Coevolution of bacteria and their viruses

Folia Microbiologica

Volumn 58, Issue 3, 2013, Pages 177-186

  Golais, František ^a   Hollý, Jaroslav ^a   Vítkovská, Jana ^a  

^a Physics and Informatics   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84876448219     PISSN: 00155632     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12223-012-0195-5     Document Type: Review

References (79)

1. Akhverdyan V, Guk ER, Tokmakova I, Stoynova NV, Yomantas YAV, Mashko SV (2011) Application of the phage Mu-driven system for the integration/amplification of target gene in the chromosome of engineered Gram-negative bacteria-mini review. Appl Microbiol Biot 91: 857-871.
2. Appleyard RK, McGregor JF, Baird KM (1956) Mutations to extended host range and the occurrence of phenotypic mixing in the temperate coliphage lambda. Virology 2: 556-574.
3. Asadulghani MD, Yoshitoshi O, Ooka T, Itoh T, Saxaguchi A, Iguchi A, Nakayama K, Hayashi T (2009) The defective prophage pool of Escherichia coli O157: prophage-prophage interactions potentiate horizontal transfer of virulence determinants. PloS Pathog 5(5): doi: 10. 1371/journal/ppat.1000408.
4. Bohannan BJM, Lenski RE (2000) Linking genetic change to community evolution: insights from studies of bacteria and bacteriophages. Ecol Lett 3: 362-377.
5. Brüssow H (2008) Phage-bacterium coevolution and application for bacterial pathogenesis. In: Hensel M (ed) Horizontal gene transfer in the evolution of pathogenesis. Cambridge University Press, Cambridge, pp 49-78.
6. Brüssow H, Canchaya C, Hardt WD (2004) Phages and evolution of bacterial pathogens from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68: 560-602.
7. Canchaya C, Proux C, Fourmous G, Bruttin A, Brüssow H (2003) Prophage genomics. Microbiol Mol Biol R 67: 238-276.
8. Chopin MC, Chopin A, Bidnenko E (2005) Phage abortive infection in lactococci: variation on a theme. Curr Opin Microbiol 8: 473-479.
9. Court DL, Oppenheim AB, Adhya SL (2007) A new look at bacteriophage lambda genetic networks. J Bacteriol 189: 298-304.
10. Craig R (1981) Function of nucleoside triphosphate and polynucleotide in Escherichia coli recA protein-directed cleavage of phage lambda repressor. J Biol Chem 256: 8039-8044.
11. Dalsgaard A, Serichantalergs O, Forslund A, Lin W, Mekalanos J, Mintz E, Shimada T, Wells JG (2001) Clinical and environmental isolates of Vibrio cholerae serogroup 0141 carry the CTX prophage and the genes encoding the toxins-coregulated pili. J Clin Microbiol 39: 4086-4092.
12. Davies BM, Waldor MK (2003) Filamentous phages linked to virulence of Vibrio cholerae. Curr Opin Microbiol 6: 35-42.
13. Deveau H, Gerueau JE, Moineau S (2010) CRISPR/CAS system and its role in phage-bacteria interactions. Ann Rev Microbiol 64: 475-493.
14. Devoret R, Pierre M, Morean PL (1983) Prophage phi80 is induced in Escherichia coli K12 recA430. Mol Gen Genet 189: 199-206.
15. Dobzhansky T (1964) Biology, molecular and organismic. Am Zool 4: 443-452.
16. Dodd IB, Reed MR, Barr Egan J (1993) The Cro-like Apl repressor of coliphage 186 is required for prophage excision and binds near the phage attachment site. Mol Microbiol 10: 1139-1150.
17. Domingues S, Chopin A, Dusko Ehrlich S, Chopin MC (2004) A phage protein confers to the lactococcal abortive infection mechanism AbiP. J Bacteriol 186: 3278-3281.
18. Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.
19. Echols H, Murialdo H (1978) Genetic map of bacteriophage lambda. Microbiol Rev 42: 577-591.
20. Edger R, Qimron V (2010) The Escherichia coli CRISPR system protects from lambda lysogenization, lysogens, and prophage induction. J Bacteriol 219: 6291-6294.
21. Eguchi Y, Ogawa T, Ogawa H (1988) Cleavage of bacteriophage phi80 cI repressor by RecA protein. J Mol Biol 5: 565-573.
22. Elliott J, Arber W (1978) Escherichia coli K-12 pel mutants which block phage lambda DNA injection coincide with ptsM which determines components of sugar transport system. Mol Gen Genet 161: 1-8.
