1887

Abstract

The complete genomic sequence of a previously characterized temperate phage of , C2, is reported. The genome is 56 538 bp and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of phage CD119 and phage EJ-1, respectively. Homologues of structural and replication proteins were found in prophages 1 and 2 of the sequenced CD630 genome. A putative holin appears unique to the phages and was functional when expressed in . Nucleotide sequence comparisons of C2 to CD119 and the CD630 prophage sequences showed relatedness between C2 and the prophages, but less so to CD119. C2 integrated into a gene encoding a putative transcriptional regulator of the family. C2, CD119 and CD630 prophage 1 genomes had a Cdu1--integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of , flanked by , has phage origins. The sequences of C2, CD119 and CD630 prophages were dissimilar. C2-related sequences were found in 84 % of 37 clinical isolates and typed reference strains.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2006/002436-0
2007-03-01
2019-11-12
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/3/676.html?itemId=/content/journal/micro/10.1099/mic.0.2006/002436-0&mimeType=html&fmt=ahah

References

  1. Abranches, J., Chen, Y. Y. & Burne, R. A. ( 2003; ). Characterization of Streptococcus mutans strains deficient in EIIAB Man of the sugar phosphotransferase system. Appl Environ Microbiol 69, 4760–4769.[CrossRef]
    [Google Scholar]
  2. Abranches, J., Candella, M. M., Wen, Z. T., Baker, H. V. & Burne, R. A. ( 2006; ). Different roles of EIIABMan and EIIGlc in regulation of energy metabolism, biofilm development, and competence in Streptococcus mutans. J Bacteriol 188, 3748–3756.[CrossRef]
    [Google Scholar]
  3. 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.[CrossRef]
    [Google Scholar]
  4. Angeletti, B., Battiloro, E., Pascale, E. & D'Ambrosio, E. ( 1995; ). Southern and Northern blot fixing by microwave oven. Nucleic Acids Res 23, 879–880.[CrossRef]
    [Google Scholar]
  5. Arous, S., Dalet, K. & Hechard, Y. ( 2004; ). Involvement of the mpo operon in resistance to class IIa bacteriocins in Listeria monocytogenes. FEMS Microbiol Lett 238, 37–41.
    [Google Scholar]
  6. Austin, S. & Abeles, A. ( 1983; ). Partition of unit-copy miniplasmids to daughter cells. II. The partition region of miniplasmid P1 encodes an essential protein and a centromere-like site at which it acts. J Mol Biol 169, 373–387.[CrossRef]
    [Google Scholar]
  7. Barbut, F., Mario, N., Delmee, M., Gozian, J. & Petit, J. C. ( 1993; ). Genomic fingerprinting of Clostridium difficile isolates by using a random amplified polymorphic DNA (RAPD) assay. FEMS Microbiol Lett 114, 161–166.[CrossRef]
    [Google Scholar]
  8. Ben-Bassat, A., Bauer, K., Chang, S. Y., Myambo, K., Boosman, A. & Chang, S. ( 1987; ). Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure. J Bacteriol 169, 751–757.
    [Google Scholar]
  9. Benson, G. ( 1999; ). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573–580.[CrossRef]
    [Google Scholar]
  10. Besemer, J. & Borodovsky, M. ( 1999; ). Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27, 3911–3920.[CrossRef]
    [Google Scholar]
  11. Birge, E. A. ( 2000; ). Bacterial and Bacteriophage Genetics, 4th edn. New York: Springer.
  12. Bourhy, P., Frangeul, L., Couve, E., Glaser, P., Saint Girons, I. & Picardeau, M. ( 2005; ). Complete nucleotide sequence of the LE1 prophage from the spirochete Leptospira biflexa and characterization of its replication and partition functions. J Bacteriol 187, 3931–3940.[CrossRef]
    [Google Scholar]
  13. Braun, V., Hundsberger, T., Leukel, P., Sauerborn, M. & von Eichel-Streiber, C. ( 1996; ). Definition of the single integration site of the pathogenicity locus in Clostridium difficile. Gene 181, 29–38.[CrossRef]
    [Google Scholar]
  14. Bruggemann, H. ( 2005; ). Genomics of clostridial pathogens: implication of extrachromosomal elements in pathogenicity. Curr Opin Microbiol 8, 601–605.[CrossRef]
