The genome and proteome of a Campylobacter coli bacteriophage vB-CcoM-IBB-35 reveal unusual features

Virology Journal

Volumn 9, Issue , 2012, Pages

  Carvalho, Carla M ^a   Kropinski, Andrew M ^b   Lingohr, Erika J ^b   Santos, Sílvio B ^a   King, Jonathan ^c   Azeredo, Joana ^a  

^a UNIVERSITY OF MINHO   (Portugal)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Bacteriophage; Campylobacter; Genome

Indexed keywords

PROTEOME; STRUCTURAL PROTEIN; VIRUS DNA; VIRUS PROTEIN;

ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; CAMPYLOBACTER COLI; DNA REPLICATION; DNA SEQUENCE; MORPHOGENESIS; NONHUMAN; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PYROSEQUENCING; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY; CHEMISTRY; GENE ORDER; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS; VIROLOGY; VIRUS GENE; VIRUS GENOME;

BACTERIA (MICROORGANISMS); CAMPYLOBACTER; CAMPYLOBACTER COLI; MYOVIRIDAE;

BACTERIOPHAGES; CAMPYLOBACTER COLI; DNA, VIRAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENE ORDER; GENES, VIRAL; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; MYOVIRIDAE; PROTEOME; SEQUENCE ANALYSIS, DNA; TANDEM MASS SPECTROMETRY; VIRAL PROTEINS;

EID: 84856191068     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-35     Document Type: Article

References (60)

