1887

Abstract

A regular update of genome annotations is a prerequisite step to help maintain the accuracy and relevance of the information they contain. Five years after the first publication of the complete genome sequence of strain 630, we manually reannotated each of the coding sequences (CDSs), using a high-level annotation platform. The functions of more than 500 genes annotated previously with putative functions were reannotated based on updated sequence similarities to proteins whose functions have been recently identified by experimental data from the literature. We also modified 222 CDS starts, detected 127 new CDSs and added the enzyme commission numbers, which were not supplied in the original annotation. In addition, an intensive project was undertaken to standardize the names of genes and gene products and thus harmonize as much as possible with the HAMAP project. The reannotation is stored in a relational database that will be available on the MicroScope web-based platform (https://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?S_id=752&wwwpkgdb=a78e3466ad5db29aa8fe49e8812de8a7). The original submission stored in the (International Nucleotide Sequence Database Collaboration) INSDC nucleotide sequence databases was also updated.

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2011-08-01
2019-09-15
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References

  1. Altschul S. F. , Gish W. , Miller W. , Myers E. W. , Lipman D. J. . ( 1990; ). Basic local alignment search tool. . J Mol Biol 215:, 403–410.[PubMed].[CrossRef]
    [Google Scholar]
  2. 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. [CrossRef].[PubMed].
    [Google Scholar]
  3. Bendtsen J. D. , Nielsen H. , Von Heijne G. , Brunak S. . ( 2004; ). Improved prediction of signal peptides: SignalP 3.0. . J Mol Biol 340:, 783–795. [CrossRef].[PubMed].
    [Google Scholar]
  4. Bocs S. , Cruveiller S. , Vallenet D. , Nuel G. , Médigue C. . ( 2003; ). AMIGene: annotation of MIcrobial Genes. . Nucleic Acids Res 31:, 3723–3726. [CrossRef].[PubMed].
    [Google Scholar]
  5. Boeckmann B. , Bairoch A. , Apweiler R. , Blatter M. C. , Estreicher A. , Gasteiger E. , Martin M. J. , Michoud K. , O’Donovan C. et al. ( 2003; ). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. . Nucleic Acids Res 31:, 365–370. [CrossRef].[PubMed].
    [Google Scholar]
  6. Carter G. P. , Lyras D. , Allen D. L. , Mackin K. E. , Howarth P. M. , O’Connor J. R. , Rood J. I. . ( 2007; ). Binary toxin production in Clostridium difficile is regulated by CdtR, a LytTR family response regulator. . J Bacteriol 189:, 7290–7301. [CrossRef].[PubMed].
    [Google Scholar]
  7. Cartman S. T. , Minton N. P. . ( 2010; ). A mariner-based transposon system for in vivo random mutagenesis of Clostridium difficile . . Appl Environ Microbiol 76:, 1103–1109. [CrossRef].[PubMed].
    [Google Scholar]
  8. Cochrane G. , Akhtar R. , Aldebert P. , Althorpe N. , Baldwin A. , Bates K. , Bhattacharyya S. , Bonfield J. , Bower L. et al. ( 2008; ). Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL nucleotide sequence database. . Nucleic Acids Res 36: database issue D5–D12. [CrossRef].[PubMed].
    [Google Scholar]
  9. Cruveiller S. , Le Saux J. , Vallenet D. , Lajus A. , Bocs S. , Médigue C. . ( 2005; ). MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes. . Nucleic Acids Res 33: web server issue W471–W479. [CrossRef].[PubMed].
    [Google Scholar]
  10. Del Papa M. F. , Perego M. . ( 2008; ). Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis . . J Bacteriol 190:, 7147–7156. [CrossRef].[PubMed].
    [Google Scholar]
  11. Elliott J. I. , Yang S. S. , Ljungdahl L. G. , Travis J. , Reilly C. F. . ( 1982; ). Complete amino acid sequence of the 4Fe-4S, thermostable ferredoxin from Clostridium thermoaceticum . . Biochemistry 21:, 3294–3298. [CrossRef].[PubMed].
