1887

Abstract

Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches, among which the Firmicutes occupy a considerable space. has been the model of Firmicutes for decades and its genome has been a reference for more than 10 years. Sequencing the genome involved more than 30 laboratories, with different expertises, in a attempt to make the most of the experimental information that could be associated with the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high-level annotation platforms, motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.

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2009-06-01
2020-01-29
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References

  1. Aguilar C., Vlamakis H., Losick R., Kolter R.. 2007; Thinking about Bacillus subtilis as a multicellular organism. Curr Opin Microbiol10:638–643
    [Google Scholar]
  2. Anagnostopoulos C., Spizizen J.. 1961; Requirements for transformation in Bacillus subtilis . J Bacteriol81:741–746
    [Google Scholar]
  3. Andre G., Even S., Putzer H., Burguiere P., Croux C., Danchin A., Martin-Verstraete I., Soutourina O.. 2008; S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum . Nucleic Acids Res36:5955–5969
    [Google Scholar]
  4. Anton B. P., Saleh L., Benner J. S., Raleigh E. A., Kasif S., Roberts R. J.. 2008; RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli . Proc Natl Acad Sci U S A105:1826–1831
    [Google Scholar]
  5. Bailly-Bechet M., Danchin A., Iqbal M., Marsili M., Vergassola M.. 2006; Codon usage domains over bacterial chromosomes. PLOS Comput Biol2:e37
    [Google Scholar]
  6. Beck L. L., Smith T. G., Hoover T. R.. 2007; Look, no hands! Unconventional transcriptional activators in bacteria. Trends Microbiol15:530–537
    [Google Scholar]
  7. Begley T. P., Chatterjee A., Hanes J. W., Hazra A., Ealick S. E.. 2008; Cofactor biosynthesis – still yielding fascinating new biological chemistry. Curr Opin Chem Biol12:118–125
    [Google Scholar]
  8. Belitsky B. R., Sonenshein A. L.. 1998; Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol180:6298–6305
    [Google Scholar]
  9. Bentley D. R.. 2006; Whole-genome re-sequencing. Curr Opin Genet Dev16:545–552
    [Google Scholar]
  10. Berger B. J., English S., Chan G., Knodel M. H.. 2003; Methionine regeneration and aminotransferases in Bacillus subtilis , Bacillus cereus , and Bacillus anthracis . J Bacteriol185:2418–2431
    [Google Scholar]
  11. Bisicchia P., Noone D., Lioliou E., Howell A., Quigley S., Jensen T., Jarmer H., Devine K. M.. 2007; The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis . Mol Microbiol65:180–200
    [Google Scholar]
  12. Bocs S., Cruveiller S., Vallenet D., Nuel G., Medigue C.. 2003; AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Res31:3723–3726
    [Google Scholar]
  13. Burguiere P., Auger S., Hullo M. F., Danchin A., Martin-Verstraete I.. 2004; Three different systems participate in l-cystine uptake in Bacillus subtilis . J Bacteriol186:4875–4884
    [Google Scholar]
  14. Carr J. F., Hamburg D. M., Gregory S. T., Limbach P. A., Dahlberg A. E.. 2006; Effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein S12. J Bacteriol188:2020–2023
    [Google Scholar]
  15. Caspi R., Foerster H., Fulcher C. A., Kaipa P., Krummenacker M., Latendresse M., Paley S., Rhee S. Y., Shearer A. G.. other authors 2008; The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res36:D623–D631
    [Google Scholar]
  16. Chapman-Smith A., Mulhern T. D., Whelan F., Cronan J. E. Jr, Wallace J. C.. 2001; The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity. Protein Sci10:2608–2617
