Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage

Journal of Bacteriology

Volumn 185, Issue 17, 2003, Pages 5220-5233

  Miller, Eric S ^a   Heidelberg, John F ^b   Eisen, Jonathan A ^b   Nelson, William C ^b   Durkin, A Scott ^b   Ciecko, Ann ^b   Feldblyum, Tamara V ^b   White, Owen ^b   Paulsen, Ian T ^b   Nierman, William C ^b   Lee, Jong ^a   Szczypinski, Bridget ^a   Fraser, Claire M ^b  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE T4; BASE PAIRING; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA DEGRADATION; DNA RECOMBINATION; DNA REPLICATION; GENE SEQUENCE; GENETIC CODE; HOST RANGE; INTRON; NONHUMAN; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE HOMOLOGY; STRUCTURAL GENE; VIBRIO; VIBRIOPHAGE KVP40; VIRUS CAPSID;

BACTERIOPHAGE T4; GENOME, VIRAL; GENOMICS; MOLECULAR SEQUENCE DATA; MYOVIRIDAE; SEQUENCE ANALYSIS, DNA; VIBRIO PARAHAEMOLYTICUS; VIRAL PROTEINS;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; UNIDENTIFIED BACTERIOPHAGE; VIBRIO;

EID: 0041386480     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.17.5220-5233.2003     Document Type: Article

References (64)

