1887

Abstract

The genome sequence of subsp. W23 has been determined. The sequence strongly suggests that W23 is a direct descendant of ATCC 6633. W23 shares a 3.6 Mb core genome with the intensively studied model organism subsp. 168, and gene order within this core has been strongly conserved. Additionally, the W23 genome has 157 accessory (that is, non-core) genome segments that are not found in 168, while the 168 genome has 141 segments not found in W23. The distribution of sequences similar to these accessory segments among other genomes of the species complex shows that those sequences having entered into the phylogeny of the complex more recently tend to be larger and more AT-rich than those having entered earlier. A simple model can account for these observations, in which parasitic or symbiotic DNAs are transferred into the genome and then are reduced in size and modified in base composition during speciation.

Funding
This study was supported by the:
  • National Sciences Foundation (Award 0234214)
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.048520-0
2011-07-01
2021-10-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/157/7/2033.html?itemId=/content/journal/micro/10.1099/mic.0.048520-0&mimeType=html&fmt=ahah

References

  1. Albertini A. M., Galizzi A. ( 1999). The sequence of the trp operon of Bacillus subtilis 168 (trpC2) revisited. Microbiology 145:3319–3320[PubMed]
    [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [View Article][PubMed]
    [Google Scholar]
  3. Anagnostopoulos C., Spizizen J. ( 1961). Requirements for transformation in Bacillus subtilis. J Bacteriol 81:741–746[PubMed]
    [Google Scholar]
  4. Auch A. F., Klenk H.-P., Göker M. ( 2010). Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2:142–148 [View Article][PubMed]
    [Google Scholar]
  5. Auchtung J. M., Lee C. A., Monson R. E., Lehman A. P., Grossman A. D. ( 2005). Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci U S A 102:12554–12559 [View Article][PubMed]
    [Google Scholar]
  6. Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I. et al. ( 2009). From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758–1775 [View Article][PubMed]
    [Google Scholar]
  7. Borisova S. A., Circello B. T., Zhang J. K., van der Donk W. A., Metcalf W. W. ( 2010). Biosynthesis of rhizocticins, antifungal phosphonate oligopeptides produced by Bacillus subtilis ATCC6633. Chem Biol 17:28–37 [View Article][PubMed]
    [Google Scholar]
  8. Borriss R., Chen X., Rueckert C., Blom J., Becker A., Baumgarth B., Fan B., Pukall R., Schumann P. et al. ( 2010). Relationship of Bacillus amyloliquefaciens clades associated with strains DSM7T and FZB42: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on their discriminating complete genome sequences. Int J Syst Evol Microbiol [View Article][PubMed]
    [Google Scholar]
  9. Brown S., Meredith T., Swoboda J., Walker S. ( 2010). Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways. Chem Biol 17:1101–1110 [View Article][PubMed]
    [Google Scholar]
  10. Burkholder P. R., Giles N. H. Jr ( 1947). Induced biochemical mutations in Bacillus subtilis.. Am J Bot 34:345–348 [View Article][PubMed]
    [Google Scholar]
  11. Buxton R. S. ( 1976). Prophage mutation causing heat inducibility of defective Bacillus subtilis bacteriophage PBSX. J Virol 20:22–28[PubMed]
    [Google Scholar]
  12. Casjens S. ( 2003). Prophages and bacterial genomics: what have we learned so far?. Mol Microbiol 49:277–300 [View Article][PubMed]
    [Google Scholar]
  13. Coley J., Tarelli E., Archibald A. R., Baddiley J. ( 1978). The linkage between teichoic acid and peptidoglycan in bacterial cell walls. FEBS Lett 88:1–9 [View Article][PubMed]
    [Google Scholar]
  14. Cutting S. M., Vander Horn P. B. ( 1990). Genetic Analysis. Molecular Biological Methods for Bacillus27–74 Harwood C. R., Cutting S. M. Chichester: Wiley;
    [Google Scholar]
