Genetic diversity among five T4-like bacteriophages

Virology Journal

Volumn 3, Issue , 2006, Pages

  Nolan, James M ^a,b   Petrov, Vasiliy ^b   Bertrand, Claire ^c   Krisch, Henry M ^c   Karam, Jim D ^b  

^a UNIVERSITY OF NEW ORLEANS   (United States)

^b TULANE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

^c UPS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; TRANSFER RNA;

AEROMONAS HYDROPHILA; AEROMONAS SALMONICIDA; ARTICLE; BACTERIAL GROWTH; BACTERIOPHAGE T4; BIOINFORMATICS; BIOMASS; CODON; COLIPHAGE; CONSENSUS; CONTROLLED STUDY; DATA BASE; DNA SEQUENCE; ECOLOGY; ESCHERICHIA COLI; GENE CONTROL; GENE ORDER; GENE SEQUENCE; GENE TRANSFER; GENETIC VARIABILITY; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PROMOTER REGION; TRANSCRIPTION REGULATION;

AEROMONAS HYDROPHILA; AEROMONAS SALMONICIDA; ANIMALS; BACTERIOPHAGE T4; BACTERIOPHAGES; BASE SEQUENCE; COLIPHAGES; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; GENOME, VIRAL; HUMANS; MICE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RNA, TRANSFER; SEQUENCE ALIGNMENT; VIRAL PROTEINS;

AEROMONAS PHAGE AEH1; AEROMONAS SALMONICIDA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33745913143     PISSN: 1743422X     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-3-30     Document Type: Article

References (54)