1. Phage genomics: small is beautiful. Brüssow H, Hendrix RW, Cell 2002 108 13 16 10.1016/S0092-8674(01)00637-7 11792317 (Pubitemid 34137008)
2. Evidence for a lineage of virulent bacteriophages that target Campylobacter. Timms AR, Cambray-Young J, Scott AE, Petty NK, Connerton PL, Clarke L, Seeger K, Quail M, Cummings N, Maskell DJ, et al. BMC Genomics 2010 11 214 10.1186/1471-2164-11-214 20353581
3. Method for bacteriophage isolation against target Campylobacter strains. Carvalho C, Susano M, Fernandes E, Santos S, Gannon B, Nicolau A, Gibbs P, Teixeira P, Azeredo J, Lett Appl Microbiol 2010 50 192 197 10.1111/j.1472-765X. 2009.02774.x 20002571
4. The in vivo efficacy of two administration routes of a phage cocktail to reduce numbers of Campylobacter coli and Campylobacter jejuni in chickens. Carvalho C, Gannon B, Halfhide D, Santos S, Hayes C, Roe J, Azeredo J, BMC Microbiol 2010 10 232 10.1186/1471-2180-10-232 20809975
5. Isolation and characterization of Campylobacter bacteriophages from retail poultry. Atterbury RJ, Connerton PL, Dodd CER, Rees CED, Connerton IF, Appl Environ Microbiol 2003 69 4511 4518 10.1128/AEM.69.8.4511-4518.2003 12902236 (Pubitemid 36992906)
6. Isolation and characterization of bacteriophages specific for Campylobacter jejuni. Hwang S, Yun J, Kim K-P, Heu S, Lee S, Ryu S, Microbiol Immunol 2009 53 559 566 10.1111/j.1348-0421.2009.00163.x 19780969
7. Jumbo bacteriophages. Hendrix RW, Curr Top Microbiol Immunol 2009 328 229 240 10.1007/978-3-540-68618-7-7 19216440
8. A selective barrier to horizontal gene transfer in the T4-type bacteriophages that has preserved a core genome with the viral replication and structural genes. Filée J, Bapteste E, Susko E, Krisch HM, Mol Biol Evol 2006 23 1688 1696 10.1093/molbev/msl036 16782763 (Pubitemid 44309762)
9. Sambrook J, Russell DW, Molecular cloning: A Laboratory Manual Cold Spring Harbor: Cold Spring Harbor Laboratory Press 3 2001
10. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Moreira D, Nucleic Acids Res 1998 26 3309 3310 10.1093/nar/26.13.3309 9628935 (Pubitemid 28288935)
11. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Lowe TM, Eddy SR, Nucleic Acids Res 1997 25 955 964 10.1093/nar/25.5.955 9023104 (Pubitemid 27298263)
12. A combined transmembrane topology and signal peptide prediction method. Käll L, Krogh A, Sonnhammer ELL, J Mol Biol 2004 338 1027 1036 10.1016/j.jmb.2004.03.016 15111065 (Pubitemid 38542831)
13. Improved prediction of signal peptides: SignalP 3.0. Bendtsen JD, Nielsen H, von Heijne G, Brunak S, J Mol Biol 2004 340 783 795 10.1016/j.jmb.2004.05. 028 15223320 (Pubitemid 38829638)
14. Mfold web server for nucleic acid folding and hybridization prediction. Zuker M, Nucleic Acids Res 2003 31 3406 3415 10.1093/nar/gkg595 12824337 (Pubitemid 37442169)
15. Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. Darling AE, Mau B, Perna NT, PLoS One 2010 5 11147 10.1371/journal.pone.0011147 20593022
16. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. Zafar N, Mazumder R, Seto D, BMC bioinform 2002 3 12 10.1186/1471-2105-3-12 (Pubitemid 38751192)
17. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Shevchenko A, Wilm M, Vorm O, Mann M, Anal Chem 1996 68 850 858 10.1021/ac950914h 8779443 (Pubitemid 26101214)
18. Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Searle BC, Proteomics 2010 10 1265 1269 10.1002/pmic.200900437 20077414
19. Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea. Kropinski AM, Prangishvili D, Lavigne R, Environ Microbiol 2009 11 2775 2777 10.1111/j.1462-2920.2009.01970.x 19519870
20. The genome and proteome of a virulent Escherichia coli O157:H7 bacteriophage closely resembling Salmonella phage Felix O1. Villegas A, She Y-M, Kropinski AM, Lingohr EJ, Mazzocco A, Ojha S, Waddell TE, Ackermann H-W, Moyles DM, Ahmed R, Johnson RP, Virol J 2009 6 41 10.1186/1743-422X-6-41 19379502
21. GeneWiz browser: an interactive tool for visualizing sequenced chromosomes. Hallin PF, Stærfeldt H-H, Rotenberg E, Binnewies TT, Benham CJ, Ussery DW, Stand Genomic Sci 2009 1 204 215 21304658
