The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination

Virology Journal

Volumn 7, Issue , 2010, Pages

  Deschavanne, Patrick ^a   Dubow, Michael S ^b   Regeard, Christophe ^b  

^a INSERM   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE; CAUDOVIRIDAE; ESCHERICHIA COLI; GENE SEQUENCE; GENOMICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; TAXONOMY; VIROGENESIS; VIRUS CELL INTERACTION; BACTERIUM; CHROMOSOME MAP; CLASSIFICATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HOST PATHOGEN INTERACTION; SPECIES DIFFERENCE; VIROLOGY; VIRUS GENOME;

BACTERIA; BACTERIOPHAGES; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOMICS; HOST-PATHOGEN INTERACTIONS; PHYLOGENY; SPECIES SPECIFICITY;

EID: 77954549736     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-7-163     Document Type: Article

References (111)

1. Bacteriophage genomics. GF Hatfull, Curr Opin Microbiol 2008 11 5 447 53 10.1016/j.mib.2008.09.004 18824125
2. Prokaryotes: the unseen majority. WB Whitman DC Coleman WJ Wiebe, Proc Natl Acad Sci USA 1998 95 12 6578 83 10.1073/pnas.95.12.6578 9618454
3. Virioplankton: viruses in aquatic ecosystems. KE Wommack RR Colwell, Microbiol Mol Biol Rev 2000 64 1 69 114 10.1128/MMBR.64.1.69-114.2000 10704475
4. Ecology of prokaryotic viruses. MG Weinbauer, FEMS Microbiol Rev 2004 28 2 127 81 10.1016/j.femsre.2003.08.001 15109783
5. Marine viruses - major players in the global ecosystem. CA Suttle, Nat Rev Microbiol 2007 5 10 801 12 10.1038/nrmicro1750 17853907
6. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. TF Thingstad R Lignell, Aquat Microb Ecol 1997 13 19 27 10.3354/ame013019
7. Are viruses driving microbial diversification and diversity? MG Weinbauer F Rassoulzadegan, Environ Microbiol 2004 6 1 1 11 10.1046/j.1462-2920.2003. 00539.x 14686936
8. Phage as agents of lateral gene transfer. C Canchaya G Fournous S Chibani-Chennoufi ML Dilmann H Brussow, Curr Opin Microbiol 2003 6 417 424 10.1016/S1369-5274(03)00086-9 12941415
9. Lysogenic conversion by a filamentous phage encoding cholera toxin. MK Waldor JJ Mekalanos, Science 1996 272 5270 1910 4 10.1126/science.272.5270.1910 8658163
10. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? M Ohnishi K Kurokawa T Hayashi, Trends Microbiol 2001 9 10 481 5 10.1016/S0966-842X(01)02173-4 11597449
11. The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. SJ Williamson DB Rusch S Yooseph AL Halpern KB Heidelberg JI Glass D Fadrosh CS Miller G Sutton M Frazier JC Venter, PLoS One 2008 3 1 1456 10.1371/journal.pone.0001456 18213365
12. Imbroglios of Viral Taxonomy: Genetic Exchange and Failings of Phenetic Approaches. JG Lawrence GF Hatfull RW Hendrix, J Bact 2002 184 4891 4905 10.1128/JB.184.17.4891-4905.2002 12169615
13. Phage Genomics: Small Is Beautiful. H Brüssow RW Hendrix, Cell 2002 108 13 16 10.1016/S0092-8674(01)00637-7 11792317
14. Nucleotide sequence of bacteriophage phi X174 DNA. F Sanger GM Air BG Barrell NL Brown AR Coulson CA Fiddes CA Hutchison PM Slocombe M Smith, Nature 1977 265 5596 687 95 10.1038/265687a0 870828
15. Propagating the missing bacteriophages: a large bacteriophage in a new class. P Serwer SJ Hayes JA Thomas SC Hardies, Virol J 2007 4 21 10.1186/1743-422X-4-21 17324288
16. 5500 Phages examined in the electron microscope. HW Ackermann, Arch Virol 2007 152 2 227 43 10.1007/s00705-006-0849-1 17051420
17. Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J Dorscht J Klumpp R Bielmann M Schmelcher Y Born M Zimmer R Calendar MJ Loessner, J Bacteriol 2009 191 23 7206 15 10.1128/JB.01041-09 19783628
18. Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. GF Hatfull SG Cresawn RW Hendrix, Res Microbiol 2008 159 5 332 9 10.1016/j.resmic.2008.04.008 18653319
19. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. T Kwan J Liu M DuBow P Gros J Pelletier, Proc Natl Acad Sci USA 2005 102 14 5174 9 10.1073/pnas.0501140102 15788529
20. Portal protein diversity and phage ecology. MB Sullivan ML Coleman V Quinlivan JE Rosenkrantz AS Defrancesco G Tan R Fu JA Lee JB Waterbury JP Bielawski SW Chisholm, Environ Microbiol 2008 10 10 2810 23 10.1111/j.1462-2920. 2008.01702.x 18673386
21. Dinucleotide relative abundance extremes: a genomic signature. S Karlin C Burge, Trends In Genetics 1995 11 283 290 10.1016/S0168-9525(00)89076-9 7482779
22. Compositional biases of bacterial genomes and evolutionary implications. S Karlin J Mrzek AM Campbell, J Bact 1997 179 3899 3913 9190805
23. Genome signature comparisons among prokaryote, plasmid and mitochondrial DNA. A Campbell J Mrzek S Karlin, Proc Nat Acad Sci USA 1999 96 9184 9189 10.1073/pnas.96.16.9184 10430917
24. Use of the genomic signature in bacterial classification and identification. T Coenye P Vandamme, Syst Appl Microbiol 2004 27 2 175 85 10.1078/072320204322881790 15046306
25. The reach of the genome signature in prokaryotes. Passel van EE Kuramae AC Luyf A Bart T Boekhout, BMC Evol Biol 2006 6 84 10.1186/1471-2148-6-84 17040564
26. Similarities and dissimilarities of phage genomes. BE Blaisdell AM Campbell S Karlin, Proc Natl Acad Sci USA 1996 93 12 5854 9 10.1073/pnas.93.12. 5854 8650182
27. Genomic signature: characterization and classification of species assessed by Chaos Game Representation of sequences. PJ Deschavanne A Giron J Vilain G Fagot B Fertil, Molecular Biology and Evolution 1999 16 1391 1399 10563018
28. Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis. V Rosas-Magallanes P Deschavanne L Quintana-Murci R Brosch B Gicquel O Neyrolles, Mol Biol Evol 2006 23 1129 1135 10.1093/molbev/msj120 16520338
29. Detection and characterization of horizontal transfers in prokaryotes using genomic signature. C Dufraigne B Fertil S Lespinats A Giron P Deschavanne, Nucleic Acids Res 2005 33 1 6 10.1093/nar/gni004 15653627
30. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. S Karlin, Trends in Microbiology 2001 9 7 335 343 10.1016/S0966-842X(01)02079-0 11435108
31. Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195. C Regeard J Maillard C Dufraigne P Deschavanne C Holliger, Appl Environ Microbiol 2005 71 6 2955 61 10.1128/AEM.71.6.2955-2961.2005 15932990
32. Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. J Becq MC Gutierrez V Rosas-Magallanes J Rauzier B Gicquel O Neyrolles P Deschavanne, Mol Biol Evol 2007 24 8 1861 71 10.1093/molbev/msm111 17545187
33. An acquisition account of genomic islands based on genome signature comparisons. MW van Passel A Bart HH Thygesen AC Luyf AH van Kampen A van der Ende, BMC Genomics 2005 6 163 10.1186/1471-2164-6-163 16297239
34. Identification of prophages in bacterial genomes by dinucleotide relative abundance difference. KV Srividhya V Alaguraj G Poornima D Kumar GP Singh L Raghavenderan AV Katta P Mehta S Krishnaswamy, PLoS One 2007 2 11 1193 10.1371/journal.pone.0001193 18030328
35. Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. DT Pride TM Wassenaar C Ghose MJ Blaser, BMC Genomics 2006 7 8 10.1186/1471-2164-7-8 16417644
36. Application of tetranucleotide frequencies for the assignment of genomic fragments. H Teeling A Meyerdierks M Bauer R Amann FO Glockner, Environ Microbiol 2004 6 9 938 47 10.1111/j.1462-2920.2004.00624.x 15305919
37. The marine viromes of four oceanic regions. FE Angly B Felts M Breitbart P Salamon RA Edwards C Carlson AM Chan M Haynes S Kelley H Liu JM Mahaffy JE Mueller J Nulton R Olson R Parsons S Rayhawk CA Suttle F Rohwer, PLoS Biol 2006 4 11 368 10.1371/journal.pbio.0040368 17090214
38. New dimensions of the virus world discovered through metagenomics. DM Kristensen AR Mushegian VV Dolja EV Koonin, Trends Microbiol 2009 19942437
39. Diversity among the tailed-bacteriophages that infect the Enterobacteriaceae. SR Casjens, Res Microbiol 2008 159 5 340 8 10.1016/j.resmic.2008.04.005 18550341
40. Complete genomic sequence of bacteriophage phiEcoM-GJ1, a novel phage that has myovirus morphology and a podovirus-like RNA polymerase. N Jamalludeen AM Kropinski RP Johnson E Lingohr J Harel CL Gyles, Appl Environ Microbiol 2008 74 2 516 25 10.1128/AEM.00990-07 18039824
41. Identification of host receptor and receptor-binding module of a newly sequenced T5-like phage EPS7. J Hong KP Kim S Heu SJ Lee S Adhya S Ryu, FEMS Microbiol Lett 2008 289 2 202 9 10.1111/j.1574-6968.2008.01397.x 19025561
42. Complete genome sequence of bacteriophage T5. J Wang Y Jiang M Vincent Y Sun H Yu Q Bao H Kong S Hu, Virology 2005 332 1 45 65 10.1016/j.virol.2004.10. 049 15661140
43. Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. D Savalia LF Westblade M Goel L Florens P Kemp N Akulenko O Pavlova JC Padovan BT Chait MP Washburn HW Ackermann A Mushegian T Gabisonia I Molineux K Severinov, J Mol Biol 2008 377 3 774 89 10.1016/j.jmb.2007.12.077 18294652
44. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. GJ Morgan GF Hatfull S Casjens RW Hendrix, J Mol Biol 2002 317 3 337 59 10.1006/jmbi.2002.5437 11922669
45. Amelioration of bacterial genomes: rates of change and exchange. J Lawrence H Ochman, Journal of Molecular Evolution 1997 44 383 397 10.1007/PL00006158 9089078
46. Gene amelioration demonstrated: the journey of nascent genes in bacteria. PR Marri GB Golding, Genome 2008 51 2 164 8 10.1139/G07-105 18356951
47. Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. S Labrie S Moineau, Virology 2002 296 2 308 20 10.1006/viro.2002.1401 12069529
48. Genome Structure of Mycobacteriophage D29: Implications for Phage Evolution. ME Ford GJ Sarkis AE Belanger RW Hendrix GF Hatfull, J Mol Biol 1998 279 143 164 10.1006/jmbi.1997.1610 9636706
49. The genome and proteome of coliphage T1. MD Roberts NL Martin AM Kropinski, Virology 2004 318 1 245 66 10.1016/j.virol.2003.09.020 14972552
50. Predominance of clones carrying Panton-Valentine leukocidin genes among methicillin-resistant Staphylococcus aureus strains isolated in Japanese hospitals from 1979 to 1985. XX Ma T Ito P Chongtrakool K Hiramatsu, J Clin Microbiol 2006 44 12 4515 27 10.1128/JCM.00985-06 17050818