    [Google Scholar]
  17. Chartier F. J., Couture M.. 2007; Substrate-specific interactions with the heme-bound oxygen molecule of nitric-oxide synthase. J Biol Chem282:20877–20886
    [Google Scholar]
  18. Christiansen L. C., Schou S., Nygaard P., Saxild H. H.. 1997; Xanthine metabolism in Bacillus subtilis : characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism. J Bacteriol179:2540–2550
    [Google Scholar]
  19. Claverys J. P., Havarstein L. S.. 2007; Cannibalism and fratricide: mechanisms and raisons d'être. Nat Rev Microbiol5:219–229
    [Google Scholar]
  20. Danchin A.. 2008; Natural selection and immortality. Biogerontology
    [Google Scholar]
  21. Danchin A.. 2009a; A phylogenetic view of bacterial ribonucleases. Prog Nucleic Acid Res Mol Biol85:1–41
    [Google Scholar]
  22. Danchin A.. 2009b; Bacteria as computers making computers. FEMS Microbiol Rev33:3–26
    [Google Scholar]
  23. Danchin A., Fang G., Noria S.. 2007; The extant core bacterial proteome is an archive of the origin of life. Proteomics7:875–889
    [Google Scholar]
  24. Dartois V., Debarbouille M., Kunst F., Rapoport G.. 1998; Characterization of a novel member of the DegS-DegU regulon affected by salt stress in Bacillus subtilis . J Bacteriol180:1855–1861
    [Google Scholar]
  25. de Lorenzo V., Danchin A.. 2008; Synthetic biology: discovering new worlds and new words. EMBO Rep9:822–827
    [Google Scholar]
  26. den Blaauwen T., de Pedro M. A., Nguyen-Disteche M., Ayala J. A.. 2008; Morphogenesis of rod-shaped sacculi. FEMS Microbiol Rev32:321–344
    [Google Scholar]
  27. Dobrindt U., Hochhut B., Hentschel U., Hacker J.. 2004; Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol2:414–424
    [Google Scholar]
  28. Dyson F. J.. 1985; Origins of Life Cambridge, UK: Cambridge University Press;
  29. Earl A. M., Losick R., Kolter R.. 2008; Ecology and genomics of Bacillus subtilis . Trends Microbiol16:269–275
    [Google Scholar]
  30. Ellermeier C. D., Hobbs E. C., Gonzalez-Pastor J. E., Losick R.. 2006; A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Cell124:549–559
    [Google Scholar]
  31. Errington J.. 2003; Regulation of endospore formation in Bacillus subtilis . Nat Rev Microbiol1:117–126
    [Google Scholar]
  32. Fang G., Rocha E., Danchin A.. 2005; How essential are nonessential genes?. Mol Biol Evol22:2147–2156
    [Google Scholar]
  33. Formstone A., Carballido-Lopez R., Noirot P., Errington J., Scheffers D. J.. 2008; Localization and interactions of teichoic acid synthetic enzymes in Bacillus subtilis . J Bacteriol190:1812–1821
    [Google Scholar]
  34. Fouet A., Arnaud M., Klier A., Rapoport G.. 1987; Bacillus subtilis sucrose-specific enzyme II of the phosphotransferase system: expression in Escherichia coli and homology to enzymes II from enteric bacteria. Proc Natl Acad Sci U S A84:8773–8777
    [Google Scholar]
  35. Frangeul L., Nelson K. E., Buchrieser C., Danchin A., Glaser P., Kunst F.. 1999; Cloning and assembly strategies in microbial genome projects. Microbiology145:2625–2634
    [Google Scholar]
  36. Frenkiel-Krispin D., Minsky A.. 2006; Nucleoid organization and the maintenance of DNA integrity in E. coli , B. subtilis and D. radiodurans . J Struct Biol156:311–319
    [Google Scholar]
  37. Frey P. A., Hegeman A. D., Ruzicka F. J.. 2008; The radical SAM superfamily. Crit Rev Biochem Mol Biol43:63–88
    [Google Scholar]