    [Google Scholar]
  15. Canchaya, C., Proux, C., Fournous, G., Bruttin, A. & Brussow, H. ( 2003; ). Prophage genomics. Microbiol Mol Biol Rev 67, 238–276.[CrossRef]
    [Google Scholar]
  16. Casjens, S. R. ( 2005; ). Comparative genomics and evolution of the tailed-bacteriophages. Curr Opin Microbiol 8, 451–458.[CrossRef]
    [Google Scholar]
  17. Casjens, S. R., Gilcrease, E. B., Winn-Stapley, D. A., Schicklmaier, P., Schmieger, H., Pedulla, M. L., Ford, M. E., Houtz, J. M., Hatfull, G. F. & Hendrix, R. W. ( 2005; ). The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J Bacteriol 187, 1091–1104.[CrossRef]
    [Google Scholar]
  18. Chaillou, S., Postma, P. W. & Pouwels, P. H. ( 2001; ). Contribution of the phosphoenolpyruvate : mannose phosphotransferase system to carbon catabolite repression in Lactobacillus pentosus. Microbiology 147, 671–679.
    [Google Scholar]
  19. Dam, M. & Gerdes, K. ( 1994; ). Partitioning of plasmid R1. Ten direct repeats flanking the parA promoter constitute a centromere-like partition site parC, that expresses incompatibility. J Mol Biol 236, 1289–1298.[CrossRef]
    [Google Scholar]
  20. Ford, M. E., Stenstrom, C., Hendrix, R. W. & Hatfull, G. F. ( 1998; ). Mycobacteriophage TM4: genome structure and gene expression. Tuber Lung Dis 79, 63–73.[CrossRef]
    [Google Scholar]
  21. Freiberg, A., Morona, R., Van den Bosch, L., Jung, C., Behlke, J., Carlin, N., Seckler, R. & Baxa, U. ( 2003; ). The tailspike protein of Shigella phage Sf6. A structural homolog of Salmonella phage P22 tailspike protein without sequence similarity in the beta-helix domain. J Biol Chem 278, 1542–1548.[CrossRef]
    [Google Scholar]
  22. Gallie, D. R. & Kado, C. I. ( 1987; ). Agrobacterium tumefaciens pTAR parA promoter region involved in autoregulation, incompatibility and plasmid partitioning. J Mol Biol 193, 465–478.[CrossRef]
    [Google Scholar]
  23. Garvey, P., Fitzgerald, G. F. & Hill, C. ( 1995; ). Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol 61, 4321–4328.
    [Google Scholar]
  24. Goh, S., Chang, B. J. & Riley, T. V. ( 2005a; ). Effect of phage infection on toxin production by Clostridium difficile. J Med Microbiol 54, 129–135.[CrossRef]
    [Google Scholar]
  25. Goh, S., Riley, T. V. & Chang, B. J. ( 2005b; ). Isolation and characterization of temperate bacteriophages of Clostridium difficile. Appl Environ Microbiol 71, 1079–1083.[CrossRef]
    [Google Scholar]
  26. Govind, R., Fralick, J. A. & Rolfe, R. D. ( 2006; ). Genomic organization and molecular characterization of Clostridium difficile bacteriophage ϕCD119. J Bacteriol 188, 2568–2577.[CrossRef]
    [Google Scholar]
  27. Hammond, G. A. & Johnson, J. L. ( 1995; ). The toxigenic element of Clostridium difficile strain VPI 10463. Microb Pathog 19, 203–213.[CrossRef]
    [Google Scholar]
  28. Haslam, S. C., Ketley, J. M., Mitchell, T. J., Stephen, J., Burdon, D. W. & Candy, D. C. ( 1986; ). Growth of Clostridium difficile and production of toxins A and B in complex and defined media. J Med Microbiol 21, 293–297.[CrossRef]
    [Google Scholar]
  29. Hendrix, R. W. ( 2002; ). Bacteriophages: evolution of the majority. Theor Popul Biol 61, 471–480.[CrossRef]
    [Google Scholar]
  30. Hundsberger, T., Braun, V., Weidmann, M., Leukel, P., Sauerborn, M. & von Eichel-Streiber, C. ( 1997; ). Transcription analysis of the genes tcdA-E of the pathogenicity locus of Clostridium difficile. Eur J Biochem 244, 735–742.[CrossRef]
    [Google Scholar]
  31. Iyer, L. M., Koonin, E. V. & Aravind, L. ( 2002; ). Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics 3, 8.[CrossRef]
    [Google Scholar]
  32. Juhala, R. J., Ford, M. E., Duda, R. L., Youlton, A., Hatfull, G. F. & Hendrix, R. W. ( 2000; ). Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J Mol Biol 299, 27–51.[CrossRef]
    [Google Scholar]
