Complete genome sequence of φHSIC, a pseudotemperate marine phage of Listonella pelagia

Applied and Environmental Microbiology

Volumn 71, Issue 6, 2005, Pages 3311-3320

  Paul, John H ^a   Williamson, Shannon J ^b   Long, Amy ^a   Authement, R Nathan ^c   John, David ^a   Segall, Anca M ^c   Rohwer, Forest L ^d   Androlewicz, Matthew ^e   Patterson, Stacey ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

^b UNIVERSITY OF DELAWARE   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

^d SAN DIEGO STATE UNIVERSITY   (United States)

^e H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENZYMES; INFORMATION ANALYSIS;

GENOME SEQUENCES; LISTONELLA PELAGIA; OPEN READING FRAMES (ORF); PSEUDOTEMPERATE MARINE PHAGE;

GENES;

AMINO ACID; DNA DIRECTED DNA POLYMERASE GAMMA; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE;

GENOME;

ARTICLE; BACTERIAL GENE; BACTERIOPHAGE; DIGESTION; ENZYME SUBUNIT; GENE SEQUENCE; GENOME; LISTONELLA; LISTONELLA PELAGIA; LYSOGENIZATION; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHIHSIC GENE; SALMONELLA; SHIGELLA;

ELECTROPHORESIS, GEL, PULSED-FIELD; GENE LIBRARY; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; SEAWATER; SEQUENCE ANALYSIS, DNA; SIPHOVIRIDAE; VIBRIONACEAE; VIRAL PROTEINS;

LISTONELLA PELAGIA; SALMONELLA; SHIGELLA; SIPHOVIRIDAE;

EID: 20444405294     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.6.3311-3320.2005     Document Type: Article

References (53)