  38. Gaidenko T. A., Kim T. J., Weigel A. L., Brody M. S., Price C. W.. 2006; The blue-light receptor YtvA acts in the environmental stress signaling pathway of Bacillus subtilis . J Bacteriol188:6387–6395
    [Google Scholar]
  39. Gilks W. R., Audit B., De Angelis D., Tsoka S., Ouzounis C. A.. 2002; Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics18:1641–1649
    [Google Scholar]
  40. Glaser P., Kunst F., Arnaud M., Coudart M. P., Gonzales W., Hullo M. F., Ionescu M., Lubochinsky B., Marcelino L.. other authors 1993; Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325 degrees to 333 degrees. Mol Microbiol10:371–384
    [Google Scholar]
  41. Goelzer A., Bekkal Brikci F., Martin-Verstraete I., Noirot P., Bessieres P., Aymerich S., Fromion V.. 2008; Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis . BMC Syst Biol2:20
    [Google Scholar]
  42. Gordon D., Abajian C., Green P.. 1998; Consed: a graphical tool for sequence finishing. Genome Res8:195–202
    [Google Scholar]
  43. Gruber T. M., Gross C. A.. 2003; Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol57:441–466
    [Google Scholar]
  44. Haldenwang W. G.. 1995; The sigma factors of Bacillus subtilis . Microbiol Rev59:1–30
    [Google Scholar]
  45. Harwood C. R., Wipat A.. 1996; Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Lett389:84–87
    [Google Scholar]
  46. Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B. L.. other authors 2006; Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2. 2006.0007
  47. Hayhurst E. J., Kailas L., Hobbs J. K., Foster S. J.. 2008; Cell wall peptidoglycan architecture in Bacillus subtilis . Proc Natl Acad Sci U S A105:14603–14608
    [Google Scholar]
  48. Helmann J. D.. 1999; Anti-sigma factors. Curr Opin Microbiol2:135–141
    [Google Scholar]
  49. Helmann J. D.. 2002; The extracytoplasmic function (ECF) sigma factors. Adv Microb Physiol46:47–110
    [Google Scholar]
  50. Herring C. D., Palsson B. O.. 2007; An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes. BMC Genomics8:274
    [Google Scholar]
  51. Hobman J. L., Penn C. W., Pallen M. J.. 2007; Laboratory strains of Escherichia coli : model citizens or deceitful delinquents growing old disgracefully?. Mol Microbiol64:881–885
    [Google Scholar]
  52. Hochgrafe F., Mostertz J., Pother D. C., Becher D., Helmann J. D., Hecker M.. 2007; S -Cysteinylation is a general mechanism for thiol protection of Bacillus subtilis proteins after oxidative stress. J Biol Chem282:25981–25985
    [Google Scholar]
  53. Hoper D., Bernhardt J., Hecker M.. 2006; Salt stress adaptation of Bacillus subtilis : a physiological proteomics approach. Proteomics6:1550–1562
    [Google Scholar]
  54. Hullo M. F., Auger S., Soutourina O., Barzu O., Yvon M., Danchin A., Martin-Verstraete I.. 2007; Conversion of methionine to cysteine in Bacillus subtilis and its regulation. J Bacteriol189:187–197
    [Google Scholar]
  55. Huse S. M., Huber J. A., Morrison H. G., Sogin M. L., Welch D. M.. 2007; Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol8:R143
    [Google Scholar]
  56. Jenkins A. L., Zhang Y., Ealick S. E., Begley T. P.. 2008; Mutagenesis studies on TenA: a thiamin salvage enzyme from Bacillus subtilis . Bioorg Chem36:29–32
    [Google Scholar]
  57. Joseph P., Fichant G., Quentin Y., Denizot F.. 2002; Regulatory relationship of two-component and ABC transport systems and clustering of their genes in the Bacillus / Clostridium group, suggest a functional link between them. J Mol Microbiol Biotechnol4:503–513
    [Google Scholar]