1. Ackermann, H.-W., and H. M. Krisch. 1997. A catalogue of T4-type bacteriophages. Arch. Virol. 142:2329-2345.
2. Alberts, B., and R. Miake-Lye. 1992. Unscrambling the puzzle of biological machines: the importance of the details. Cell 68:415-420.
3. Ang, D., A. Richardson, M. P. Mayer, F. Keppel, H. Krisch, and C. Georgopoulos. 2001. Pseudo-T-even bacteriophage RB49 encodes CocO, a cochaperonin for GroEL, which can substitute for Escherichia coli's GroES and bacteriophage T4's Gp31. J. Biol. Chem. 276:8720-8726.
4. Bateman, A., E. Bírney, R. Durbin, S. R. Eddy, R. D. Finn, and E. L. Sonnhammer. 1999. Pfam 3.1: 1313 multiple alignments and profile hidden Markov models match the majority of proteins. Nucleic Acids Res. 27:260-262.
5. Bhagwat, M., and N. G. Nossal. 2001. Bacteriophage T4 RNase H removes both RNA primers and adjacent DNA from the 5′ end of lagging-strand fragments. J. Biol. Chem. 276:28516-28524.
6. Bradley, D. E. 1967. Ultrastructure of bacteriophage and bacteriocins. Bacteriol. Rev. 31:230-314.
7. Claros, M. G., and G. von Heijne. 1994. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10:685-686.
8. Desplats, C., C. Dez, F. Tetart, H. Eleaume, and H. M. Krisch. 2002. Snapshot of the genome of the pseudo-T-even bacteriophage RB49. J. Bacteriol. 184:2789-2804.
9. Eddy, S. R. 1995. Multiple alignment with hidden Markov models. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3:114-120.
10. Ermolaeva, M. D., H. G. Khalak, O. White, H. O. Smith, and S. L. Salzberg, 2000. Prediction of transcription terminators in bacterial genomes. J. Mol. Biol. 301:27-33.
11. Frank, A. C., and J. R. Lobry. 2000. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16:560-561.
12. 70 and T4 gp55 promoter recognition proteins. J. Biol. Chem. 273:34042-34048.
13. Greenberg, R. G., P. He, J. Hilfinger, and M.-J. Tseng. 1994. Deoxynucleoside triphosphate synthesis and phage T4 DNA replication, p. 14-27. In J. D. Karam, J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular biology of bacteriophage T4. ASM Press, Washington, D.C.
14. Haft, D. H., B. J. Loftus, D. L. Richardson, F. Yang, J. A. Eisen, I. T. Paulsen, and O. White. 2001. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29:41-43.
15. Hambly, E., F. Tetart, C. Desplats, W. H. Wilson, H. M. Krisch, and N. H. Mann. 2001. A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc. Natl. Acad. Sci. USA 98:11411-11416.
16. Heidelberg, J. F., J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, L. Umayam, S. R. Gill, K. E. Nelson, T. D. Read, H. Tettelin, D. Richardson, M. D. Ermolaeva, J. Vamathevan, S. Bass, H. Qin, I. Dragoi, P. Sellers, L. McDonald, T. Utterback, R. D. Fleishmann, W. C. Nierman, O. White, S. L. Salzberg, H. O. Smith, R. R. Colwell, J. J. Mekalanos, J. C. Venter, and C. M. Fraser. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
17. Henning, U., and S. Hashemolhosseini. 1994. Receptor recognition by Teven-type coliphages, p. 291-298. In J. D. Karam, J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular biology of bacteriophage T4. ASM Press, Washington, D.C.
18. Herr, A. J., N. M. Wills, C. C. Nelson, R. F. Gesteland, and J. F. Atkins. 2001. Drop-off during ribosome hopping. J. Mol. Biol. 311:445-452.
19. Hinton, D. M., and S. Vuthoori. 2000. Efficient inhibition of Escherichia coli RNA polymerase by the bacteriophage T4 AsiA protein requires that AsiA binds first to free sigma70. J. Mol. Biol. 304:731-739.
20. Huang, W. M. 1986. Nucleotide sequence of a type II DNA topoisomerase gene, bacteriophage T4 gene 39. Nucleic Acids Res. 14:7751-7765.
21. Huang, W. M., S. Z. Ao, S. Casjens, R. Orlandi, R. Zeikus, R. Weiss, D. Winge, and M. Fang. 1988. A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60. Science 239:1005-1012.
22. Iida, S., R. Hiestand-Nauer, H. Sandmeier, H. Lehnherr, and W. Arber. 1998. Accessory-genes in the darA operon of bacteriophage P1 affect antirestriction function, generalized transduction, head morphogenesis, and host cell lysis. Virology 251:49-58.
23. Inoue, T., S. Matsuzaki, and S. Tanaka. 1995. A 26-kDa outer membrane protein, OmpK, common to Vibrio species is the receptor for a broad-hostrange vibriophage, KVP40. FEMS Microbiol. Lett. 125:101-105.
24. Inoue, T., S. Matsuzaki, and S. Tanaka. 1995. Cloning and sequence analysis of Vibrio parahaemolyticus ompK gene encoding a 26-kDa outer membrane protein, OmpK, that serves as receptor for a broad-host-range vibriophage, KVP40. FEMS Microbiol. Lett. 134:245-249.
25. Jones, C. E., T. C. Mueser, K. C. Dudas, K. N. Kreuzer, and N. G. Nossal. 2001. Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: a versatile couple with roles in replication and recombination. Proc. Natl. Acad. Sci. USA 98:8312-8318.
26. Kano-Sueoka, T., J. R. Lobry, and N. Sueoka. 1999. Intra-strand biases in bacteriophage T4 genome. Gene 238:59-64.
27. Karam, J. D., J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.). 1994. Molecular biology of bacteriophage T4. ASM Press, Washington, D.C.
28. Karlin, S., A. M. Campbell, and J. Mrazek. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32:185-225.
29. Kolesky, S., M. Ouhammouch, E. N. Brody, and E. P. Geiduschek. 1999. Sigma competition: the contest between bacteriophage T4 middle and late transcription. J. Mol. Biol. 291:267-281.
30. Kreuzer, K. N. 1998. Bacteriophage T4, a model system for understanding the mechanism of type II topoisomerase inhibitors. Biochim. Biophys. Acta 1400:339-347.
31. Kreuzer, K. N., and S. W. Morrical. 1994. Initiation of DNA replication, p. 28-42. In J. D. Karam, J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular biology of bacteriophage T4. ASM Press, Washington, D.C.
32. Kricker, M., and K. Carlson. 1994. Isolation of T4 phage DNA, p. 455-456. In J. D. Karam, J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
