1887

Abstract

The 34 734-bp integrative and potentially conjugative element (putative ICE) ICE has been previously found to be site-specifically integrated in the 3′ end of the locus of CNRZ368. Four types of genomic islands related to ICE are integrated in the same position in seven other strains of . One of these elements, ICE, harbours conjugation and recombination modules closely related to those of ICE and excises by site-specific recombination. Two other types of elements, CIME19258 and CIME302, are flanked by site-specific attachment sites closely related to and of ICE and ICE, whereas ΔCIME308 only possesses a putative site; none of these three elements carry complete conjugation and recombination modules. ICE contains a functional internal recombination site, ′, that is almost identical to of CIME19258. The recombination between ′ and of ICE leads to the excision of the expected circular molecule (putative ICE); a -mobilizable element (CIME) flanked by an site and an ′ site remains integrated into the 3′ end of . Furthermore, sequences that could be truncated sites were found within ICE, ICE and CIME302. All together, these data suggest that these genomic islands evolved by deletion and tandem accretion of ICEs and CIMEs resulting from site-specific recombination. A model for this evolution is proposed and its application to other genomic islands is discussed.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.26883-0
2004-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/4/mic1500759.html?itemId=/content/journal/micro/10.1099/mic.0.26883-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Zhang Z., Miller W., Lipman D. J., Schäffer A. A., Zhang J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  2. Bentley S. D., Chater K. F., Cerdeno-Tarraga A. M.40 other authors 2002; Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147 [CrossRef]
    [Google Scholar]
  3. Besemer J., Borodovsky M. 1999; Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920 [CrossRef]
    [Google Scholar]
  4. Boccard F., Smokvina T., Pernodet J. L., Friedmann A., Guérineau M. 1989; The integrated conjugative plasmid pSAM2 of Streptomyces ambofaciens is related to temperate bacteriophages. EMBO J 8:973–980
    [Google Scholar]
  5. Bourgoin F., Panis C., Decaris B., Guédon G., Pébay M., Roussel Y. 1996; Characterization of a mosaic ISS1 element and evidence for the recent horizontal transfer of two different types of ISS1 betweenStreptococcus thermophilus and Lactococcus lactis. Gene 178:15–23 [CrossRef]
    [Google Scholar]
  6. Bourgoin F., Decaris B., Guédon G., Gintz B. 1998; Characterization of a novel insertion sequence, IS1194, in Streptococcus thermophilus. Plasmid 40:44–49 [CrossRef]
    [Google Scholar]
  7. Bourgoin F., Pluvinet A., Gintz B., Decaris B., Guédon G. 1999; Are horizontal transfers involved in the evolution of the Streptococcus thermophilus exopolysaccharide synthesis loci?. Gene 233:151–161 [CrossRef]
    [Google Scholar]
  8. Brassinga A. K., Hiltz M. F., Sisson G. R., Morash M. G., Hill N., Garduno E., Edelstein P. H., Garduno R. A., Hoffman P. S. 2003; A 65-kilobase pathogenicity island is unique to Philadelphia-1 strains of Legionella pneumophila. J Bacteriol 185:4630–4637 [CrossRef]
    [Google Scholar]
  9. Burrus V., Roussel Y., Decaris B., Guédon G. 2000; Characterization of a novel integrative element, ICESt1, in the lactic acid bacterium Streptococcus thermophilus. Appl Environ Microbiol 66:1749–1753 [CrossRef]
    [Google Scholar]
  10. Burrus V., Bontemps C., Decaris B., Guédon G. 2001; Characterization of a novel type II restriction-modification system, Sth368I, encoded by the integrative element ICESt1 ofStreptococcus thermophilus CNRZ368. Appl Environ Microbiol 67:1522–1528 [CrossRef]
