1887

Abstract

A temperate transposable bacteriophage (MP22) was isolated from a Korean clinical isolate of . It has a coliphage -like morphology and a double-stranded DNA genome. The complete nucleotide sequence and annotation of the MP22 genome and its characteristics are presented. The MP22 genome is 36 409 bp long with a G+C content of 64.2 mol%. The genome contains 51 proposed ORFs, of which 48 (94 %) display synteny and significant nucleotide and protein sequence similarity to the corresponding ORFs of the closely related phage, D3112. Three of the predicted ORFs are unique proteins, whose functions are yet to be revealed. The phage c repressors exhibit striking dissimilarities and, when present as a single gene, did not show cross-immunity. In contrast, although an MP22 lysogen could be productively infected with D3112, MP22 could not grow on a D3112 lysogen, indicating a role of other D3112 genes in superinfection exclusion.

Keyword(s): TFP, type four pili
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/007260-0
2007-09-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/9/2885.html?itemId=/content/journal/micro/10.1099/mic.0.2007/007260-0&mimeType=html&fmt=ahah

References

  1. Bibb M. J., Findlay P. R., Johnson M. W. 1984; The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene 30:157–166
    [Google Scholar]
  2. Bodey G. P., Bolivar R., Fainstein V., Jadeja L. 1983; Infections caused by Pseudomonas aeruginosa. Rev Infect Dis 5:279–313
    [Google Scholar]
  3. Boles B. R., Thoendel M., Singh P. K. 2004; Self-generated diversity produces “insurance effects” in biofilm communities. Proc Natl Acad Sci U S A 101:16630–16635
    [Google Scholar]
  4. Bradley D. E. 1967; Ultrastructure of bacteriophage and bacteriocins. Bacteriol Rev 31:230–314
    [Google Scholar]
  5. Bradley D. E. 1973a; A pilus-dependent Pseudomonas aeruginosa bacteriophage with a long noncontractile tail. Virology 51:489–492
    [Google Scholar]
  6. Bradley D. E. 1973b; The length of the filamentous Pseudomonas aeruginosa bacteriophage Pf. J Gen Virol 20:249–252
    [Google Scholar]
  7. Braid M. D., Silhavy J. L., Kitts C. L., Cano R. J., Howe M. M. 2004; Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa. J Bacteriol 186:6560–6574
    [Google Scholar]
  8. Budzik J. M., Rosche W. A., Rietsch A., O'Toole G. A. 2004; Isolation and characterization of a generalized transducing phage for Pseudomonas aeruginosa strains PAO1 and PA14. J Bacteriol 186:3270–3273
    [Google Scholar]
  9. Byrne M., Kropinski A. M. 2005; The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116. Gene 346:187–194
    [Google Scholar]
  10. Choi K. H., Kumar A., Schweizer H. P. 2006; A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: application for DNA fragment transfer between chromosomes and plasmid transformation. J Microbiol Methods 64:391–397
    [Google Scholar]
  11. Costerton J. W., Stewart P. S., Greenberg E. P. 1999; Bacterial biofilms: a common cause of persistent infections. Science 284:1318–1322
    [Google Scholar]
  12. Darling A. C., Mau B., Blattner F. R., Perna N. T. 2004; Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403
    [Google Scholar]
  13. Darzins A., Casadaban M. J. 1989a; Mini-D3112 bacteriophage transposable elements for genetic analysis of Pseudomonas aeruginosa. J Bacteriol 171:3909–3916
    [Google Scholar]
  14. Darzins A., Casadaban M. J. 1989b; In vivo cloning of Pseudomonas aeruginosa genes with mini-D3112 transposable bacteriophage. J Bacteriol 171:3917–3925
    [Google Scholar]
  15. Daw M. A., Falkiner F. R. 1996; Bacteriocins: nature, function and structure. Micron 27:467–479
    [Google Scholar]
  16. Drenkard E., Ausubel F. M. 2002; Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation. Nature 416:740–743
    [Google Scholar]
  17. Govan J. R., Deretic V. 1996; Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol Rev 60:539–574
    [Google Scholar]
  18. Groisman E. A., Casadaban M. J. 1987; In vivo DNA cloning with a mini-Mu replicon cosmid and a helper lambda phage. Gene 51:77–84
    [Google Scholar]
  19. Hagens S., Habel A., von Ahsen U., von Gabain A., Blasi U. 2004; Therapy of experimental Pseudomonas infections with a nonreplicating genetically modified phage. Antimicrob Agents Chemother 48:3817–3822