    [Google Scholar]
  12. Even S. , Pellegrini O. , Zig L. , Labas V. , Vinh J. , Bréchemmier-Baey D. , Putzer H. . ( 2005; ). Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. . Nucleic Acids Res 33:, 2141–2152. [CrossRef].[PubMed].
    [Google Scholar]
  13. Ferguson S. A. , Keis S. , Cook G. M. . ( 2006; ). Biochemical and molecular characterization of a Na+-translocating F1F0-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum . . J Bacteriol 188:, 5045–5054. [CrossRef].[PubMed].
    [Google Scholar]
  14. Fonknechten N. , Perret A. , Perchat N. , Tricot S. , Lechaplais C. , Vallenet D. , Vergne C. , Zaparucha A. , Le Paslier D. et al. ( 2009; ). A conserved gene cluster rules anaerobic oxidative degradation of l-ornithine. . J Bacteriol 191:, 3162–3167. [CrossRef].[PubMed].
    [Google Scholar]
  15. Fonknechten N. , Chaussonnerie S. , Tricot S. , Lajus A. , Andreesen J. R. , Perchat N. , Pelletier E. , Gouyvenoux M. , Barbe V. et al. ( 2010; ). Clostridium sticklandii, a specialist in amino acid degradation: revisiting its metabolism through its genome sequence. . BMC Genomics 11:, 555. [CrossRef].[PubMed].
    [Google Scholar]
  16. Fox K. A. , Ramesh A. , Stearns J. E. , Bourgogne A. , Reyes-Jara A. , Winkler W. C. , Garsin D. A. . ( 2009; ). Multiple posttranscriptional regulatory mechanisms partner to control ethanolamine utilization in Enterococcus faecalis . . Proc Natl Acad Sci U S A 106:, 4435–4440. [CrossRef].[PubMed].
    [Google Scholar]
  17. Jain S. , Graham R. L. , McMullan G. , Ternan N. G. . ( 2010; ). Proteomic analysis of the insoluble subproteome of Clostridium difficile strain 630. . FEMS Microbiol Lett 312:, 151–159. [CrossRef].[PubMed].
    [Google Scholar]
  18. Janvilisri T. , Scaria J. , Chang Y. F. . ( 2010; ). Transcriptional profiling of Clostridium difficile and Caco-2 cells during infection. . J Infect Dis 202:, 282–290. [CrossRef].[PubMed].
    [Google Scholar]
  19. Lawley T. D. , Croucher N. J. , Yu L. , Clare S. , Sebaihia M. , Goulding D. , Pickard D. J. , Parkhill J. , Choudhary J. , Dougan G. . ( 2009; ). Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores. . J Bacteriol 191:, 5377–5386. [CrossRef].[PubMed].
    [Google Scholar]
  20. Lima T. , Auchincloss A. H. , Coudert E. , Keller G. , Michoud K. , Rivoire C. , Bulliard V. , De Castro E. , Lachaize C. et al. ( 2009; ). HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. . Nucleic Acids Res 37: database issue D471–D478. [CrossRef].[PubMed].
    [Google Scholar]
  21. Luo C. , Hu G. Q. , Zhu H. . ( 2009; ). Genome reannotation of Escherichia coli CFT073 with new insights into virulence. . BMC Genomics 10:, 552. [CrossRef].[PubMed].
    [Google Scholar]
  22. Marsden G. L. , Davis I. J. , Wright V. J. , Sebaihia M. , Kuijper E. J. , Minton N. P. . ( 2010; ). Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile . . BMC Genomics 11:, 389. [CrossRef].[PubMed].
    [Google Scholar]
  23. Miura M. , Kato H. , Matsushita O. . ( 2010; ). A novel virulence factor SRL modulates toxin B sensitivity of intestinal epithelial cells. . In 3rd International Clostridium difficile Symposium, Bled, Slovenia, 22–24 September 2010. Basel:: European Society of Clinical Microbiology and Infectious Diseases;.