  58. Julkowska D., Obuchowski M., Holland I. B., Seror S. J.. 2005; Comparative analysis of the development of swarming communities of Bacillus subtilis 168 and a natural wild type: critical effects of surfactin and the composition of the medium. J Bacteriol187:65–76
    [Google Scholar]
  59. Kazmierczak M. J., Wiedmann M., Boor K. J.. 2005; Alternative sigma factors and their roles in bacterial virulence. Microbiol Mol Biol Rev69:527–543
    [Google Scholar]
  60. Kiley P. J., Beinert H.. 2003; The role of Fe–S proteins in sensing and regulation in bacteria. Curr Opin Microbiol6:181–185
    [Google Scholar]
  61. Knizewski L., Ginalski K.. 2007; Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding. Cell Cycle6:1666–1670
    [Google Scholar]
  62. Kobayashi K., Ogura M., Yamaguchi H., Yoshida K., Ogasawara N., Tanaka T., Fujita Y.. 2001; Comprehensive DNA microarray analysis of Bacillus subtilis two-component regulatory systems. J Bacteriol183:7365–7370
    [Google Scholar]
  63. Kobayashi K., Ehrlich S. D., Albertini A., Amati G., Andersen K. K., Arnaud M., Asai K., Ashikaga S., Aymerich S.. other authors 2003; Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A100:4678–4683
    [Google Scholar]
  64. Kroos L., Yu Y. T.. 2000; Regulation of sigma factor activity during Bacillus subtilis development. Curr Opin Microbiol3:553–560
    [Google Scholar]
  65. Kunst F., Ogasawara N., Moszer I., Albertini A. M., Alloni G., Azevedo V., Bertero M. G., Bessieres P., Bolotin A.. other authors 1997; The complete genome sequence of the Gram-positive bacterium Bacillus subtilis . Nature390:249–256
    [Google Scholar]
  66. Kurland C. G., Canback B., Berg O. G.. 2007; The origins of modern proteomes. Biochimie89:1454–1463
    [Google Scholar]
  67. Kurtz S., Phillippy A., Delcher A. L., Smoot M., Shumway M., Antonescu C., Salzberg S. L.. 2004; Versatile and open software for comparing large genomes. Genome Biol5:R12
    [Google Scholar]
  68. Lechat P., Hummel L., Rousseau S., Moszer I.. 2008; GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res36:D469–D474
    [Google Scholar]
  69. Lewis R. J., Brannigan J. A., Offen W. A., Smith I., Wilkinson A. J.. 1998; An evolutionary link between sporulation and prophage induction in the structure of a repressor : anti-repressor complex. J Mol Biol283:907–912
    [Google Scholar]
  70. Lima T., Auchincloss A. H., Coudert E., Keller G., Michoud K., Rivoire C., Bulliard V., de Castro E., Lachaize C.. other authors 2009; HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res37:D471–D478
    [Google Scholar]
  71. Margulies M., Egholm M., Altman W. E., Attiya S., Bader J. S., Bemben L. A., Berka J., Braverman M. S., Chen Y. J.. other authors 2005; Genome sequencing in microfabricated high-density picolitre reactors. Nature437:376–380
    [Google Scholar]
  72. Mechold U., Fang G., Ngo S., Ogryzko V., Danchin A.. 2007; YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Res35:4552–4561
    [Google Scholar]
  73. Medigue C., Rose M., Viari A., Danchin A.. 1999; Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence. Genome Res9:1116–1127
    [Google Scholar]
  74. Meerak J., Yukphan P., Miyashita M., Sato H., Nakagawa Y., Tahara Y.. 2008; Phylogeny of gamma-polyglutamic acid-producing Bacillus strains isolated from a fermented locust bean product manufactured in West Africa. J Gen Appl Microbiol54:159–166
    [Google Scholar]
  75. Merkl R.. 2004; SIGI: score-based identification of genomic islands. BMC Bioinformatics5:22
    [Google Scholar]
