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Filamentous phage integration requires the host recombinases XerC and XerD

Abstract

Many bacteriophages and animal viruses integrate their genomes into the chromosomal DNA of their hosts as a method of promoting vertical transmission. Phages that integrate in a site-specific fashion encode an integrase enzyme that catalyses recombination between the phage and host genomes1,2. CTXφ is a filamentous bacteriophage that contains the genes encoding cholera toxin, the principal virulence factor of the diarrhoea-causing Gram-negative bacterium Vibrio cholerae3. CTXφ integrates into the V. cholerae genome in a site-specific manner4,5; however, the 6.9-kilobase (kb) CTXφ genome does not encode any protein with significant homology to known recombinases. Here we report that XerC and XerD, two chromosome-encoded recombinases that ordinarily function to resolve chromosome dimers at the dif recombination site6, are essential for CTXφ integration into the V. cholerae genome. The CTXφ integration site was found to overlap with the dif site of the larger of the two V. cholerae chromosomes. Examination of sequences of the integration sites of other filamentous phages indicates that the XerCD recombinases also mediate the integration of these phage genomes at dif-like sites in various bacterial species.

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Figure 1: Site-specific integration of CTXφ DNA into chrI of strain 2740-80.
Figure 4: Sequences of the chrI and chrII dif/attB regions.
Figure 2: Analysis of pCTX-Kn integration in 2740-80 derivatives. pCTX-Kn was introduced into several 2740-80 derivatives and total DNA was prepared from KnR transformants.
Figure 3: Filamentation in V. cholerae xer and dif mutants.
Figure 5: Alignment of dif-like chromosome junction sequences of various filamentous prophages.

References

  1. Nash, H. A. in Escherichia coli and Salmonella (ed. Neidhardt, F. C.) 2363–2376 (ASM Press, Washington DC, 1996)

    Google Scholar 

  2. Campbell, A. M. Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174, 7495–7499 (1992)

    CAS  Article  Google Scholar 

  3. Waldor, M. K. & Mekalanos, J. J. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272, 1910–1914 (1996)

    ADS  CAS  Article  Google Scholar 

  4. Pearson, G. D., Woods, A., Chiang, S. L. & Mekalanos, J. J. CTX genetic element encodes a site-specific recombination system and an intestinal colonization factor. Proc. Natl Acad. Sci. USA 90, 3750–3754 (1993)

    ADS  CAS  Article  Google Scholar 

  5. Davis, B. M., Kimsey, H. H., Chang, W. & Waldor, M. K. The Vibrio cholerae O139 Calcutta bacteriophage CTXφ is infectious and encodes a novel repressor. J. Bacteriol. 181, 6779–6787 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Blakely, G. et al. Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell 75, 351–361 (1993)

    CAS  Article  Google Scholar 

  7. Heidelberg, J. F. et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483 (2000)

    ADS  CAS  Article  Google Scholar 

  8. Kuempel, P. L., Henson, J. M., Dircks, L., Tecklenburg, M. & Lim, D. F. dif, a recA-independent recombination site in the terminus region of the chromosome of Escherichia coli. New Biol. 3, 799–811 (1991)

    CAS  PubMed  Google Scholar 

  9. Davis, B. M., Moyer, K. E., Boyd, E. F. & Waldor, M. K. CTX prophages in classical biotype Vibrio cholerae: functional phage genes but dysfunctional phage genomes. J. Bacteriol. 182, 6992–6998 (2000)

    CAS  Article  Google Scholar 

  10. Tecklenburg, M., Naumer, A., Nagappan, O. & Kuempel, P. The dif resolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location. Proc. Natl Acad. Sci. USA 92, 1352–1356 (1995)

    ADS  CAS  Article  Google Scholar 

  11. Steiner, W., Liu, G., Donachie, W. D. & Kuempel, P. The cytoplasmic domain of FtsK protein is required for resolution of chromosome dimers. Mol. Microbiol. 31, 579–583 (1999)

    CAS  Article  Google Scholar 

  12. Moyer, K. E., Kimsey, H. H. & Waldor, M. K. Evidence for a rolling-circle mechanism of phage DNA synthesis from both replicative and integrated forms of CTXφ. Mol. Microbiol. 41, 311–323 (2001)

    CAS  Article  Google Scholar 

  13. Davis, B. M. & Waldor, M. K. CTXφ contains a hybrid genome derived from tandemly integrated elements. Proc. Natl Acad. Sci. USA 97, 8572–8577 (2000)

    ADS  CAS  Article  Google Scholar 

  14. Parkhill, J. et al. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523–527 (2001)

    ADS  CAS  Article  Google Scholar 

  15. Lin, N. T., Chang, R. Y., Lee, S. J. & Tseng, Y. H. Plasmids carrying cloned fragments of RF DNA from the filamentous phage φLf can be integrated into the host chromosome via site-specific integration and homologous recombination. Mol. Genet. Genom. 266, 425–435 (2001)

    CAS  Article  Google Scholar 

  16. Dai, H., Chow, T. Y., Liao, H. J., Chen, Z. Y. & Chiang, K. S. Nucleotide sequences involved in the neolysogenic insertion of filamentous phage Cf16-v1 into the Xanthomonas campestris pv. citri chromosome. Virology 167, 613–620 (1988)

    CAS  PubMed  Google Scholar 

  17. Simpson, A. J. et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406, 151–157 (2000)

    ADS  CAS  Article  Google Scholar 

  18. Dillard, J. P. & Seifert, H. S. A variable genetic island specific for Neisseria gonorrhaae is involved in providing DNA for natural transformation and is found more often in disseminated infection isolates. Mol. Microbiol. 41, 263–277 (2001)

    CAS  Article  Google Scholar 

  19. Metcalf, W. W. et al. Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteria. Plasmid 35, 1–13 (1996)

    CAS  Article  Google Scholar 

  20. Lessl, M. et al. Dissection of IncP conjugative plasmid transfer: definition of the transfer region Tra2 by mobilization of the Tra1 region in trans. J. Bacteriol. 174, 2493–2500 (1992)

    CAS  Article  Google Scholar 

  21. Horton, R. M., Hunt, H. D., Ho, S. N., Pullen, J. K. & Pease, L. R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61–68 (1989)

    CAS  Article  Google Scholar 

  22. Butterton, J. R. et al. Heterologous antigen expression in Vibrio cholerae vector strains. Infect. Immun. 63, 2689–2696 (1995)

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank L. Arciszewska, A. Camilli, A. Campbell, B. Davis, A. Kane, D. Raychaudhuri, M. Russel and A. Sonenshein for helpful suggestions, and E. Vimr for communication of unpublished observations. We are grateful to A. Kane and the New England Medical Center GRASP Center for the preparation of plates and media. We acknowledge the support of NIH, Howard Hughes Medical Institute and the Pew Foundation.

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Correspondence to Matthew K. Waldor.

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Huber, K., Waldor, M. Filamentous phage integration requires the host recombinases XerC and XerD. Nature 417, 656–659 (2002). https://doi.org/10.1038/nature00782

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