1. Ackermann, H. W., and M. S. DuBow. 1987. Viruses of prokaryotes, vol. I. General properties of bacteriophages. CRC Press, Inc., Boca Raton, Fla.
2. Altermann, E., J. R. Klein, and B. Henrich. 1999. Primary structure and features of the genome of the Lactobacillus gasseri temperate bacteriophage φadh. Gene 236:333-346.
3. Aravind, L., K. S. Makarova, and E. V. Koonin. 2000. Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution, and evolutionary trajectories. Nucleic Acids Res. 28:3417-3432.
4. Beres, S. B., G. L. Sylva, K. D. Barbian, B. Lei, J. S. Hoff, N. D. Mammarella, M. Y. Liu, J. C. Smoot, S. F. Porcella, L. D. Parkins, D. S. Campbell, T. M. Smith, J. K. McCormick, D. Y. Leung, P. M. Schlievert, and J. M. Musser. 2002. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc. Natl. Acad. Sci. USA 99:10078-10083,
5. Black, L. W. 1989. DNA packaging in dsDNA bacteriophages. Annu. Rev. Microbiol. 43:267-292.
6. Breitbart, M., B. Felts, J. M. Mahaffy, J. Nulton, P. Salamon, and F. Rohwer. 2004. Diversity and population structure of a near-shore marine-sediment viral community. Proc. R. Soc. Lond. Ser. B 271:565-574.
7. Büchen-Osmond, C. 2002. ICTVdB: the universal virus database of the International Committee on Taxonomy of Viruses. Index of viruses. [Online.] http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/ICTVindex.htm.
8. Burr, S. E., K. Stuber, and J. Frey. 2003. The ADP-ribosylating toxin, AexT, from Aeromonas salmonicida subsp. salmonicida is translocated via a type III secretion pathway. J. Bacteriol. 185:6583-6591.
9. Casjens, S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49:277-300.
10. Casjens, S., D. A. Winn-Stapley, E. B. Gilcrease, R. Morona, C. Kulewein, J. E. H. Chua, P. A. Manning, W. Inwood, and A. J. Clark. 2004. The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging. J. Mol. Biol. 339:379-394.
11. Chen, F., and J. Lu. 2002. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68:2589-2594.
12. Clark, A. J., W. Inwood, T. Cloutier, and T. S. Dhillon. 2001. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. J. Mol. Biol. 311:657-679.
13. Deng, W., V. Burland, G. Plunkett III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plana, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner, and R. D. Perry. 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184:4601-4611.
14. Dickman, M. J., S. M. Ingleston, S. E. Sedelnikova, J. B. Rafferty, R. G. Lloyd, J. A. Grasby, and D. P. Hornby. 2002. The RuvABC resolvasome. Eur. J. Biochem. 269:5492-5501.
15. Esposito, D., and J. J. Scocca. 1997. The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res. 25:3605-3614.
16. Farto, R., M. J. Perez, A. Fernandez-Briera, and T. P. Nieto. 2002. Purification and partial characterization of a fish lethal extracellular protease from Vibrio pelagius. Vet. Microbiol. 89:181-194.
17. Ferretti, J. J., W. M. McShan, D. Ajdic, D. Savic, G. Savic, K. Lyon, C. Primeaux, S. S. Sezate, A. N. Surorov, S. Kenton, H. Lai, S. Lin, Y. Qian, H. G. Jia, F. Z. Najar, Q. Ren, H. Zhu, L. Song, J. White, X. Yuan, S. W. Clifton, B. A. Roe, and R. E. McLaughlin. 2001. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 98:4658-4663.
18. Groth, A. C., and M. P. Calos. 2004. Phage integrases: biology and applications. J. Mol. Biol. 335:667-678.
19. Han, S., A. S. Arvai, S. B. Clancy, and J. A. Tainer. 2001. Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis. J. Mol. Biol. 305:95-107.
20. Hendrix, R. W. 1988. Tail length determination in double-stranded DNA bacteriophages. Curr. Top. Microbiol. Immunol. 136:21-29.
21. Inal, J. M., and K. V. Karunakaran. 1996. φ20, a temperate bacteriophage isolated from Bacillus anthracis, exists as a plasmidial prophage. Curr. Microbiol. 32:171-175.
22. Jiang, S. C., and J. H. Paul. 1998. Gene transfer by transduction in the marine environment. Appl. Environ. Microbiol. 64:2780-2787.
23. Jiang, S. C., and J. H. Paul. 1996. Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Mar. Ecol. Prog. Ser. 142:27-38.
24. Jiang, S. C., and J. H. Paul. 1998. Significance of lysogeny in the marine environment: studies with isolates and a model for viral production. Microb. Ecol. 35:235-243.
25. Jiang, S. C., C. A. Kellogg, and J. H. Paul. 1998. Characterization of marine temperate phage-host systems isolated from Mamala Bay, Oahu, Hawaii. Appl. Environ. Microbiol. 64:535-542.
26. Kapfhammer, D., J. Blass, S. Evers, and J. Reidl. 2002. Vibrio cholerae phage K139: complete genome sequence and comparative phage genomics of related phages. J. Bacteriol. 184:6592-6601.