51. Two different Panton-Valentine leukocidin phage lineages predominate in Japan. XX Ma T Ito Y Kondo M Cho Y Yoshizawa J Kaneko A Katai M Higashiide S Li K Hiramatsu, J Clin Microbiol 2008 46 10 3246 58 10.1128/JCM.00136-08 18685010
52. Prophages of Staphylococcus aureus Newman and their contribution to virulence. T Bae T Baba K Hiramatsu O Schneewind, Mol Microbiol 2006 62 4 1035 47 10.1111/j.1365-2958.2006.05441.x 17078814
53. Phage conversion of Panton-Valentine leukocidin in Staphylococcus aureus: molecular analysis of a PVL-converting phage, phiSLT. S Narita J Kaneko J Chiba Y Piemont S Jarraud J Etienne Y Kamio, Gene 2001 268 1-2 195 206 10.1016/S0378-1119(01)00390-0 11368915
54. Complete nucleotide sequence and molecular characterization of two lytic Staphylococcus aureus phages: 44AHJD and P68. D Vybiral M Takac M Loessner A Witte U von Ahsen U Blasi, FEMS Microbiol Lett 2003 219 2 275 83 10.1016/S0378-1097(03)00028-4 12620632
55. Prophage, phiPV83-pro, carrying panton-valentine leukocidin genes, on the Staphylococcus aureus P83 chromosome: comparative analysis of the genome structures of phiPV83-pro, phiPVL, phi11, and other phages. D Zou J Kaneko S Narita Y Kamio, Biosci Biotechnol Biochem 2000 64 12 2631 43 10.1271/bbb.64.2631 11210127
56. Comparative Genomic Analysis of 60 Mycobacteriophage Genomes: Genome Clustering, Gene Acquisition, and Gene Size. GF Hatfull D Jacobs-Sera JG Lawrence WH Pope DA Russell CC Ko RJ Weber MC Patel KL Germane RH Edgar NN Hoyte CA Bowman AT Tantoco EC Paladin MS Myers AL Smith MS Grace TT Pham MB O'Brien AM Vogelsberger AJ Hryckowian JL Wynalek H Donis-Keller MW Bogel CL Peebles SG Cresawn RW Hendrix, J Mol Biol 2010 20064525
57. Origins of Highly Mosaic Mycobacteriophage Genomes. ML Pedulla ME Ford JM Houtz T Karthikeyan C Wadsworth JA Lewis D Jacobs-Sera J Falbo J Gross NR Pannunzio W Brucker V Kumar J Kandasamy L Keenan S Bardarov J Kriakov JG Lawrence WR Jacobs RW Hendrix GF Hatfull, Cell 2003 113 171 182 10.1016/S0092-8674(03)00233-2 12705866
58. Genome organization and characterization of mycobacteriophage Bxb1. J Mediavilla S Jain J Kriakov ME Ford RL Duda WR Jacobs Jr RW Hendrix GF Hatfull, Mol Microbiol 2000 38 5 955 70 10.1046/j.1365-2958.2000.02183.x 11123671
59. Mycobacteriophage TM4: genome structure and gene expression. ME Ford C Stenstrom RW Hendrix GF Hatfull, Tuber Lung Dis 1998 79 2 63 73 10.1054/tuld.1998.0007 10645443
60. Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination. P Morris LJ Marinelli D Jacobs-Sera RW Hendrix GF Hatfull, J Bacteriol 2008 190 6 2172 82 10.1128/JB.01657-07 18178732
61. Comparative genomic analysis of mycobacteriophage Tweety: evolutionary insights and construction of compatible site-specific integration vectors for mycobacteria. TT Pham D Jacobs-Sera ML Pedulla RW Hendrix GF Hatfull, Microbiology 2007 153 Pt 8 2711 23 10.1099/mic.0.2007/008904-0 17660435
62. Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. T Kwan J Liu M Dubow P Gros J Pelletier, J Bacteriol 2006 188 3 1184 7 10.1128/JB.188.3.1184-1187.2006 16428425
63. DNA sequence-based analysis of the Pseudomonas species. M Mulet J Lalucat E Garcia-Valdes, Environ Microbiol 2010 20192968
64. Genome sequence comparison and superinfection between two related Pseudomonas aeruginosa phages, D3112 and MP22. YJ Heo IY Chung KB Choi GW Lau YH Cho, Microbiology 2007 153 Pt 9 2885 95 10.1099/mic.0.2007/007260-0 17768233
65. Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa. MD Braid JL Silhavy CL Kitts RJ Cano MM Howe, J Bacteriol 2004 186 19 6560 74 10.1128/JB.186.19.6560-6574.2004 15375138
66. Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the phiKMV subgroup within the T7 supergroup. PJ Ceyssens R Lavigne W Mattheus A Chibeu K Hertveldt J Mast J Robben G Volckaert, J Bacteriol 2006 188 19 6924 31 10.1128/JB.00831-06 16980495
67. Characteristics of a novel Pseudomonas aeruginosa bacteriophage, PAJU2, which is genetically related to bacteriophage D3. J Uchiyama M Rashel T Matsumoto Y Sumiyama H Wakiguchi S Matsuzaki, Virus Res 2009 139 1 131 4 10.1016/j.virusres.2008.10.005 19010363
68. The genome and structural proteome of YuA, a new Pseudomonas aeruginosa phage resembling M6. PJ Ceyssens V Mesyanzhinov N Sykilinda Y Briers B Roucourt R Lavigne J Robben A Domashin K Miroshnikov G Volckaert K Hertveldt, J Bacteriol 2008 190 4 1429 35 10.1128/JB.01441-07 18065532
69. Whole genome sequencing of a novel temperate bacteriophage of P. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome. Y Tan K Zhang X Rao X Jin J Huang J Zhu Z Chen X Hu X Shen L Wang F Hu, Cell Microbiol 2007 9 2 479 91 10.1111/j.1462-5822.2006. 00804.x 16965514
70. The intron-containing genome of the lytic Pseudomonas phage LUZ24 resembles the temperate phage PaP3. PJ Ceyssens K Hertveldt HW Ackermann JP Noben M Demeke G Volckaert R Lavigne, Virology 2008 377 2 233 8 10.1016/j.virol.2008.04.038 18519145
71. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. AM Kropinski, J Bacteriol 2000 182 21 6066 74 10.1128/JB.182.21.6066-6074.2000 11029426
72. DNA sequence of satellite bacteriophage P4. C Halling R Calendar GE Christie EC Dale G Deho S Finkel J Flensburg D Ghisotti ML Kahn KB Lane,, et al. Nucleic Acids Res 1990 18 6 1649 10.1093/nar/18.6.1649 2183201
73. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. MI Pajunen MR Elizondo M Skurnik J Kieleczawa IJ Molineux, J Mol Biol 2002 319 5 1115 32 10.1016/S0022-2836(02)00384-4 12079351
74. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. AJ Clark W Inwood T Cloutier TS Dhillon, J Mol Biol 2001 311 4 657 79 10.1006/jmbi.2001.4868 11518522
75. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. D Scholl C Merril, J Bacteriol 2005 187 24 8499 503 10.1128/JB.187.24.8499-8503.2005 16321955
76. Genomic Sequences of Bacteriophages HK97 and HK022: Pervasive Genetic Mosaicism in the Lambdoid Bacteriophages. RJ Juhala ME Ford RL Duda A Youlton GF Hatfull RW Hendrix, J Mol Biol 2000 299 27 51 10.1006/jmbi.2000.3729 10860721
77. Coliphage BA14: a new relative of phage T7. H Mertens R Hausmann, J Gen Virol 1982 62 Pt 2 331 41 10.1099/0022-1317-62-2-331 6292354
78. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. JJ Dunn FW Studier, J Mol Biol 1983 166 4 477 535 10.1016/S0022-2836(83)80282-4 6864790
79. The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. J Recktenwald H Schmidt, Infect Immun 2002 70 4 1896 908 10.1128/IAI.70.4.1896-1908.2002 11895953
80. Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. D Scholl J Kieleczawa P Kemp J Rush CC Richardson C Merril S Adhya IJ Molineux, J Mol Biol 2004 335 5 1151 71 10.1016/j.jmb.2003.11.035 14729334