  15. Deng Y., Zhu Y., Wang P., Zhu L., Zheng J., Li R., Ruan L., Peng D., Sun M. ( 2011). Complete genome sequence of Bacillus subtilis BSn5, an endophytic bacterium of Amorphophallus konjac with antimicrobial activity for the plant pathogen Erwinia carotovora subsp. carotovora. J Bacteriol 193:2070–2071 [View Article][PubMed]
    [Google Scholar]
  16. Duitman E. H., Hamoen L. W., Rembold M., Venema G., Seitz H., Saenger W., Bernhard F., Reinhardt R., Schmidt M. et al. ( 1999). The mycosubtilin synthetase of Bacillus subtilis ATCC6633: a multifunctional hybrid between a peptide synthetase, an amino transferase, and a fatty acid synthase. Proc Natl Acad Sci U S A 96:13294–13299 [View Article][PubMed]
    [Google Scholar]
  17. Fan L., Bo S., Chen H., Ye W., Kleinschmidt K., Baumann H. I., Imhoff J. F., Kleine M., Cai D. ( 2011). Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b, isolated from the Indian ocean. J Bacteriol 193:1276–1277 [View Article][PubMed]
    [Google Scholar]
  18. Farmer J. L., Rothman F. ( 1965). Transformable thymine-requiring mutant of Bacillus subtilis. J Bacteriol 89:262–263[PubMed]
    [Google Scholar]
  19. Felsenstein J. ( 1989). phylip – phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  20. Gogarten J. P., Townsend J. P. ( 2005). Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687 [View Article][PubMed]
    [Google Scholar]
  21. Guindon S., Gascuel O. ( 2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [View Article][PubMed]
    [Google Scholar]
  22. Hemphill H. E., Whiteley H. R. ( 1975). Bacteriophages of Bacillus subtilis. Bacteriol Rev 39:257–315[PubMed]
    [Google Scholar]
  23. Jansen E. F., Hirschmann D. J. ( 1944). Subtilin – an antibacterial product of Bacillus subtilis. Culturing conditions and properties. Arch Biochem Biophys 4:297–309
    [Google Scholar]
  24. Kavenoff R. ( 1972). Characterization of the Bacillus subtilis W23 genome by sedimentation. J Mol Biol 72:801–806 [View Article][PubMed]
    [Google Scholar]
  25. Kellerman K. F., McBeth I. G. ( 1912). The fermentation of cellulose. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 2 34:485–494
    [Google Scholar]
  26. Koonin E. V., Wolf Y. I. ( 2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36:6688–6719 [View Article][PubMed]
    [Google Scholar]
  27. Kopac S., Cohan F. M. ( 2011). A theory-based pragmatism for discovering and classifying newly divergent bacterial species. Genetics and Evolution of Infectious Diseases21–41 Tibayrenc M. London: Elsevier; [View Article]
    [Google Scholar]
  28. Latreille P., Norton S., Goldman B. S., Henkhaus J., Miller N., Barbazuk B., Bode H. B., Darby C., Du Z. et al. ( 2007). Optical mapping as a routine tool for bacterial genome sequence finishing. BMC Genomics 8:321 [View Article][PubMed]
    [Google Scholar]
  29. Lawrence J. G., Ochman H. ( 1997). Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383–397 [View Article][PubMed]
    [Google Scholar]
  30. Lawrence J. G., Ochman H. ( 1998). Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95:9413–9417 [View Article][PubMed]
    [Google Scholar]
  31. Lazarevic V., Soldo B., Düsterhöft A., Hilbert H., Mauël C., Karamata D. ( 1998). Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPβ. Proc Natl Acad Sci U S A 95:1692–1697 [View Article][PubMed]
    [Google Scholar]
  32. Lazarevic V., Abellan F.-X., Möller S. B., Karamata D., Mauël C. ( 2002). Comparison of ribitol and glycerol teichoic acid genes in Bacillus subtilis W23 and 168: identical function, similar divergent organization, but different regulation. Microbiology 148:815–824[PubMed]
    [Google Scholar]
  33. Löytynoja A., Goldman N. ( 2010). webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics 11:579 [View Article][PubMed]
    [Google Scholar]
  34. Minnig K., Lazarevic V., Soldo B., Mauël C. ( 2005). Analysis of teichoic acid biosynthesis regulation reveals that the extracytoplasmic function sigma factor σM is induced by phosphate depletion in Bacillus subtilis W23. Microbiology 151:3041–3049 [View Article][PubMed]