27. Katsura, I. 1987. Determination of bacteriophage λ tail length by a protein ruler. Nature 327:73-75.
28. Kumar, S., K. Tamura, and M. Nei. 1993. MEGA: molecular evolutionary genetic analysis. The Pennsylvania State University, University Park, Pa.
29. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
30. Lin, H., V. B. Rao, and L. W. Black. 1999. Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4. J. Mol. Biol. 289:249-260.
31. Martinez-Jimenez, M. I., P. Mesa, and J. C. Alonso. 2002. Bacillus subtilis tau subunit of DNA polymerase III interacts with bacteriophage SPP1 replicative DNA helicase G40P. Nucleic Acids Res. 30:5056-5064.
32. McDaniel, L., L. A. Houchin, S. J. Williamson, and J. H. Paul. 2002. Lysogeny in marine Synechococcus populations. Nature 415:496.
33. Moebus, K. 1997. Investigations of the marine lysogenic bacterium H24. II. Development of pseudolysogeny in nutrient broth rich culture. Mar. Ecol. Prog. Ser. 148:229-240.
34. Munro, J., J. Oakey, E. Bromage, and L. Owens. 2003. Experimental bacteriophage-mediated virulence in strains of Vibrio harveyi. Dis. Aquat. Organ. 54:187-194.
35. Oakey, H. J., B. R. Cullen, and L. Owens. 2002. The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML. J. Appl. Microbiol. 93:1089-1098.
36. Ortmann, A. C., J. E. Lawrence, and C. A. Suttle. 2002. Lysogeny and lytic viral production during a bloom of the cyanobacterium Synechococcus spp. Microb. Ecol. 43:225-231.
37. Parkhill, J., B. W. Wren, N. R. Thomson, R. W. Titball, M. T. G. Holden, M. B. Prentice, M. Sebaihia, K. D. James, C. Churcher, K. L. Mungall, S. Baker, D. Basham, S. D. Bentley, K. Brooks, A. M. Cerdeno-Tarraga, T. Chillingworth, A. Cronin, R. M. Davies, P. Davis, G. Dougan, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, S. Leather, A. V. Karlyshev, S. Moule, P. C. F. Oyston, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523-527.
38. Paul, J. H., and S. C. Jiang. 2001. Lysogeny and transduction. Methods Microbiol. 30:105-125.
39. Paul, J. H., and B. Myers. 1982. The fluorometric determination of DNA in aquatic microorganisms employing Hoechst 33258. Appl. Environ. Microbiol. 43:1393-1399.
40. Paul, J. H., J. B. Rose, S. C. Jiang, C. A. Kellogg, and L. Dickson. 1993. Distribution of viral abundance in the reef environment of Key Largo, Florida. Appl. Environ. Microbiol. 59:718-724.
41. Pedersen, M., S. Ostergaard, J. Bresciani, and F. K. Vogensen. 2000. Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly. Virology 276:315-328.
42. Ripp, S., and R. V. Miller. 1998. Dynamics of the pseudolysogenic response in slowly growing Pseudomonas aeruginosa cells. Microbiology 144:2225-2232.
43. Rohwer, F., and R. Edwards. 2002. The phage proteomic tree: a genome-based taxonomy for phage. J. Bacteriol. 184:4529-4535.
44. Seguritan, V., I.-W. Feng, F. Rohwer, M. Swift, and A. N. Segall. 2003. Genome sequences of two closely related Vibrio parahaemolyticus phages, VP16T and VP16C. J. Bacteriol. 185:6434-6447.
45. Simidu, U., K. Kta-Tsukamoto, T. Yasumoto, and M. Yotsu. 1990. Taxonomy of four marine bacterial strains that produce tetrodotoxin. Int. J. Syst. Bacteriol. 40:331-336.
46. Southworth, M. W., and F. B. Perler. 2002. Protein splicing of the Deinococcus radiodurans strain R1 Snf2 intein. J. Bacteriol. 184:6387-6388.
47. Sumby, P., and M. K. Waldor. 2003. Transcription of the toxin genes present within the staphylococcal phage φSa3ms is intimately linked with the phage's life cycle. J. Bacteriol. 185:6841-6851.
48. Villamil, L., A. Figueras, A. E. Toranzo, M. Planas, and B. Novoa. 2003. Isolation of a highly pathogenic Vibrio pelagius strain associated with mass mortalities of turbot, Scophthalmus maximus (L.), larvae. J. Fish Dis. 26:293-303.
49. Weinbauer, M. G., and C. A. Suttle. 1996. Potential significance of lysogeny to bacteriophage production and bacterial mortality in coastal waters of the Gulf of Mexico. Appl. Environ. Microbiol. 62:4374-4380.
50. Weinbauer, M. G., and C. A. Suttle. 1999. Lysogeny and prophage induction in coastal and offshore bacterial communities. Aquat. Microb. Ecol. 18:217-225.
51. Williamson, S., M. R. McLaughlin, and J. H. Paul. 2001. Interaction of the phage HSIC with its host. Lysogeny or pseudolysogeny? Appl. Environ. Microbiol. 67:1682-1688.
52. Wilson, W. H., S. Turner., and N. H. Mann. 1998. Population dynamics of phytoplankton and viruses in phosphate-limited mesocosm and their effect on DMSP and DMS production. Estuar. Coast. Shelf Sci. 46:49-59.
53. Wommack, K. E., and R. R. Colwell. 2000. Viroplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.