    [Google Scholar]
  11. Burrus V., Pavlovic G., Decaris B., Guédon G. 2002a; Conjugative transposons: the tip of the iceberg. Mol Microbiol 46:601–610 [CrossRef]
    [Google Scholar]
  12. Burrus V., Pavlovic G., Decaris B., Guédon G. 2002b; The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration. Plasmid 48:77 [CrossRef]
    [Google Scholar]
  13. Carias L. L., Rudin S. D., Donskey C. J., Rice L. B. 1998; Genetic linkage and cotransfer of a novel, vanB-containing transposon (Tn5382) and a low-affinity penicillin-binding protein 5 gene in a clinical vancomycin-resistant Enterococcus faecium isolate. J Bacteriol 180:4426–4434
    [Google Scholar]
  14. Charron-Bourgoin F., Pluvinet A., Morel C., Guédon G., Decaris B. 2001; Polymorphism of eps loci involved in exopolysaccharide synthesis of Streptococcus thermophilus. Lait 81:281–288 [CrossRef]
    [Google Scholar]
  15. Christie P. J., Dunny G. M. 1986; Identification of regions of the Streptococcus faecalis plasmid pCF-10 that encode antibiotic resistance and pheromone response functions. Plasmid 15:230–241 [CrossRef]
    [Google Scholar]
  16. Churchward G. 2002; Conjugative transposons and related mobile elements. In Mobile DNA II pp. 177–191 Edited by Craig N. L., Craigie R., Gellert M., Lambowitz M. L. Washington DC: American Society for Microbiology;
    [Google Scholar]
  17. Clewell D. B., Flannagan F. E. 1993; The conjugative transposons of Gram-positive bacteria. In Bacterial Conjugation pp. 369–388 Edited by Clewell D. B. New York: Plenum;
    [Google Scholar]
  18. Dodd I. B., Egan J. B. 1990; Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res 18:5019–5026 [CrossRef]
    [Google Scholar]
  19. Dower W. J., Miller J. F., Ragsdale C. W. 1988; High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16:6127–6145 [CrossRef]
    [Google Scholar]
  20. Galas D. J., Chandler M. 1989; Bacterial insertion sequences. In Mobile DNA pp. 109–162 Edited by Berg D. E., Howe M. M. Washington DC: American Society for Microbiology;
    [Google Scholar]
  21. Garnier F., Taourit S., Glaser P., Courvalin P., Galimand M. 2000; Characterization of transposon Tn1549,conferring VanB-type resistance in Enterococcus spp. Microbiology 146:1481–1489
    [Google Scholar]
  22. Gasson M. J., Swindell S., Maeda S., Dodd H. M. 1992; Molecular rearrangement of lactose plasmid DNA associated with high-frequency transfer and cell aggregation in Lactococcus lactis 712. Mol Microbiol 6:3213–3223 [CrossRef]
    [Google Scholar]
  23. Guédon G., Bourgoin F., Pébay M., Roussel Y., Colmin C., Simonet J. M., Decaris B. 1995; Characterization and distribution of two insertion sequences, IS1191 and iso-IS981, in Streptococcus thermophilus: does intergeneric transfer of insertion sequences occur in lactic acid bacteria co-cultures?. Mol Microbiol 16:69–78 [CrossRef]
    [Google Scholar]
  24. Hacker J., Kaper J. B. 2000; Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679 [CrossRef]
    [Google Scholar]
  25. Hacker J., Blum-Oehler G., Muhldorfer I., Tschape H. 1997; Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 23:1089–1097 [CrossRef]
    [Google Scholar]
  26. Hochhut B., Waldor M. K. 1999; Site-specific integration of the conjugal Vibrio cholerae SXT element into prfC. Mol Microbiol 32:99–110 [CrossRef]
    [Google Scholar]
  27. Hochhut B., Marrero J., Waldor M. K. 2000; Mobilization of plasmids and chromosomal DNA mediated by the SXT element, a constin found in Vibrio cholerae O139. J Bacteriol 182:2043–2047 [CrossRef]
    [Google Scholar]