  76. Montorsi M., Lorenzetti R.. 1993; Heat-stable and heat-labile thymidylate synthases B of Bacillus subtilis : comparison of the nucleotide and amino acid sequences. Mol Gen Genet239:1–5
    [Google Scholar]
  77. Moszer I., Rocha E. P., Danchin A.. 1999; Codon usage and lateral gene transfer in Bacillus subtilis . Curr Opin Microbiol2:524–528
    [Google Scholar]
  78. Moszer I., Jones L. M., Moreira S., Fabry C., Danchin A.. 2002; SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res30:62–65
    [Google Scholar]
  79. Nakano M. M., Zuber P.. 1998; Anaerobic growth of a “strict aerobe” ( Bacillus subtilis . Annu Rev Microbiol52:165–190
    [Google Scholar]
  80. Nakano M. M., Geng H., Nakano S., Kobayashi K.. 2006; The nitric oxide-responsive regulator NsrR controls ResDE-dependent gene expression. J Bacteriol188:5878–5887
    [Google Scholar]
  81. Nandy S. K., Bapat P. M., Venkatesh K. V.. 2007; Sporulating bacteria prefers predation to cannibalism in mixed cultures. FEBS Lett581:151–156
    [Google Scholar]
  82. Nicolas P., Bize L., Muri F., Hoebeke M., Rodolphe F., Ehrlich S. D., Prum B., Bessieres P.. 2002; Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res30:1418–1426
    [Google Scholar]
  83. Ning Z., Cox A. J., Mullikin J. C.. 2001; SSAHA: a fast search method for large DNA databases. Genome Res11:1725–1729
    [Google Scholar]
  84. Nitschke P., Guerdoux-Jamet P., Chiapello H., Faroux G., Henaut C., Henaut A., Danchin A.. 1998; Indigo: a World-Wide-Web review of genomes and gene functions. FEMS Microbiol Rev22:207–227
    [Google Scholar]
  85. Noirot-Gros M. F., Dervyn E., Wu L. J., Mervelet P., Errington J., Ehrlich S. D., Noirot P.. 2002; An expanded view of bacterial DNA replication. Proc Natl Acad Sci U S A99:8342–8347
    [Google Scholar]
  86. Ogura M., Tanaka T.. 2009; The Bacillus subtilis late competence operon comE is transcriptionally regulated by yutB and under post-transcription initiation control by comN ( yrzD ). J Bacteriol191:949–958
    [Google Scholar]
  87. Paley S. M., Karp P. D.. 2006; The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res34:3771–3778
    [Google Scholar]
  88. Pascal G., Medigue C., Danchin A.. 2005; Universal biases in protein composition of model prokaryotes. Proteins60:27–35
    [Google Scholar]
  89. Petersohn A., Brigulla M., Haas S., Hoheisel J. D., Volker U., Hecker M.. 2001; Global analysis of the general stress response of Bacillus subtilis . J Bacteriol183:5617–5631
    [Google Scholar]
  90. Piggot P. J., Hilbert D. W.. 2004; Sporulation of Bacillus subtilis . Curr Opin Microbiol7:579–586
    [Google Scholar]
  91. Rajagopala S. V., Titz B., Goll J., Parrish J. R., Wohlbold K., McKevitt M. T., Palzkill T., Mori H., Finley R. L. Jr, Uetz P.. 2007; The protein network of bacterial motility. Mol Syst Biol3:128
    [Google Scholar]
  92. Raschle T., Amrhein N., Fitzpatrick T. B.. 2005; On the two components of pyridoxal 5′-phosphate synthase from Bacillus subtilis . J Biol Chem280:32291–32300
    [Google Scholar]
  93. Reder A., Hoper D., Weinberg C., Gerth U., Fraunholz M., Hecker M.. 2008; The Spx paralogue MgsR (YqgZ) controls a subregulon within the general stress response of Bacillus subtilis . Mol Microbiol69:1104–1120
    [Google Scholar]
  94. Reuter K., Mofid M. R., Marahiel M. A., Ficner R.. 1999; Crystal structure of the surfactin synthetase-activating enzyme Sfp: a prototype of the 4′-phosphopantetheinyl transferase superfamily. EMBO J18:6823–6831
    [Google Scholar]
