Genome sequence comparison and superinfection between two related Pseudomonas aeruginosa phages, D3112 and MP22

Microbiology

Volumn 153, Issue 9, 2007, Pages 2885-2895

  Heo, Yun Jeong ^a   Chung, In Young ^a   Choi, Kelly B ^a   Lau, Gee W ^b   Cho, You Hee ^a  

^a Sogang University   (South Korea)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DOUBLE STRANDED DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIOPHAGE; BACTERIOPHAGE D3112; BACTERIOPHAGE MP22; CONTROLLED STUDY; GENE FUNCTION; GENE ISOLATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC IDENTIFICATION; KOREA; MICROMORPHOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PSEUDOMONAS AERUGINOSA; SUPERINFECTION;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; GENOME, VIRAL; HUMANS; LYSOGENY; MOLECULAR SEQUENCE DATA; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS PHAGES; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, DNA; VIRAL PROTEINS;

ENTEROBACTERIA PHAGE LAMBDA; PSEUDOMONAS AERUGINOSA;

EID: 34948870403     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.2007/007260-0     Document Type: Article

References (44)

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.
2. Bodey, G. P., Bolivar, R., Fainstein, V. & Jadeja, L. (1983). Infections caused by Pseudomonas aeruginosa. Rev Infect Dis 5, 279-313.
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.
4. Bradley, D. E. (1967). Ultrastructure of bacteriophage and bacteriocins. Bacteriol Rev 31, 230-314.
5. Bradley, D. E. (1973a). A pilus-dependent Pseudomonas aeruginosa bacteriophage with a long noncontractile tail. Virology 51, 489-492.
6. Bradley, D. E. (1973b). The length of the filamentous Pseudomonas aeruginosa bacteriophage Pf. J Gen Virol 20, 249-252.
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.
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.
9. Byrne, M. & Kropinski, A. M. (2005). The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116. Gene 346, 187-194.
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.
11. Costerton, J. W., Stewart, P. S. & Greenberg, E. P. (1999). Bacterial biofilms: a common cause of persistent infections. Science 284, 1318-1322.
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.
13. Darzins, A. & Casadaban, M. J. (1989a). Mini-D3112 bacteriophage transposable elements for genetic analysis of Pseudomonas aeruginosa. J Bacteriol 171, 3909-3916.
14. Darzins, A. & Casadaban, M. J. (1989b). In vivo cloning of Pseudomonas aeruginosa genes with mini-D3112 transposable bacteriophage. J Bacteriol 171, 3917-3925.
15. Daw, M. A. & Falkiner, F. R. (1996). Bacteriocins: nature, function and structure. Micron 27, 467-479.
16. Drenkard, E. & Ausubel, F. M. (2002). Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation. Nature 416, 740-743.
17. Govan, J. R. & Deretic, V. (1996). Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol Rev 60, 539-574.
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.
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.
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.
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.
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.
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.
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.
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.
26. Kropinski, A. M. (2000). Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J Bacteriol 182, 6066-6074.
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.
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.
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.
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.
31. Marrs, C. F. & Howe, M. M. (1990). Kinetics and regulation of transcription of bacteriophage Mu. Virology 174, 192-203.
32. Pabo, C. O. & Sauer, R. T. (1992). Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 61, 1053-1095.
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.
34. Rohwer, F. & Edwards, R. (2002). The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184, 4529-4535.
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.
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.
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.
39. Sulakvelidze, A., Alavidze, Z. & Morris, J. G., Jr (2001). Bacteriophage therapy. Antimicrob Agents Chemother 45, 649-659.
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.
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.
42. Wang, I. N., Smith, D. L. & Young, R. (2000). Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol 54, 799-825.
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.
44. Xu, J., Hendrix, R. W. & Duda, R. L. (2004). Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol Cell 16, 11-21.