    [Google Scholar]
  20. Heo Y.-J., Ko K. S., Song J.-H., Cho Y.-H. 2005; Profiling pyocins and competitive growth advantages in various Pseudomonas aeruginosa strains. J Microbiol Biotechnol 15:1368–1376
    [Google Scholar]
  21. Heo Y.-J., Chung I.-Y., Choi K. B., Cho Y.-H. 2007; R-type pyocin is required for competitive growth advantage between Pseudomonas aeruginosa strains. J Microbiol Biotechnol 17:180–185
    [Google Scholar]
  22. Hoang T. T., Karkhoff-Schweizer R. R., Kutchma A. J., Schweizer H. P. 1998; A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212:77–86
    [Google Scholar]
  23. Hoang T. T., Kutchma A. J., Becher A., Schweizer H. P. 2000; Integration-proficient plasmids for Pseudomonas aeruginosa: site-specific integration and use for engineering of reporter and expression strains. Plasmid 43:59–72
    [Google Scholar]
  24. Isono K., McIninch J. D., Borodovsky M. 1994; Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark. DNA Res 1:263–269
    [Google Scholar]
  25. Kielhofner M., Atmar R. L., Hamill R. J., Musher D. M. 1992; Life-threatening Pseudomonas aeruginosa infections in patients with human immunodeficiency virus infection. Clin Infect Dis 14:403–411
    [Google Scholar]
  26. Kropinski A. M. 2000; Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J Bacteriol 182:6066–6074
    [Google Scholar]
  27. Krylov V. N., Akhverdian V. Z., Bogush V. G., Khrenova E. A., Reulets M. A. 1985; Modular structure of the genes of phages-transposons of Pseudomonas aeruginosa. Genetika 21:724–734
    [Google Scholar]
  28. Levin M. E., Hendrix R. W., Casjens S. R. 1993; A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein. J Mol Biol 234:124–139
    [Google Scholar]
  29. 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
    [Google Scholar]
  30. Ma J., Campbell A., Karlin S. 2002; Correlations between Shine–Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol 184:5733–5745
    [Google Scholar]
  31. Marrs C. F., Howe M. M. 1990; Kinetics and regulation of transcription of bacteriophage Mu. Virology 174:192–203
    [Google Scholar]
  32. Pabo C. O., Sauer R. T. 1992; Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 61:1053–1095
    [Google Scholar]
  33. Rahme L. G., Ausubel F. M., Cao H., Drenkard E., Goumnerov B. C., Lau G. W., Mahajan-Miklos S., Plotnikova J., Tan M. W. other authors 2000; Plants and animals share functionally common bacterial virulence factors. Proc Natl Acad Sci U S A 97:8815–8821
    [Google Scholar]
  34. Rohwer F., Edwards R. 2002; The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184:4529–4535
    [Google Scholar]
  35. Roncero C., Darzins A., Casadaban M. J. 1990; Pseudomonas aeruginosa transposable bacteriophages D3112 and B3 require pili and surface growth for adsorption. J Bacteriol 172:1899–1904
    [Google Scholar]
  36. Salmon K. A., Freedman O., Ritchings B. W., DuBow M. S. 2000; Characterization of the lysogenic repressor (c) gene of the Pseudomonas aeruginosa transposable bacteriophage D3112. Virology 272:85–97
    [Google Scholar]
  37. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  38. Shine J., Dalgarno L. 1975; Determinant of cistron specificity in bacterial ribosomes. Nature 254:34–38
    [Google Scholar]
  39. Sulakvelidze A., Alavidze Z., Morris J. G. Jr 2001; Bacteriophage therapy. Antimicrob Agents Chemother 45:649–659
    [Google Scholar]
  40. Summer E. J., Gonzalez C. F., Carlisle T., Mebane L. M., Cass A. M., Savva C. G., LiPuma J., Young R. 2004; Burkholderia cenocepacia phage BcepMu and a family of Mu-like phages encoding potential pathogenesis factors. J Mol Biol 340:49–65
    [Google Scholar]
  41. 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
    [Google Scholar]
  42. Wang I. N., Smith D. L., Young R. 2000; Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol 54:799–825
    [Google Scholar]
  43. Wang P. W., Chu L., Guttman D. S. 2004; Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J Bacteriol 186:400–410
    [Google Scholar]
  44. Xu J., Hendrix R. W., Duda R. L. 2004; Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell 16:11–21
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2007/007260-0
Loading
/content/journal/micro/10.1099/mic.0.2007/007260-0
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