22. An analysis of initiation codon utilization in the Domain Bacteria-concerns about the quality of bacterial genome annotation. Villegas A, Kropinski AM, Microbiol 2008 154 2559 2661 10.1099/mic.0.2008/021360-0
23. Bacteriophage T4 Genome. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ru W, Microbiol Mol Biol Rev 2003 67 86 156 10.1128/MMBR.67.1.86- 156.2003 12626685 (Pubitemid 36314786)
24. T4 phage deoxyribonucleotide-synthesizing enzyme complex. Further studies on enzyme composition and regulation. Allen JR, Lasser GW, Goldman Da, Booth JW, Mathews CK, J Biol Chem 1983 258 5746 5753 6853543 (Pubitemid 13096494)
25. Characteristics of a bacteriophage T4-induced complex synthesizing deoxyribonucleotides. Chiu CS, Cook KS, Greenberg GR, J Biol Chem 1982 257 15087 15097 6757252 (Pubitemid 13164859)
26. Bacteriophage T4 nrdA and nrdB genes, encoding ribonucleotide reductase, are expressed both separately and coordinately: characterization of the nrdB promoter. Tseng MJ, He P, Hilfinger JM, Greenberg GR, J Bacteriol 1990 172 6323 6332 2228963 (Pubitemid 20372772)
27. Bacteriophage T4 gene 55.9 encodes an activity required for anaerobic ribonucleotide reduction. Young P, Ohman M, Sjöberg BM, J Biol Chem 1994 269 27815 27818 7961708 (Pubitemid 24354501)
28. Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580. Young P, Andersson J, Sahlin M, Sjöberg BM, J Biol Chem 1996 271 20770 20775 10.1074/jbc.271.34.20770 8702830 (Pubitemid 26281862)
29. Biochemical characterization of two thymidylate synthases in Corynebacterium glutamicum NCHU 87078. Kan S-C, Liu J-S, Hu H-Y, Chang C-M, Lin W-D, Wang W-C, Hsu W-H, Biochimica et Biophysica Acta (BBA)-Proteins & Proteomic 2010 1804 1751 1759 10.1016/j.bbapap.2010.05.006 22289879
30. Isolation of mutants of bacteriophage T4 unable to induce thymidine kinase activity. II. Location of the structural gene for thymidine kinase. Chace KV, Hall DH, J Virol 1975 15 855 860 1090751
31. Recombination-dependent DNA replication in bacteriophage T4. Mosig G, Annu Rev Genet 1998 32 379 413 10.1146/annurev.genet.32.1.379 9928485 (Pubitemid 29045318)
32. Molecular architecture of bacteriophage T4. Mesyanzhinov VV, Leiman PG, Kostyuchenko VA, Kurochkina LP, Miroshnikov KA, Sykilinda NN, Shneider MM, Biochemistry Biokhimiia 2004 69 1190 1202 10.1007/s10541-005-0064-9 15627372 (Pubitemid 40050037)
33. Interactions of bacteriophage T4-coded primase (gp61) with the T4 replication helicase (gp41) and DNA in primosome formation. Jing DH, Dong F, Latham GJ, von Hippel PH, J Biol Chem 1999 274 27287 27298 10.1074/jbc.274.38. 27287 10480949 (Pubitemid 29440081)
34. Molecular architecture of the prolate head of bacteriophage T4. Fokine A, Chipman PR, Leiman PG, Mesyanzhinov VV, Rao VB, Rossmann MG, Proc Natl Acad Sci USA 2004 101 6003 6008 10.1073/pnas.0400444101 15071181 (Pubitemid 38520518)
35. Protein-protein interactions in the bacteriophage T4 replisome. The leading strand holoenzyme is physically linked to the lagging strand holoenzyme and the primosome. Ishmael FT, Trakselis MA, Benkovic SJ, J Biol Chem 2003 278 3145 3152 10.1074/jbc.M209858200 12427736 (Pubitemid 36801225)
36. Structure and mechanism of DNA topoisomerase II. Berger JM, Gamblin SJ, Harrison SC, Wang JC, Nature 1996 379 225 232 10.1038/379225a0 8538787 (Pubitemid 26025206)
37. Bacteriophage T4 UvsW protein is a helicase involved in recombination, repair and the regulation of DNA replication origins. Carles-Kinch K, George JW, Kreuzer KN, EMBO J 1997 16 4142 4151 10.1093/emboj/16.13.4142 9233823 (Pubitemid 27281029)
38. UvsW protein regulates replication by unwinding R-loops UvsW protein regulates bacteriophage T4 origin-dependent replication by unwinding R-loops. Dudas KC, Kreuzer KN, Mol Cell Biol 2001 21 2706 2715 10.1128/MCB.21.8.2706- 2715.2001 11283250 (Pubitemid 32244915)
39. Bacteriophage T4 gp2 interferes with cell viability and with bacteriophage lambda Red recombination. Appasani K, Thaler DS, Goldberg EB, J Bacteriol 1999 181 1352 1355 9973367 (Pubitemid 29119579)