  28. Hochhut B., Beaber J. W., Woodgate R., Waldor M. K. 2001a; Formation of chromosomal tandem arrays of the SXT element and R391, two conjugative chromosomally integrating elements that share an attachment site. J Bacteriol 183:1124–1132 [CrossRef]
    [Google Scholar]
  29. Hochhut B., Lotfi Y., Mazel D., Faruque S. M., Woodgate R., Waldor M. K. 2001b; Molecular analysis of antibiotic resistance gene clusters in Vibrio cholerae O139 and O1 SXT constins. Antimicrob Agents Chemother 45:2991–3000 [CrossRef]
    [Google Scholar]
  30. Hopwood D. A., Bibb M. J., Chater K. F.7 other authors 1985 Genetic Manipulation of Streptomyces: a Laboratory Manual Norwich: The John Innes Institute;
  31. Immonen T., Wahlstrom G., Takala T., Saris P. E. 1998 Evidence for a mosaic structure of the Tn5481in Lactococcus lactis N8. DNA Seq 9 245–261
    [Google Scholar]
  32. Kelly W. J., Davey G. P., Ward L. J. 2000; Novel sucrose transposons from plant strains of Lactococcus lactis. FEMS Microbiol Lett 190:237–240 [CrossRef]
    [Google Scholar]
  33. Kleckner N., Chalmers R. M., Kwon D., Sakai J., Bolland S. 1996; Tn10 and IS10 transposition and chromosome rearrangements: mechanism and regulationin vivo and in vitro. Curr Top Microbiol Immunol 204:49–82
    [Google Scholar]
  34. Manganelli R., Romano L., Ricci S., Zazzi M., Pozzi G. 1995; Dosage of Tn916 circular intermediates in Enterococcus faecalis. Plasmid 34:48–57 [CrossRef]
    [Google Scholar]
  35. McDougal L. K., Tenover F. C., Lee L. N., Rasheed J. K., Patterson J. E., Jorgensen J. H., LeBlanc D. J. 1998; Detection of Tn917-like sequences within a Tn916-like conjugative transposon (Tn3872) in erythromycin-resistant isolates ofStreptococcus pneumoniae. Antimicrob Agents Chemother 42:2312–2318
    [Google Scholar]
  36. Merlin C., Mahillon J., Nesvera J., Toussaint A. 2000; Gene recruiters and transporters: the modular structure of bacterial elements. In The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread pp. 363–408 Edited by Thomas C. M. Newark: Hardwood Academic Publishers;
    [Google Scholar]
  37. Nielsen H., Krogh A. 1998; Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 6:122–130
    [Google Scholar]
  38. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. 1997; Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10:1–6 [CrossRef]
    [Google Scholar]
  39. Nobusato A., Uchiyama I., Ohashi S., Kobayashi I. 2000; Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 259:99–108 [CrossRef]
    [Google Scholar]
  40. Osborn M. A., Boltner D. 2002; When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum. Plasmid 48:202–212 [CrossRef]
    [Google Scholar]
  41. Paulsen I. T., Banerjei L., Myers G. S.27 other authors 2003; Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299:2071–2074 [CrossRef]
    [Google Scholar]
  42. Pembroke J. T., MacMahon C., McGrath B. 2002; The role of conjugative transposons in the Enterobacteriaceae. Cell Mol Life Sci 59:2055–2064 [CrossRef]
    [Google Scholar]
  43. Pickard D., Wain J., Baker S.12 other authors 2003; Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J Bacteriol 185:5055–5065 [CrossRef]
    [Google Scholar]
  44. Pingoud A., Jeltsch A. 2001; Structure and function of type II restriction endonucleases. Nucleic Acids Res 29:3705–3727 [CrossRef]
    [Google Scholar]
  45. Possoz C., Ribard C., Gagnat J., Pernodet J. L., Guérineau M. 2001; The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer. Mol Microbiol 42:159–166
    [Google Scholar]
  46. Ravatn R., Studer S., Springael D., Zehnder A. J., van der Meer J. R. 1998; Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. Strain B13. J Bacteriol 180:4360–4369
    [Google Scholar]