23. Erikson V, Lindberg AA (1976) Adsorption of phage P22 to Salmonella typhimurium. J Gen Virol 34: 207-221.
24. Esquinas-Rychen M, Erni B (2001) Facilitation of bacteriophage lambda DNA injection by injection by inner membrane proteins of the bacterial phosphoenol-pyruvate: carbohydrate phosphotransferase system (PTS). J Mol Microb Biotech 3: 361-370.
25. Golais F, Sabó A (1988) Koevolution von Virus und Wirtszelle. Biol Zbl 197: 267-280.
26. Gómez P, Buckling A (2011) Bacteria-phage antagonistic coevolution in soil. Science 332: 106-109.
27. Hall AR, Scanlan PD, Buckling A (2011) Bacteria-phage coevolution and the emergence of generalist pathogens. Am Nat 177: 44-53.
28. Hendrix RW (2002) Bacteriophages. Evolution of the majority. Theor Popul Biol 61: 471-480.
29. + gene in the ultraviolet mutagenesis of lambda in different genetic systems. J Mol Biol 23: 117-133.
30. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and Archaea. Science 327: 167-170.
31. Incardona NL, Selvidge L (1973) Mechanisms of adsorption and eclipse of bacteriophage phiX174. II. Attachment and eclipse with isolated Escherichia coli cell wall lipopolysaccharide. J Virol 11: 775-782.
32. Janion C (2008) Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli. Int J Biol Sci 4: 338-344.
33. Jay GS, Lloyd EA (1999) Individuality and adaptations across levels of selection. How shall we name and generalize the unit of Darwinism? P Natl Acad Sci USA 96: 11904-11909.
34. Kimsey HH, Waldor MK (2009) Vibrio cholerae LexA coordinates CTX prophage gene expression. J Bacteriol 191: 6788-6795.
35. Koudelka AP, Hufnagel LA, Koudelka GB (2004) Purification and characterization of the repressor of the Shiga toxin-encoding bacteriophage 933 W: DNA binding, gene regulation and autocleavage. J Bacteriol 186: 7659-7669.
36. Krüger DH, Bickle TA (1983) Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction system of their hosts. Microbiol Rev 47: 345-360.
37. Kutschera V, Niklas KJ (2004) The modern theory of biological evolution: an expanded synthesis. Naturwissenschaften 91: 255-276.
38. Labrie SJ, Samson JE, Moineau S (2010) Bacteria-phage resistance mechanisms. Nat Rev Microbiol 8: 317-327.
39. Ladero V, Garcia P, Bascarán V, Herrero M, Alvarez MA, Suarez JE (1998) Identification of the repressor-encoding gene of the Lactobacillus gene A2. J Bacteriol 180: 3474-3476.
40. Lamont I, Richardson H, Carter DR, Egan JB (1993) Genes for the establishment and maintenance of lysogeny by the temperate coliphage 186. J Bacteriol 175: 5286-5288.
41. Lemire S, Figueroa-Bossi N, Bossi L (2011) Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PloS Genet 7(6): e1002149. doi: 10. 1371/journal. pgen. 10002149.
42. Lewin B (2008a) Phage strategies. In: Genes IX. Jones and Bartlett Publ. pp 349-375.
43. Lewin B (2008b) Transposons. In: Genes IX. Jones and Bartlett Publ. pp 521-549.
44. Los M, Wegrzyn G (2012) Pseudolysogeny. Adv Virus Res 82: 333-343.
45. Los JM, Los M, Wegrzyn G (2011) Bacteria carrying Shiga toxin genes: genomic variations, detection and potential treatment of pathogenic bacteria. Future Microbiol 6: 909-924.
46. Mardanov AV, Ravin NV (2007) The antirepressor needed for induction of linear plasmid-prophage N15 belongs to the SOS regulon. J Bacteriol 189: 6333-6338.
47. Marrafini LA, Sontheimer EJ (2010) Self versus non-self versus discrimination during CRISPR RNA-directed immunity. Nature 463: 568-572.
48. Mayr E (1985) Natürliche Auslese. Naturwissenschaften 72: 231-236.
49. Mayr E (1997) The objects of selection. P Natl Acad Sci USA 94: 2091-2094.
50. Mayr E (2001) What evolution is. Basic Books, New York.
51. Mayr E (2004) What makes biology unique? Cambridge University Press, Cambridge.
52. Michel B (2005) After 30 years study, the bacterial SOS response still surprises us. PloS Biol 3(7): e255. doi: 10. 1371/journal. pbio. 0030255.