1. Büchen-Osmond C: T4-like viruses. ICTVdB - The Universal Virus Database, version 3 [http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/].
2. Ackermann HW, Krisch HM: A catalogue of T4-type bacteriophages. Arch Virol 1997, 142(12):2329-2345.
3. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W: Bacteriophage T4 Genome. Microbiol Mol Biol Rev 2003, 67(1):86-156.
4. Hendrix RW: Bacteriophage genomics. Curr Opin Microbiol 2003, 6(5):506-511.
5. Grossi GF, Macchiato MF, Gialanella G: Circular permutation analysis of phage T4 DNA by electron microscopy. Z Naturforsch [C] 1983, 38(3-4):294-296.
6. Mosig G: Homologous recombination. In Molecular Biology of Bacteriophage T4 Edited by: Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Eiserling FA, Black LW, Spicer EK, Kutter E, Carlson K, Miller ES. Washington, D.C. , American Society for Microbiology; 1994:54-82.
7. Miller ES, Heidelberg JF, Eisen JA, Nelson WC, Durkin AS, Ciecko A, Feldblyum TV, White O, Paulsen IT, Nierman WC, Lee J, Szczypinski B, Fraser CM: Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage. J Bacteriol 2003, 185(17):5220-5233.
8. Mann NH, Clokie MR, Millard A, Cook A, Wilson WH, Wheatley PJ, Letarov A, Krisch HM: The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains. J Bacteriol 2005, 187(9):3188-3200.
9. Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW: Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol 2005, 3(5):e144.
10. Desplats C, Krisch HM: The diversity and evolution of the T4-type bacteriophages. Res Microbiol 2003, 154(4):259-267.
11. Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M: Improving gene annotation of complete viral genomes. Nucleic Acids Res 2003, 31(23):7041-7055.
12. Besemer J, Lomsadze A, Borodovsky M: GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001, 29(12):2607-2618.
13. Petrov V, Nolan JM, Bertrand C, Chin Levy D, Desplat C, Krisch H, Karam J: Divergence of the DNA replication genes among T4-like phage genomes. J Mol Biol 2006, in press:.
14. Edgar RS, Lielausis I: Temperature-Sensitive Mutants Of Bacteriophage T4d: Their Isolation And Genetic Characterization. Genetics 1964, 49:649-662.
15. Kawabata T, Arisaka F, Nishikawa K: Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches. Gene 2000, 259(1-2):223-233.
16. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH: CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002, 30(1):281-283.
17. Sickmier EA, Kreuzer KN, White SW: The crystal structure of the UvsW helicase from bacteriophage T4. Structure 2004, 12(4):583-592.
18. Kano-Sueoka T, Lobry JR, Sueoka N: Intra-strand biases in bacteriophage T4 genome. Gene 1999, 238(1):59-64.
19. Sharp PM, Li WH: The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15(3):1281-1295.
20. Xu W, Gauss P, Shen J, Dunn CA, Bessman MJ: The gene e.1 (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 2002, 277(26):23181-23185.
21. Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340(4):783-795.
22. Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305(3):567-580.
23. Magnani E, Sjolander K, Hake S: From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell 2004, 16(9):2265-2277.
24. Rice P, Longden I, Bleasby A: EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 2000, 16(6):276-277.
25. Tiemann B, Depping R, Gineikiene E, Kaliniene L, Nivinskas R, Ruger W: ModA and ModB, two ADP-ribosyltransferases encoded by bacteriophage T4: catalytic properties and mutation analysis. J Bacteriol 2004, 186(21):7262-7272.
26. Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH, Gourse RL: Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev 1999, 13(16):2134-2147.
27. Ross W, Aiyar SE, Salomon J, Gourse RL: Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J Bacteriol 1998, 180(20):5375-5383.
28. Estrem ST, Gaal T, Ross W, Gourse RL: Identification of an UP element consensus sequence for bacterial promoters. Proc Natl Acad Sci U S A 1998, 95(17):9761-9766.
29. Desplats C, Dez C, Tetart F, Eleaume H, Krisch HM: Snapshot of the genome of the pseudo-T-even bacteriophage RB49. J Bacteriol 2002, 184(10):2789-2804.
30. Hinton DM, Pande S, Wais N, Johnson XB, Vuthoori M, Makela A, Hook-Barnard I: Transcriptional takeover by sigma appropriation: remodelling of the sigma70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and co-activator AsiA. Microbiology 2005, 151(Pt 6):1729-1740.
31. Li N, Sickmier EA, Zhang R, Joachimiak A, White SW: The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the 'double wing' motif. Mol Microbiol 2002, 43(5):1079-1088.
32. Adelman K, Brody EN, Buckle M: Stimulation of bacteriophage T4 middle transcription by the T4 proteins MotA and AsiA occurs at two distinct steps in the transcription cycle. Proc Natl Acad Sci U S A 1998, 95(26):15247-15252.
33. Truncaite L, Piesiniene L, Kolesinskiene G, Zajanckauskaite A, Driukas A, Klausa V, Nivinskas R: Twelve new MotA-dependent middle promoters of bacteriophage T4: consensus sequence revised. J Mol Biol 2003, 327(2):335-346.
34. Hinton DM, Vuthoori S: Efficient inhibition of Escherichia coli RNA polymerase by the bacteriophage T4 AsiA protein requires that AsiA binds first to free sigma70. J Mol Biol 2000, 304(5):731-739.
35. Pineda M, Gregory BD, Szczypinski B, Baxter KR, Hochschild A, Miller ES, Hinton DM: A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a Transcription inhibitor and co-activator of bacteriophage T4. J Mol Biol 2004, 344(5):1183-1197.
36. Williams KP, Kassavetis GA, Herendeen DR, Geiduschek EP: Regulation of late-gene expression. In Molecular Biology of Bacteriophage T4 Edited by: Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Eiserling FA, Black LW, Spicer EK, Kutter E, Carlson K, Miller ES. Washington, DC , American Society for Microbiology; 1994:161-175.
37. Salzberg SL: ELPH, a motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites. [http://www.cbcb.umd.edu/software/ ELPH/].
38. Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL: Prediction of transcription terminators in bacterial genomes. J Mol Biol 2000, 301(1):27-33.
39. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964.
40. Nureki O, Niimi T, Muramatsu T, Kanno H, Kohno T, Florentz C, Giege R, Yokoyama S: Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli. J Mol Biol 1994, 236(3):710-724.
41. Guthrie C, McClain WH: Rare transfer ribonucleic acid essential for phage growth. Nucleotide sequence comparison of normal and mutant T4 isoleucine-accepting transfer ribonucleic acid. Biochemistry 1979, 18(17):3786-3795.
42. Fukada K, Abelson J: DNA sequence of a T4 transfer RNA gene cluster. J Mol Biol 1980, 139(3):377-391.
43. Muramatsu T, Nishikawa K, Nemoto F, Kuchino Y, Nishimura S, Miyazawa T, Yokoyama S: Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 1988, 336(6195):179-181.
44. Plunkett G, Rose DJ, Durfee TJ, Blattner FR: Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J Bacteriol 1999, 181(6):1767-1778.
45. Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, Brucker W, Kumar V, Kandasamy J, Keenan L, Bardarov S, Kriakov J, Lawrence JG, Jacobs WRJ, Hendrix RW, Hatfull GF: Origins of highly mosaic mycobacteriophage genomes. Cell 2003, 113(2):171-182.
46. Hendrix RW, Lawrence JG, Hatfull GF, Casjens S: The origins and ongoing evolution of viruses. Trends Microbiol 2000, 8(11):504-508.
47. Wu H, Sampson L, Parr R, Casjens S: The DNA site utilized by bacteriophage P22 for initiation of DNA packaging. Mol Microbiol 2002, 45(6):1631-1646.
48. Mosig G, Gewin J, Luder A, Colowick N, Vo D: Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer. Proc Natl Acad Sci U S A 2001, 98(15):8306-8311.
49. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL: Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999, 27(23):4636-4641.
50. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
51. Stein LD, Mungall C, Shu SQ, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S: The Generic Genome Browser: A Building Block for a Model Organism System Database. Genome Res 2002, 12(10):1599-1610.
52. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.
53. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30(1):276-280.
54. Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004, 14(6):1188-1190.