  95. Reyes D. Y., Zuber P.. 2008; Activation of transcription initiation by Spx: formation of transcription complex and identification of a cis -acting element required for transcriptional activation. Mol Microbiol69:765–779
    [Google Scholar]
  96. Rocha E.. 2002; Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?. Trends Microbiol10:393–395
    [Google Scholar]
  97. Rocha E. P., Viari A., Danchin A.. 1998; Oligonucleotide bias in Bacillus subtilis : general trends and taxonomic comparisons. Nucleic Acids Res26:2971–2980
    [Google Scholar]
  98. Rocha E. P., Danchin A., Viari A.. 1999a; Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes. Mol Biol Evol16:1219–1230
    [Google Scholar]
  99. Rocha E. P., Danchin A., Viari A.. 1999b; Translation in Bacillus subtilis : roles and trends of initiation and termination, insights from a genome analysis. Nucleic Acids Res27:3567–3576
    [Google Scholar]
  100. Roll-Hansen N.. 1979; Experimental method and spontaneous generation: the controversy between Pasteur and Pouchet, 1859–64. J Hist Med Allied Sci34:273–292
    [Google Scholar]
  101. Saier M. H. Jr, Goldman S. R., Maile R. R., Moreno M. S., Weyler W., Yang N., Paulsen I. T.. 2002; Transport capabilities encoded within the Bacillus subtilis genome. J Mol Microbiol Biotechnol4:37–67
    [Google Scholar]
  102. Saito S., Kakeshita H., Nakamura K.. 2009; Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis . Gene428:2–8
    [Google Scholar]
  103. Sauer U., Eikmanns B. J.. 2005; The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev29:765–794
    [Google Scholar]
  104. Saunders C. W., Schmidt B. J., Mirot M. S., Thompson L. D., Guyer M. S.. 1984; Use of chromosomal integration in the establishment and expression of blaZ , a Staphylococcus aureus beta-lactamase gene, in Bacillus subtilis . J Bacteriol157:718–726
    [Google Scholar]
  105. Sekowska A.. 1999; Une rencontre du métabolisme du soufre et de l'azote; le métabolisme des polyamines chez Bacillus subtilis PhD thesis Université de Versailles Saint-Quentin-en-Yvelines;
  106. Sekowska A., Kung H. F., Danchin A.. 2000; Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction. J Mol Microbiol Biotechnol2:145–177
    [Google Scholar]
  107. Sekowska A., Robin S., Daudin J. J., Henaut A., Danchin A.. 2001; Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis . Genome Biol2:RESEARCH0019
    [Google Scholar]
  108. Sekowska A., Denervaud V., Ashida H., Michoud K., Haas D., Yokota A., Danchin A.. 2004; Bacterial variations on the methionine salvage pathway. BMC Microbiol4:9
    [Google Scholar]
  109. Simpson A. J.. 2001; Genome sequencing networks. Nat Rev Genet2:979–983
    [Google Scholar]
  110. Singh K. D., Schmalisch M. H., Stulke J., Gorke B.. 2008; Carbon catabolite repression in Bacillus subtilis : quantitative analysis of repression exerted by different carbon sources. J Bacteriol190:7275–7284
    [Google Scholar]
  111. Sinha S. C., Sprang S. R.. 2006; Structures, mechanism, regulation and evolution of class III nucleotidyl cyclases. Rev Physiol Biochem Pharmacol157:105–140
    [Google Scholar]
  112. Sneath P. H. A.. 1986; Endospore-forming Gram-positive rods and cocci. In Bergey's Manual of Systematic Bacteriolog y pp1105–1139 Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins Co;
    [Google Scholar]
  113. Sonenshein A. L.. 2007; Control of key metabolic intersections in Bacillus subtilis . Nat Rev Microbiol5:917–927
    [Google Scholar]
  114. Soupene E., van Heeswijk W. C., Plumbridge J., Stewart V., Bertenthal D., Lee H., Prasad G., Paliy O., Charernnoppakul P., Kustu S.. 2003; Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J Bacteriol185:5611–5626