    [Google Scholar]
  24. Petty N. K. . ( 2010; ). Genome annotation: man versus machine. . Nat Rev Microbiol 8:, 762. [CrossRef].[PubMed].
    [Google Scholar]
  25. Ren Q. , Chen K. , Paulsen I. T. . ( 2007; ). TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. . Nucleic Acids Res 35: Database issue D274–D279. [CrossRef].[PubMed].
    [Google Scholar]
  26. Rupnik M. , Dupuy B. , Fairweather N. F. , Gerding D. N. , Johnson S. , Just I. , Lyerly D. M. , Popoff M. R. , Rood J. I. et al. ( 2005; ). Revised nomenclature of Clostridium difficile toxins and associated genes. . J Med Microbiol 54:, 113–117. [CrossRef].[PubMed].
    [Google Scholar]
  27. Sebaihia M. , Wren B. W. , Mullany P. , Fairweather N. F. , Minton N. , Stabler R. , Thomson N. R. , Roberts A. P. , Cerdeño-Tárraga A. M. et al. ( 2006; ). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. . Nat Genet 38:, 779–786. [CrossRef].[PubMed].
    [Google Scholar]
  28. Shahbabian K. , Jamalli A. , Zig L. , Putzer H. . ( 2009; ). RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis . . EMBO J 28:, 3523–3533. [CrossRef].[PubMed].
    [Google Scholar]
  29. Sonnhammer E. L. , Von Heijne G. , Krogh A. . ( 1998; ). A hidden Markov model for predicting transmembrane helices in protein sequences. . Proc Int Conf Intell Syst Mol Biol 6:, 175–182.[PubMed].
    [Google Scholar]
  30. Stabler R. A. , He M. , Dawson L. , Martin M. , Valiente E. , Corton C. , Lawley T. D. , Sebaihia M. , Quail M. A. et al. ( 2009; ). Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. . Genome Biol 10:, R102. [CrossRef].[PubMed].
    [Google Scholar]
  31. Twine S. M. , Reid C. W. , Aubry A. , McMullin D. R. , Fulton K. M. , Austin J. , Logan S. M. . ( 2009; ). Motility and flagellar glycosylation in Clostridium difficile . . J Bacteriol 191:, 7050–7062. [CrossRef].[PubMed].
    [Google Scholar]
  32. UPC ( 2011; ). Ongoing and future developments at the Universal Protein Resource. . Nucleic Acids Res 39: database issue D214–D219. [CrossRef].[PubMed].
    [Google Scholar]
  33. Vallenet D. , Labarre L. , Rouy Z. , Barbe V. , Bocs S. , Cruveiller S. , Lajus A. , Pascal G. , Scarpelli C. , Médigue C. . ( 2006; ). MaGe: a microbial genome annotation system supported by synteny results. . Nucleic Acids Res 34:, 53–65. [CrossRef].[PubMed].
    [Google Scholar]
  34. Vallenet D. , Engelen S. , Mornico D. , Cruveiller S. , Fleury L. , Lajus A. , Rouy Z. , Roche D. , Salvignol G. et al. ( 2009; ). MicroScope: a platform for microbial genome annotation and comparative genomics. . Database (Oxford) 2009:, bap021.[PubMed].[CrossRef]
    [Google Scholar]
  35. Yu N. Y. , Wagner J. R. , Laird M. R. , Melli G. , Rey S. , Lo R. , Dao P. , Sahinalp S. C. , Ester M. et al. ( 2010; ). PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. . Bioinformatics 26:, 1608–1615. [CrossRef].[PubMed].
    [Google Scholar]
  36. Zdobnov E. M. , Apweiler R. . ( 2001; ). InterProScan – an integration platform for the signature-recognition methods in InterPro. . Bioinformatics 17:, 847–848. [CrossRef].[PubMed].
    [Google Scholar]
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