53. Mizuuchi K, Craigie R (1986) Mechanism of bacteriophage Mu transposition. Annu Rev Genet 20: 385-429.
54. Molineux IJ (1991) Host-parasite interactions: recent developments in the genetic of abortive phage infections. New Biol 3: 230-236.
55. Morgan AD, Bonsall MB, Buckling A (2010) Impact of bacterial mutation rate on coevolutionary dynamics between bacteria and phages. Evolution 64: 2980-2987.
56. Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284: 604-607.
57. Pal C, Maciá MD, Oliver A, Schachar I, Buckling A (2007) Coevolution with viruses drives the evolution of bacterial mutation rates. Nature 450: 1079-1081.
58. Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B, Fenton A, Hall N, Brockhurst MA (2010) Antagonistic coevolution accelerates molecular evolution. Nature 464: 275-278.
59. Pawlowski DR, Koudelka GP (2004) The preferred substrate for RecA-mediated cleavage of bacteriophage 434 repressor is the DNA-bound dimer. J Bacteriol 186: 1-7.
60. Pruteanu M, Baker T (2009) Proteolysis in the SOS response and metal homeostasis in Escherichia coli. Res Microbiol 160: 677-683.
61. Quinones M, Kimsey HH, Waldor MK (2005) LexA cleavage is required for CTX prophage induction. Mol Cell 17: 291-300.
62. Radman M (1975) Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis. Basic Life Sci 5A: 355-367.
63. Rakhuba DV, Kolomiets EI, Szwajcer DE, Novik GI (2010) Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol J Microbiol 59: 145-155.
64. Ranquet C, Toussaint A, de Jong H, Maenhaut-Michel G, Geiselmann J (2005) Control of phage Mu lysogenic repression. J Mol Biol 353: 186-195.
65. Ravin NV (2011) N15: the linear phage-plasmid. Plasmid 65: 102-109.
66. Ripp S, Miller RV (1997) The role of pseudolysogeny in bacteriophage-host interactions in a natural freshwater environment. Microbiology 143: 2065-2070.
67. Stern A, Sorek R (2010) The phage-host arms race: shaping the evolution of microbes. Bioessays 33: 43-51.
68. Susskind M, Botstein D (1978) Molecular genetics of bacteriophage P22. Microbiol Rev 42: 385-413.
69. Szybalski EH, Szybalski W (1979) A comprehensive molecular map of bacteriophage lambda. Gene 7: 217-270.
70. Turner M (2011) Phage on the rampage. Antibiotic use may have driven the development of Europe's deadly E. coli. Nature. doi: 10. 1038/news 2011. 360.
71. Vale PF, Little TJ (2010) CRISPR-mediated phage resistance and the ghost of evolution past. P Roy Soc B 277: 2097-2103.
72. van Valen L (1973) A new evolutionary law. Evol Theor 1: 1-30.
73. Wang J, Michel V, Hoffnung M, Charbit A (1998) Cloning of the J gene of bacteriophage lambda, expression, solubilization of the J protein: first in vitro studies on the interaction between J and LamB, its cell surface receptor. Res Microbiol 149: 611-624.
74. Wang X, Kim Y, Ma Q, Hoon HS, Pokusaeva K, Sturino JM, Wood TK (2010) Cryptic prophages help bacteria cope with adverse environments. Nature Commun 1: 147. doi: 10. 1038/ncomms1146.
75. Wegrzyn G, Licznerska K, Wegrzyn A (2012) Phage lambda-new insights into regulatory circuits. Adv Virus Res 82: 155-178.
76. Werts C, Michel V, Hoffnung M, Charbit A (1994) Adsorption of bacteriophage lambda on the lamB protein of Escherichia coli K-12: point mutations in gene J of lambda responsible for extended host range. J Bacteriol 176: 4941-4947.
77. Williams N, Fox DK, Shea C, Roseman S (1986) Pel, the protein that permit lambda DNA penetration of Escherichia coli, is encoded by a gene in ptsM and is required for mannose utilization by the phosphotransferase system. P Natl Acad Sci USA 83: 8934-8938.
78. Wilson G, Murray NE (1991) Restriction and modification systems. Annu Rev Genet 25: 585-627.
79. Woolhouse MEJ, Webster JP, Domingo E, Charlesworth B, Levin BR (2002) Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nature Genet 32: 569-571.