    [Google Scholar]
  115. Srivatsan A., Han Y., Peng J., Tehranchi A. K., Gibbs R., Wang J. D., Chen R.. 2008; High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet4:e1000139
    [Google Scholar]
  116. Sterk P., Kersey P. J., Apweiler R.. 2006; Genome reviews: standardizing content and representation of information about complete genomes. OMICS10:114–118
    [Google Scholar]
  117. Tadesse S., Graumann P. L.. 2007; DprA/Smf protein localizes at the DNA uptake machinery in competent Bacillus subtilis cells. BMC Microbiol7:105
    [Google Scholar]
  118. Tamames J., Gonzalez-Moreno M., Mingorance J., Valencia A., Vicente M.. 2001; Bringing gene order into bacterial shape. Trends Genet17:124–126
    [Google Scholar]
  119. Tamburini E., Leon A. G., Perito B., Mastromei G.. 2003; Characterization of bacterial pectinolytic strains involved in the water retting process. Environ Microbiol5:730–736
    [Google Scholar]
  120. Tanous C., Soutourina O., Raynal B., Hullo M. F., Mervelet P., Gilles A. M., Noirot P., Danchin A., England P., Martin-Verstraete I.. 2008; The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis . J Biol Chem283:35551–35560
    [Google Scholar]
  121. Tozzi M. G., Camici M., Mascia L., Sgarrella F., Ipata P. L.. 2006; Pentose phosphates in nucleoside interconversion and catabolism. FEBS J273:1089–1101
    [Google Scholar]
  122. Vallenet D., Labarre L., Rouy Z., Barbe V., Bocs S., Cruveiller S., Lajus A., Pascal G., Scarpelli C., Medigue C.. 2006; MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res34:53–65
    [Google Scholar]
  123. Van Arsdell S. W., Perkins J. B., Yocum R. R., Luan L., Howitt C. L., Chatterjee N. P., Pero J. G.. 2005; Removing a bottleneck in the Bacillus subtilis biotin pathway: BioA utilizes lysine rather than S -adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction. Biotechnol Bioeng91:75–83
    [Google Scholar]
  124. van Schaik W., Abee T.. 2005; The role of sigmaB in the stress response of Gram-positive bacteria – targets for food preservation and safety. Curr Opin Biotechnol16:218–224
    [Google Scholar]
  125. Wang Z. Q., Lawson R. J., Buddha M. R., Wei C. C., Crane B. R., Munro A. W., Stuehr D. J.. 2007; Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase. J Biol Chem282:2196–2202
    [Google Scholar]
  126. Yamazaki S., Yamazaki J., Nishijima K., Otsuka R., Mise M., Ishikawa H., Sasaki K., Tago S., Isono K.. 2006; Proteome analysis of an aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1. Mol Cell Proteomics5:811–823
    [Google Scholar]
  127. You C., Lu H., Sekowska A., Fang G., Wang Y., Gilles A. M., Danchin A.. 2005; The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis . BMC Microbiol5:57
    [Google Scholar]
  128. You C., Sekowska A., Francetic O., Martin-Verstraete I., Wang Y., Danchin A.. 2008; Spx mediates oxidative stress regulation of the methionine sulfoxide reductases operon in Bacillus subtilis . BMC Microbiol8:128
    [Google Scholar]
  129. Yudkin M. D., Clarkson J.. 2005; Differential gene expression in genetically identical sister cells: the initiation of sporulation in Bacillus subtilis . Mol Microbiol56:578–589
    [Google Scholar]
  130. Zeigler D. R., Pragai Z., Rodriguez S., Chevreux B., Muffler A., Albert T., Bai R., Wyss M., Perkins J. B.. 2008; The origins of 168, W23, and other Bacillus subtilis legacy strains. J Bacteriol190:6983–6995
    [Google Scholar]
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