  33. Kanamaru, S., Ishiwata, Y., Suzuki, T., Rossmann, M. G. & Arisaka, F. ( 2005; ). Control of bacteriophage T4 tail lysozyme activity during the infection process. J Mol Biol 346, 1013–1020.[CrossRef]
    [Google Scholar]
  34. Kwan, T., Liu, J., DuBow, M., Gros, P. & Pelletier, J. ( 2005; ). The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci U S A 102, 5174–5179.[CrossRef]
    [Google Scholar]
  35. Kyte, J. & Doolittle, R. F. ( 1982; ). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105–132.[CrossRef]
    [Google Scholar]
  36. Laemmli, U. K. ( 1970; ). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.[CrossRef]
    [Google Scholar]
  37. Lemee, L., Bourgeois, I., Ruffin, E., Collignon, A., Lemeland, J. F. & Pons, J. L. ( 2005; ). Multilocus sequence analysis and comparative evolution of virulence-associated genes and housekeeping genes of Clostridium difficile. Microbiology 151, 3171–3180.[CrossRef]
    [Google Scholar]
  38. Loo, V. G., Poirier, L., Miller, M. A., Oughton, M., Libman, M. D., Michaud, S., Bourgault, A. M., Nguyen, T., Frenette, C. & other authors ( 2005; ). A predominantly clonal multi-institutional outbreak of Clostridium difficile-associated diarrhea with high morbidity and mortality. N Engl J Med 353, 2442–2449.[CrossRef]
    [Google Scholar]
  39. Lowe, T. M. & Eddy, S. R. ( 1997; ). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25, 955–964.[CrossRef]
    [Google Scholar]
  40. Mahdi, A. A., Sharples, G. J., Mandal, T. N. & Lloyd, R. G. ( 1996; ). Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J Mol Biol 257, 561–573.[CrossRef]
    [Google Scholar]
  41. Mani, N. & Dupuy, B. ( 2001; ). Regulation of toxin synthesis in Clostridium difficile by an alternative RNA polymerase sigma factor. Proc Natl Acad Sci U S A 98, 5844–5849.[CrossRef]
    [Google Scholar]
  42. Matamouros, S., Govind, R. & Dupuy, B. ( 2006; ). TcdC inhibits toxin synthesis in Clostridium difficile. In 5th International Meeting on the Molecular Biology and Pathogenesis of the Clostridia, p. 64. Nottingham, UK.
  43. McDonald, L. C., Killgore, G. E., Thompson, A., Owens, R. C., Jr, Kazakova, S. V., Sambol, S. P., Johnson, S. & Gerding, D. N. ( 2005; ). An epidemic, toxin gene-variant strain of Clostridium difficile. N Engl J Med 353, 2433–2441.[CrossRef]
    [Google Scholar]
  44. Muhlenhoff, M., Stummeyer, K., Grove, M., Sauerborn, M. & Gerardy-Schahn, R. ( 2003; ). Proteolytic processing and oligomerization of bacteriophage-derived endosialidases. J Biol Chem 278, 12634–12644.[CrossRef]
    [Google Scholar]
  45. Muyombwe, A., Tanji, Y. & Unno, H. ( 1999; ). Cloning and expression of a gene encoding the lytic functions of Bacillus amyloliquefaciens phage: evidence of an auxiliary lysis system. J Biosci Bioeng 88, 221–225.[CrossRef]
    [Google Scholar]
  46. Ochman, H., Gerber, A. S. & Hartl, D. L. ( 1988; ). Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621–623.
    [Google Scholar]
  47. Pedulla, M. L., Ford, M. E., Houtz, J. M., Karthikeyan, T., Wadsworth, C., Lewis, J. A., Jacobs-Sera, D., Falbo, J., Gross, J. & other authors ( 2003; ). Origins of highly mosaic mycobacteriophage genomes. Cell 113, 171–182.[CrossRef]
    [Google Scholar]
  48. Radnedge, L., Davis, M. A. & Austin, S. J. ( 1996; ). P1 and P7 plasmid partition: ParB protein bound to its partition site makes a separate discriminator contact with the DNA that determines species specificity. EMBO J 15, 1155–1162.
    [Google Scholar]
  49. Reizer, J., Bachem, S., Reizer, A., Arnaud, M., Saier, M. H., Jr & Stulke, J. ( 1999; ). Novel phosphotransferase system genes revealed by genome analysis – the complete complement of PTS proteins encoded within the genome of Bacillus subtilis. Microbiology 145, 3419–3429.
    [Google Scholar]
  50. Romero, P., Lopez, R. & Garcia, E. ( 2004; ). Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an atypical pneumococcus. Virology 322, 239–252.[CrossRef]
    [Google Scholar]
