscopy, circular dichroism and tryptophan fluorescence studies . Protein MC1 has a low amount of alpha-helix but contains antiparallel beta-sheet strands . The larger hydrophobic cluster which contains tryptophan at position 61 appears buried in the protein . Addition of salts induces the unfolding of the protein and makes the tryptophan indole ring more rigid . With respect to its primary structure and its conformation, protein MC1 appears radically different from the chromosomal DNA-binding protein II (also called HU-type protein) in eubacteria. Nature, 1990 May 3, 345(6270), 60 - 3 Genetic diversity in Sargasso Sea bacterioplankton; Giovannoni SJ et al.; Bacterioplankton are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities . Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques . Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species . We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction . The analysis indicates the presence of a novel microbial group, the SAR11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community . A second cluster of lineages related to the oxygenic phototrophs--cyanobacteria, prochlorophytes and chloroplasts--was also observed . However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats . The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors. J Clin Periodontol, 1990 May, 17(5), 288 - 91 Serum antibodies and loss of periodontal bone in patients with rheumatoid arthritis; Tolo K et al.; The number of teeth, % of alveolar bone loss, serum IgG, and serum antibodies to Bacteroides gingivalis, Capnocytophaga ochracea and Eubacterium saburreum were recorded in 37 patients diagnosed with rheumatoid arthritis (RA) and in an age- and sex-matched control group of 37 individuals free from RA . The RA group had a significantly increased loss of teeth and loss of alveolar bone compared to the control group . The RA patients also had a significantly increased level of serum IgG . In the total material, 26% of the variation in loss of alveolar bone was accounted for by age, diagnosis of rheumatoid arthritis, and levels of antibodies against B . gingivalis and E . saburreum . In the RA group, 48% of this variation was accounted for by age, total serum IgG and IgG antibodies to B . gingivalis and E . saburreum. Mol Gen Genet, 1990 May, 221(3), 315 - 21 Structure of the archaebacterial 7S RNA molecule; Kaine BP; The genes encoding the 7S RNAs of the archaebacteria Archaeoglobus fulgidus, Methanosarcina acetivorans, Sulfolobus, solfataricus, and Thermococcus celer have been isolated . All four genes occur as single genomic copies and are flanked by sequences containing potential signals for transcriptional promotion and termination . The genes encode RNA molecules approximately 300 nucleotides in length which conform strictly to a model of secondary structure common to all described archaebacterial 7S RNAs . Archaebacterial 7S RNAs exhibit a strong similarity to eukaryotic 7S RNAs in terms of overall secondary structure, while primary sequence conservation is limited to a specific structural domain of the molecule . This domain displays strong primary and secondary structural similarity to features of small eubacterial RNAs, including the small cytoplasmic (sc) RNA of Bacillus subtilis and the 4.5S RNA of Escherichia coli . Conservation of this structural domain among divergent RNA molecules across three kingdoms suggests that these RNAs are the descendants of a unique subcellular structure present before the divergence of the archaebacterial, eubacterial and eukaryotic kingdoms. J Mol Evol, 1990 May, 30(5), 463 - 76 Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins; Van de Peer Y et al.; A tree was constructed from a structurally conserved area in an alignment of 83 small ribosomal subunit sequences of eukaryotic, archaebacterial, eubacterial, plastidial, and mitochondrial origin . The algorithm involved computation and optimization of a dissimilarity matrix . According to the tree, only plant mitochondria belong to the eubacterial primary kingdom, whereas animal, fungal, algal, and ciliate mitochondria branch off from an internal node situated between the tree primary kingdoms . This result is at variance with a parsimony tree of similar size published by Cedergren et al . (J Mol Evol 28:98-112, 1988), which postulates the mitochondria to be monophyletic and to belong to the eubacterial primary kingdom . The discrepancy does not follow from the use of conflicting sequence alignments, hence it must be due to the use of different treeing algorithms . We tested our algorithm on a set of sequences resulting from a simulated evolution and found it capable of faithfully reconstructing a branching topology that involved very unequal evolutionary rates . The use of more limited or more extended areas of the complete sequence alignment, comprising only very conserved or also more variable portions of the small ribosomal subunit structure, does have some inf