    [Google Scholar]
  35. Nakamura L. K., Roberts M. S., Cohan F. M. ( 1999). Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacteriol 49:1211–1215 [View Article][PubMed]
    [Google Scholar]
  36. Nester E. W., Lederberg J. ( 1961). Linkage of genetic units of Bacillus subtilis in DNA transformation. Proc Natl Acad Sci U S A 47:52–55 [View Article][PubMed]
    [Google Scholar]
  37. Qian Z., Yin Y., Zhang Y., Lu L., Li Y., Jiang Y. ( 2006). Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication. BMC Genomics 7:74 [View Article][PubMed]
    [Google Scholar]
  38. Reslewic S., Zhou S., Place M., Zhang Y., Briska A., Goldstein S., Churas C., Runnheim R., Forrest D. et al. ( 2005). Whole-genome shotgun optical mapping of Rhodospirillum rubrum. Appl Environ Microbiol 71:5511–5522 [View Article][PubMed]
    [Google Scholar]
  39. Rocha E. P. C., Danchin A. ( 2002). Base composition bias might result from competition for metabolic resources. Trends Genet 18:291–294 [View Article][PubMed]
    [Google Scholar]
  40. Rooney A. P., Price N. P. J., Ehrhardt C., Swezey J. L., Bannan J. D. ( 2009). Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov. Int J Syst Evol Microbiol 59:2429–2436 [View Article][PubMed]
    [Google Scholar]
  41. Seaman E., Tarmy E., Marmur J. ( 1964). Inducible phages of Bacillus subtilis. Biochemistry 3:607–613 [View Article][PubMed]
    [Google Scholar]
  42. Shaver Y. J., Nagpal M. L., Rudner R., Nakamura L. K., Fox K. F., Fox A. ( 2002). Restriction fragment length polymorphism of rRNA operons for discrimination and intergenic spacer sequences for cataloging of Bacillus subtilis sub-groups. J Microbiol Methods 50:215–223 [View Article][PubMed]
    [Google Scholar]
  43. Smith N. R., Gordon R. E., Clark F. E. ( 1952). Aerobic Sporeforming Bacteria. Washington, DC: United States Department of Agriculture;
    [Google Scholar]
  44. Spizizen J. ( 1958). Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Proc Natl Acad Sci U S A 44:1072–1078 [View Article][PubMed]
    [Google Scholar]
  45. Spizizen J. ( 1984). Citation classic – transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonucleate. Curr Contents Life Sci 19:15
    [Google Scholar]
  46. 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 Genet 4:e1000139 [View Article][PubMed]
    [Google Scholar]
  47. Takemaru K.-i., Mizuno M., Sato T., Takeuchi M., Kobayashi Y. ( 1995). Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis. Microbiology 141:323–327 [View Article][PubMed]
    [Google Scholar]
  48. Thorne C. B. ( 1962). Transduction in Bacillus subtilis. J Bacteriol 83:106–111[PubMed]
    [Google Scholar]
  49. Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P., Bingen E., Bonacorsi S., Bouchier C. et al. ( 2009). Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344 [View Article][PubMed]
    [Google Scholar]
  50. Widom R. L., Jarvis E. D., LaFauci G., Rudner R. ( 1988). Instability of rRNA operons in Bacillus subtilis. J Bacteriol 170:605–610[PubMed]
    [Google Scholar]
  51. Wood H. E., Devine K. M., McConnell D. J. ( 1990). Characterisation of a repressor gene (xre) and a temperature-sensitive allele from the Bacillus subtilis prophage, PBSX. Gene 96:83–88 [View Article][PubMed]
    [Google Scholar]
  52. Wozniak R. A. F., Waldor M. K. ( 2010). Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 8:552–563 [View Article][PubMed]
    [Google Scholar]
  53. Zeigler D. R. ( 2003). Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900 [View Article][PubMed]
    [Google Scholar]
  54. Zeigler D. R., Prágai 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 Bacteriol 190:6983–6995 [View Article][PubMed]
    [Google Scholar]
  55. Zerbino D. R., Birney E. ( 2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.048520-0
Loading
/content/journal/micro/10.1099/mic.0.048520-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Supplementary material 3

PDF

Supplementary material 4

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error