  51. Rupnik, M., Avesani, V., Janc, M., von Eichel-Streiber, C. & Delmee, M. ( 1998; ). A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates. J Clin Microbiol 36, 2240–2247.
    [Google Scholar]
  52. Rupnik, M., Brazier, J., Duerden, B., Grabnar, M. & Stubbs, S. ( 2001; ). Comparison of toxinotyping and PCR ribotyping of Clostridium difficile strains and description of novel toxinotypes. Microbiology 147, 439–447.
    [Google Scholar]
  53. Rupnik, M., Dupuy, B., Fairweather, N. F., Gerding, D. N., Johnson, S., Just, I., Lyerly, D. M., Popoff, M. R., Rood, J. I. & other authors ( 2005; ). Revised nomenclature of Clostridium difficile toxins and associated genes. J Med Microbiol 54, 113–117.[CrossRef]
    [Google Scholar]
  54. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  55. Sebaihia, M., Wren, B. W., Mullany, P., Fairweather, N. F., Minton, N., Stabler, R., Thomson, N. R., Roberts, A. P., Cerdeno-Tarraga, A. M. & other authors ( 2006; ). The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38, 779–786.[CrossRef]
    [Google Scholar]
  56. Sharples, G. J., Bolt, E. L. & Lloyd, R. G. ( 2002; ). RusA proteins from the extreme thermophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions. Mol Microbiol 44, 549–559.[CrossRef]
    [Google Scholar]
  57. Sheehan, M. M., Stanley, E., Fitzgerald, G. F. & van Sinderen, D. ( 1999; ). Identification and characterization of a lysis module present in a large proportion of bacteriophages infecting Streptococcus thermophilus. Appl Environ Microbiol 65, 569–577.
    [Google Scholar]
  58. Shepherd, A. J., Gorse, D. & Thornton, J. M. ( 1999; ). Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci 8, 1045–1055.[CrossRef]
    [Google Scholar]
  59. Tan, K. S., Wee, B. Y. & Song, K. P. ( 2001; ). Evidence for holin function of tcdE gene in the pathogenicity of Clostridium difficile. J Med Microbiol 50, 613–619.
    [Google Scholar]
  60. Tatusova, T. A. & Madden, T. L. ( 1999; ). BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174, 247–250.[CrossRef]
    [Google Scholar]
  61. Wang, I. N., Smith, D. L. & Young, R. ( 2000; ). Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol 54, 799–825.[CrossRef]
    [Google Scholar]
  62. Warny, M., Pepin, J., Fang, A., Killgore, G., Thompson, A., Brazier, J., Frost, E. & McDonald, L. C. ( 2005; ). Toxin production by an emerging strain of Clostridium difficile associated with outbreaks of severe disease in North America and Europe. Lancet 366, 1079–1084.[CrossRef]
    [Google Scholar]
  63. Yamaichi, Y. & Niki, H. ( 2000; ). Active segregation by the Bacillus subtilis partitioning system in Escherichia coli. Proc Natl Acad Sci U S A 97, 14656–14661.[CrossRef]
    [Google Scholar]
  64. Young, R. ( 1992; ). Bacteriophage lysis: mechanism and regulation. Microbiol Rev 56, 430–481.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2006/002436-0
Loading
/content/journal/micro/10.1099/mic.0.2006/002436-0
Loading

Data & Media loading...

Supplements

Translated ORFs of φC2, amino acid sequence similarity and predicted molecular function of gene products. [ Word file] (145 kb) Cumulative GC skew of the φC2 genome, where analysis began at the 3' end of the putative integrase gene (nt 35184). The minimum and maximum points are indicated in yellow and correspond to putative origin and terminus of replication, respectively. GC skew is in blue and cumulative GC skew is in red. [ PDF] (185 kb)

WORD

Translated ORFs of φC2, amino acid sequence similarity and predicted molecular function of gene products. [ Word file] (145 kb) Cumulative GC skew of the φC2 genome, where analysis began at the 3' end of the putative integrase gene (nt 35184). The minimum and maximum points are indicated in yellow and correspond to putative origin and terminus of replication, respectively. GC skew is in blue and cumulative GC skew is in red. [ PDF] (185 kb)

PDF
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