  47. Reimmann C., Haas D. 1993; Mobilization of chromosomes and nonconjugative plasmids by cointegrative mechanisms. In Bacterial Conjugation pp. 137–188 Edited by Clewell D. B. New York: Plenum;
    [Google Scholar]
  48. Roberts A. P., Johanesen P. A., Lyras D., Mullany P., Rood J. I. 2001; Comparison of Tn5397 from Clostridium difficile, Tn916 from Enterococcus faecalis and the CW459tet(M) element from Clostridium perfringens shows that they have similar conjugation regions but different insertion and excision modules. Microbiology 147:1243–1251
    [Google Scholar]
  49. Rocha E. P., Danchin A., Viari A. 1999; Functional and evolutionary roles of long repeats in prokaryotes. Res Microbiol 150:725–733 [CrossRef]
    [Google Scholar]
  50. Salyers A. A., Shoemaker N. B., Li L. Y. 1995a; In the driver's seat: the Bacteroides conjugative transposons and the elements they mobilize. J Bacteriol 177:5727–5731
    [Google Scholar]
  51. Salyers A. A., Shoemaker N. B., Stevens A. M., Li L. Y. 1995b; Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol Rev 59:579–590
    [Google Scholar]
  52. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  53. Schirawski J., Hagens W., Fitzgerald G. F., Van Sinderen D. 2002; Molecular characterization of cadmium resistance in Streptococcus thermophilus strain 4134: an example of lateral gene transfer. Appl Environ Microbiol 68:5508–5516 [CrossRef]
    [Google Scholar]
  54. Scott J. R., Churchward G. G. 1995; Conjugative transposition. Annu Rev Microbiol 49:367–397 [CrossRef]
    [Google Scholar]
  55. Seubert A., Hiestand R., De La Cruz F., Dehio C. 2003; A bacterial conjugation machinery recruited for pathogenesis. Mol Microbiol 49:1253–1266 [CrossRef]
    [Google Scholar]
  56. Shankar N., Baghdayan A. S., Gilmore M. S. 2002; Modulation of virulence within a pathogenicity island in vancomycin-resistant Enterococcus faecalis. Nature 417:746–750 [CrossRef]
    [Google Scholar]
  57. Smith C. J., Tribble G. D., Bayley D. P. 1998; Genetic elements of Bacteroides species: a moving story. Plasmid 40:12–29 [CrossRef]
    [Google Scholar]
  58. Sullivan J. T., Trzebiatowski J. R., Cruickshank R. W.11 other authors 2002; Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 184:3086–3095 [CrossRef]
    [Google Scholar]
  59. Terzaghi B. E., Sandine W. E. 1975; Improved medium for lactic streptococci and their bacteriophages. Appl Microbiol Lett 50:807–813
    [Google Scholar]
  60. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  61. Toussaint A., Merlin C. 2002; Mobile elements as a combination of functional modules. Plasmid 47:26–35 [CrossRef]
    [Google Scholar]
  62. Toussaint A., Merlin C., Monchy S., Benotmane M. A., Leplae R., Mergeay M., Springael D. 2003; The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol 69:4837–4845 [CrossRef]
    [Google Scholar]
  63. Tusnady G. E., Simon I. 1998; Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 283:489–506 [CrossRef]
    [Google Scholar]
  64. van der Meer J. R., Sentchilo V. 2003; Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 14:1–7 [CrossRef]
    [Google Scholar]
  65. Whittle G., Hund B. D., Shoemaker N. B., Salyers A. A. 2001; Characterization of the 13-kilobase ermF region of the Bacteroides conjugative transposon CTnDOT. Appl Environ Microbiol 67:3488–3495 [CrossRef]
    [Google Scholar]
  66. Xu J., Bjursell M. K., Himrod J., Deng S., Carmichael L. K., Chiang H. C., Hooper L. V., Gordon J. I. 2003; A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074–2076 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.26883-0
Loading
/content/journal/micro/10.1099/mic.0.26883-0
Loading

Data & Media loading...

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