33. Kunisawa, T. 1992. Synonymous codon preferences in bacteriophage T4: a distinctive use of transfer RNAs from T4 and from its host Escherichia coli. J. Theor. Biol. 159:287-298.
34. Kutter, E., T. White, M. Kashlev, M. Uzan, J. McKinney, and B. Guttman. 1994. Effects on host genome structure and expression, p. 357-368. In J. D. Karam, J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular biology of bacteriophage T4. ASM Press, Washington, D.C.
35. Landthaler, M., and D. A. Shub. 1999. Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Proc. Natl. Acad. Sci. USA 96:7005-7010.
36. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
37. Martin, P. R., R. J. Shea, and M. H. Mulks. 2001. Identification of a plasmid-encoded gene from Haemophilus ducreyi which confers NAD independence. J. Bacteriol. 183:1168-1174.
38. Matsuzaki; S., T. Inoue, and S. Tanaka. 1998. A vibriophage, KVP40, with major capsid protein homologous to gp23* of coliphage T4. Virology 242: 314-318.
39. Matsuzaki, S., M. Kuroda, S. Kimura, and S. Tanaka. 1999. Major capsid proteins of certain Vibrio and Aeromonas phages are homologous to the equivalent protein, gp23, of coliphage T4. Arch. Virol. 144:1647-1651.
40. Matsuzaki, S., M. Kuroda, S. Kimura, and S. Tanaka. 1999. Vibriophage KVP40 and coliphage T4 genomes share a homologous 7-kbp region immediately upstream of the gene encoding the major capsid protein. Arch. Virol. 144:2007-2012.
41. Matsuzaki, S., S. Tanaka, T. Koga, and T. Kawata. 1992. A broad-host-range vibriophage, KVP40, isolated from sea water. Microbiol. Immunol. 36:93-97.
42. Miller, E. S., and C. E. Jozwik. 1990. Sequence analysis of conserved regA and variable orf43.1 genes in T4-like bacteriophages. J. Bacteriol. 172:5180-5186.
43. Miller, E. S., J. D. Karam, and E. K. Spicer. 1994. Control of translation initiation: mRNA structure and protein repressors, p. 193-205. In J. D. Karam, J. W. Drake, K. N. Kreuzer, G. Mosig, D. Hall, F. A. Eiserling, L. W. Black, E. K. Spicer, E. Kutter, K. Carlson, and E. S. Miller (ed.), Molecular biology of bacteriophage T4. ASM Press, Washington, D.C.
44. Miller, E. S., E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa, and W. Ruger. 2003. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67:86-156.
45. Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
46. Pearson, W. R. 2000. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132:185-219.
47. Penfound, T., and J. W. Foster. 1996. Biosynthesis and recycling of NAD, p. 721-730. In F. C. Niedhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, D.C.
48. Picardeau, M., J. R. Lobry, and B. J. Hinnebusch. 2000. Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Genome Res. 10:1594-1604.
49. Raffaelli, N., T. Lorenzi, A. Amici, M. Emanuelli, S. Ruggieri, and G. Magni. 1999. Synechocystis sp. slr0787 protein is a novel bifunctional enzyme endowed with both nicotinamide mononucleotide adenylyltrransferase and "Nudix" hydrolase activities. FEBS Lett. 444:222-226.
50. Raffaelli, N., T. Lorenzi, P. L. Mariani, M. Emanuelli, A. Amici, S. Ruggieri, and G. Magni. 1999. The Escherichia coli NadR regulator is endowed with nicotinamide mononucleotide adenylyltransferase activity. J. Bacteriol. 181: 5509-5511.
51. Reanney, D.C., and H. W. Ackermann. 1982. Comparative biology and evolution of bacteriophages. Adv. Virus Res. 27:205-280.
52. Salzberg, S. L., A. L. Delcher, S. Kasif, and O. White. 1998. Microbial gene identification with interpolated Markov models. Nucleic Acids Res. 26:544-548.
53. Severinova, E., K. Severinov, and S.A. Darst. 1998. Inhibition of Escherichia coli RNA polymerase by bacteriophage T4 AsiA. J. Mol. Biol. 279:9-18.
54. Sharma, M., R. L. Ellis, and D. M. Hinton. 1992. Identification of a family of bacteriophage T4 genes encoding proteins similar to those present in group I introns of fungi and phage. Proc. Natl. Acad. Sci. USA 89:6658-6662.
55. Sharma, M., P. Marshall, and D. M. Hinton. 1999. Binding of the bacteriophage T4 transcriptional activator. MotA, to T4 middle promoter DNA: evidence for both major and minor groove contacts. J. Mol. Biol. 290:905-915.
56. Sieber, P., A. Lindemann, M. Boehm, G. Seidel, U. Herzing, P. van der Heusen, R. Muller, W. Ruger, R. Jaenicke, and P. Rosch. 1998. Overexpression and structural characterization of the phage T4 protein DsbA. Biol. Chem. 379:51-58.
57. Tetart, F., C. Desplats, M. Kutateladze, C. Monod, H. W. Ackermann, and H. M. Krisch. 2001. Phylogeny of the major head and tail genes of the wide-ranging T4-type bacteriophages. J. Bacteriol. 183:358-366.
58. Tettelin, H., D. Radune, S. Kasif, H. Khouri, and S. L. Salzberg. 1999. Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62:500-507.
59. Tiemann, B., R. Depping, and W. Ruger. 1999. Overexpression, purification, and partial characterization of ADP-ribosyltransferases ModB and ModB of bacteriophage T4. Gene Expr. 8:187-196.
60. Wilkens, K., B. Tiemann, F. Bazan, and W. Ruger. 1997. ADP-ribosylation and early transcription regulation by bacteriophage T4. Adv. Exp. Med. Biol. 419:71-82.
61. Xu, W., P. Gauss, J. Shen, C. A. Dunn, and M. J. Bessman. 2002. The gene e.I (nudE.1) of T4 bacteriophage designates a new member of the Nudix hydrolase superfamily active on flavin adenine dinucleotide, adenosine 5′-triphospho-5′-adenosine, and ADP-ribose. J. Biol. Chem. 277:23181-23185.
62. Yarmolinsky, M. B., and N. Sternberg. 1988. Bacteriophage P1, p. 291-438. In R. Calendar (ed.), The bacteriophages. Plenum Press, New York, N.Y.
63. Yeh, L. S., T. Hsu, and J. D. Karam. 1998. Divergence of a DNA replication gene cluster in the T4-related bacteriophage RB69. J. Bacteriol. 180:2005-2013.
64. Young, K. K., G. J. Edlin, and G. G. Wilson. 1982. Genetic analysis of bacteriophage T4 transducing bacteriophages. J. Virol. 41:345-347.