81. Evolution of bacteriophages infecting encapsulated bacteria: lessons from Escherichia coli K1-specific phages. K Stummeyer D Schwarzer H Claus U Vogel R Gerardy-Schahn M Muhlenhoff, Mol Microbiol 2006 60 5 1123 35 10.1111/j.1365-2958.2006.05173.x 16689790
82. The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1. A Wietzorrek H Schwarz C Herrmann V Braun, J Bacteriol 2006 188 4 1419 36 10.1128/JB.188.4.1419-1436.2006 16452425
83. Nucleotide sequence of bacteriophage lambda DNA. F Sanger AR Coulson GF Hong DF Hill GB Petersen, J Mol Biol 1982 162 4 729 73 10.1016/0022-2836(82) 90546-0 6221115
84. The TolC protein of Escherichia coli serves as a cell-surface receptor for the newly characterized TLS bacteriophage. GJ German R Misra, J Mol Biol 2001 308 4 579 85 10.1006/jmbi.2001.4578 11350161
85. The Shiga toxin 1-converting bacteriophage BP-4795 encodes an NleA-like type III effector protein. K Creuzburg J Recktenwald V Kuhle S Herold M Hensel H Schmidt, J Bacteriol 2005 187 24 8494 8 10.1128/JB.187.24.8494-8498.2005 16321954
86. Genome analysis of a novel Shiga toxin 1 (Stx1)-converting phage which is closely related to Stx2-converting phages but not to other Stx1-converting phages. T Sato T Shimizu M Watarai M Kobayashi S Kano T Hamabata Y Takeda S Yamasaki, J Bacteriol 2003 185 13 3966 71 10.1128/JB.185.13.3966-3971.2003 12813092
87. Sequence analysis of Stx2-converting phage VT2-Sa shows a great divergence in early regulation and replication regions. H Miyamoto W Nakai N Yajima A Fujibayashi T Higuchi K Sato A Matsushiro, DNA Res 1999 6 4 235 40 10.1093/dnares/6.4.235 10492170
88. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. G Plunkett DJ Rose TJ Durfee FR Blattner, J Bacteriol 1999 181 6 1767 78 10074068
89. Distinctiveness of the genomic sequence of Shiga toxin 2-converting phage isolated from Escherichia coli O157:H7 Okayama strain as compared to other Shiga toxin 2-converting phages. T Sato T Shimizu M Watarai M Kobayashi S Kano T Hamabata Y Takeda S Yamasaki, Gene 2003 309 1 35 48 10.1016/S0378-1119(03) 00487-6 12727356
90. Rothman-Denes, The bacteriophage N4-coded single-stranded DNA-binding protein (N4SSB) is the transcriptional activator of Escherichia coli RNA polymerase at N4 late promoters. NY Cho M Choi LB Rothman-Denes, J Mol Biol 1995 246 4 461 71 10.1006/jmbi.1994.0098 7877167
91. Genome of bacteriophage P1. MB Lobocka DJ Rose G Plunkett M Rusin A Samojedny H Lehnherr MB Yarmolinsky FR Blattner, J Bacteriol 2004 186 21 7032 68 10.1128/JB.186.21.7032-7068.2004 15489417
92. Snapshot of the genome of the pseudo-T-even bacteriophage RB49. C Desplats C Dez F Tetart H Eleaume HM Krisch, J Bacteriol 2002 184 10 2789 804 10.1128/JB.184.10.2789-2804.2002 11976309
93. Bacteriophage T4 genome. ES Miller E Kutter G Mosig F Arisaka T Kunisawa W Ruger, Microbiol Mol Biol Rev 2003 67 1 86 156 table of contents 10.1128/MMBR.67.1.86-156.2003 12626685
94. Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli. S Zuber C Ngom-Bru C Barretto A Bruttin H Brussow E Denou, J Bacteriol 2007 189 22 8206 14 10.1128/JB.00838-07 17693496
95. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. T Kwan J Liu M DuBow P Gros J Pelletier, Proc Natl Acad Sci USA 2005 102 14 5174 9 10.1073/pnas.0501140102 15788529
96. Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage phiPVL carrying Panton-Valentine leukocidin genes. J Kaneko T Kimura S Narita T Tomita Y Kamio, Gene 1998 215 1 57 67 10.1016/S0378-1119(98)00278-9 9666077
97. Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325. JJ Iandolo V Worrell KH Groicher Y Qian R Tian S Kenton A Dorman H Ji S Lin P Loh S Qi H Zhu BA Roe, Gene 2002 289 1-2 109 18 10.1016/S0378-1119(02)00481-X 12036589
98. Experimental protection of mice against lethal Staphylococcus aureus infection by novel bacteriophage phi MR11. S Matsuzaki M Yasuda H Nishikawa M Kuroda T Ujihara T Shuin Y Shen Z Jin S Fujimoto MD Nasimuzzaman H Wakiguchi S Sugihara T Sugiura S Koda A Muraoka S Imai, J Infect Dis 2003 187 4 613 24 10.1086/374001 12599078
99. Phage conversion of exfoliative toxin A production in Staphylococcus aureus. T Yamaguchi T Hayashi H Takami K Nakasone M Ohnishi K Nakayama S Yamada H Komatsuzawa M Sugai, Mol Microbiol 2000 38 4 694 705 10.1046/j.1365-2958.2000. 02169.x 11115106
100. Transducing particles of Staphylococcus aureus pathogenicity island SaPI1 are comprised of helper phage-encoded proteins. SM Tallent TB Langston RG Moran GE Christie, J Bacteriol 2007 189 20 7520 4 10.1128/JB.00738-07 17693489
101. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. M Kuroda,, et al. Lancet 2001 357 9264 1225 40 10.1016/S0140-6736(00)04403-2 11418146
102. Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G+C content. S O'Flaherty A Coffey R Edwards W Meaney GF Fitzgerald RP Ross, J Bacteriol 2004 186 9 2862 71 10.1128/JB.186.9.2862-2871.2004 15090528
103. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. GF Hatfull ML Pedulla D Jacobs-Sera PM Cichon A Foley ME Ford RM Gonda JM Houtz AJ Hryckowian VA Kelchner S Namburi KV Pajcini MG Popovich DT Schleicher BZ Simanek AL Smith GM Zdanowicz V Kumar CL Peebles WR Jacobs Jr JG Lawrence RW Hendrix, PLoS Genet 2006 2 6 92 10.1371/journal.pgen. 0020092 16789831
104. Genetic transformation of mycobacteria. GF Hatfull, Trends in Microbiology 1993 310 4 10.1016/0966-842X(93)90008-F 8162416
105. The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. K Nakayama S Kanaya M Ohnishi Y Terawaki T Hayashi, Mol Microbiol 1999 31 2 399 419 10.1046/j.1365-2958.1999.01158.x 10027959
106. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. ME Zegans JC Wagner KC Cady DM Murphy JH Hammond GA O'Toole, J Bacteriol 2009 191 1 210 9 10.1128/JB.00797-08 18952788
107. Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. PW Wang L Chu DS Guttman, J Bacteriol 2004 186 2 400 10 10.1128/JB.186.2.400-410.2004 14702309
108. The genome of bacteriophage phiKMV, a T7-like virus infecting Pseudomonas aeruginosa. R Lavigne MV Burkal'tseva J Robben NN Sykilinda LP Kurochkina B Grymonprez B Jonckx VN Krylov VV Mesyanzhinov G Volckaert, Virology 2003 312 1 49 59 10.1016/S0042-6822(03)00123-5 12890620
109. The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116. M Byrne AM Kropinski, Gene 2005 346 187 94 10.1016/j.gene.2004.11.001 15716012
110. Genome comparison of Pseudomonas aeruginosa large phages. K Hertveldt R Lavigne E Pleteneva N Sernova L Kurochkina R Korchevskii J Robben V Mesyanzhinov VN Krylov G Volckaert, J Mol Biol 2005 354 3 536 45 10.1016/j.jmb.2005.08.075 16256135
111. The genome of bacteriophage phiKZ of Pseudomonas aeruginosa. VV Mesyanzhinov J Robben B Grymonprez VA Kostyuchenko MV Bourkaltseva NN Sykilinda VN Krylov G Volckaert, J Mol Biol 2002 317 1 1 19 10.1006/jmbi.2001.5396 11916376