40. Bacteriophage T4 self-assembly: in vitro reconstitution of recombinant gp2 into infectious phage. Wang GR, Vianelli A, Goldberg EB, J Bacteriol 2000 182 672 679 10.1128/JB.182.3.672-679.2000 10633100 (Pubitemid 30053997)
41. Assembly and infection process of bacteriophage T4. Arisaka F, Chaos (Woodbury, NY) 2005 15 047502 10.1063/1.2142136 (Pubitemid 43037851)
42. Isolation and characterization of T4 bacteriophage gp17 terminase, a large subunit multimer with enhanced ATPase activity. Baumann RG, Black LW, J Biol Chem 2003 278 4618 4627 10.1074/jbc.M208574200 12466275 (Pubitemid 36800960)
43. The functional domains of bacteriophage t4 terminase. Kanamaru S, Kondabagil K, Rossmann MG, Rao VB, J Biol Chem 2004 279 40795 40801 10.1074/jbc.M403647200 15265872 (Pubitemid 39287676)
44. Complete genome of the broad-host-range Erwinia amylovora phage phiEa21-4 and its relationship to Salmonella phage Felix O1. Lehman SM, Kropinski AM, Castle AJ, Svircev AM, Appl Environ Microbiol 2009 75 2139 2147 10.1128/AEM.02352-08 19181832
45. Complete genomic sequence of bacteriophage Felix O1. Whichard JM, Weigt LA, Borris DJ, Li LL, Zhang Q, Kapur V, Pierson FW, Lingohr EJ, She Y-M, Kropinski AM, Sriranganathan N, Viruses 2010 2 710 730 10.3390/v2030710 21994654
46. Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function. Friedrich NC, Torrents E, Gibb EA, Sahlin M, Sjöberg B-M, Edgell DR, Proc Natl Acad Sci USA 2007 104 6176 6181 10.1073/pnas.0609915104 17395719 (Pubitemid 47186068)
47. Commentary lightning strikes twice: intron-intein coincidence. Derbyshire V, Belfort M, Proc Natl Acad Sci USA 1998 95 1356 1357 10.1073/pnas.95.4.1356 9465018 (Pubitemid 28103395)
48. Group I introns and inteins: disparate origins but convergent parasitic strategies. Raghavan R, Minnick MF, J Bacteriol 2009 191 6193 6202 10.1128/JB.00675-09 19666710
49. Distribution, sequence homology, and homing of group I introns among T-even-like bacteriophages: evidence for recent transfer of old introns. Sandegren L, Sjöberg B-M, J Biol Chem 2004 279 22218 22227 10.1074/jbc.M400929200 15026408 (Pubitemid 38679417)
50. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE, Nucleic Acids Res 2001 29 1097 1106 10.1093/nar/29.5.1097 11222759 (Pubitemid 32186195)
51. S-adenosylmethionine as an oxidant: the radical SAM superfamily. Wang SC, Frey PA, Trends Biochem Sci 2007 32 101 110 10.1016/j.tibs.2007.01.002 17291766 (Pubitemid 46367690)
52. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, et al. Nucleic Acids Res 2008 36 465 W469 10.1093/nar/gkn180 18424797
53. Phages will out: strategies of host cell lysis. Young I, Wang I, Roof WD, Trends Microbiol 2000 8 120 128 10.1016/S0966-842X(00)01705-4 10707065 (Pubitemid 30155487)
54. Bacteriophage lysis: mechanism and regulation. Young R, Microbiol Rev 1992 56 430 481 1406491
55. Holins: form and function in bacteriophage lysis. Young R, Bläsi U, FEMS Microbiol Rev 1995 17 191 205 10.1016/0168-6445(94)00079-4 7669346
56. Genetic analysis of the T4 holin: timing and topology. Ramanculov E, Young R, Gene 2001 265 25 36 10.1016/S0378-1119(01)00365-1 11255004 (Pubitemid 32209247)
57. LmbE proteins from Bacillus cereus are de-N-acetylases with broad substrate specificity and are highly similar to proteins in Bacillus anthracis. Deli A, Koutsioulis D, Fadouloglou VE, Spiliotopoulou P, Balomenou S, Arnaouteli S, Tzanodaskalaki M, Mavromatis K, Kokkinidis M, Bouriotis V, FEBS J 2010 277 2740 2753 10.1111/j.1742-4658.2010.07691.x 20491912
58. Deacetylation reaction catalyzed by Salmonella phage c341 and its baseplate parts. Iwashita S, Kanegasaki S, J Biol Chem 1976 251 5361 5365 956188
59. Disruption of Vi bacteriophage III and localization of its deacetylase activity. Kwiatkowski B, Beilharz H, Stirm S, J Gen Virol 1975 29 267 280 10.1099/0022-1317-29-3-267 1468
60. Overexpression of UDP-glucose dehydrogenase in Escherichia coli results in decreased biosynthesis of K5 polysaccharide. Roman E, Roberts I, Lidholt K, Kusche-Gullberg M, Biochem J 2003 374 767 772 10.1042/BJ20030365 12775214 (Pubitemid 37163923)