Genetic and life-history traits associated with the distribution of prophages in bacteria

ISME Journal

Volumn 10, Issue 11, 2016, Pages 2744-2754

  Touchon, Marie ^a   Bernheim, Aude ^a   Rocha, Eduardo P C ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE; BACTERIUM; GENETIC ANALYSIS; GENOME; GROWTH RATE; LIFE HISTORY TRAIT; PATHOGENICITY; SPATIAL DISTRIBUTION;

BACTERIA (MICROORGANISMS);

BACTERIAL GENOME; BACTERIUM; CLASSIFICATION; CRISPR CAS SYSTEM; GENETICS; ISOLATION AND PURIFICATION; LIFE HISTORY TRAIT; LYSOGENIZATION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROPHAGE; VIROLOGY;

BACTERIA; BASE SEQUENCE; CRISPR-CAS SYSTEMS; GENOME, BACTERIAL; LIFE HISTORY TRAITS; LYSOGENY; PROPHAGES;

EID: 84961711517     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2016.47     Document Type: Article

References (74)

1. Abby SS, Neron B, Menager H, Touchon M, Rocha EP. (2014). MacSyFinder: A program to Mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One 9: e110726
2. Abedon ST. (2008). Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses. Cambridge University Press: Cambridge, NY, USA
3. Abedon ST, Lejeune JT. (2005). Why bacteriophage encode exotoxins and other virulence factors. Evol Bioinform Online 1: 97-110
4. Akerlund T, Nordstrom K, Bernander R. (1995). Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli. J Bacteriol 177: 6791-6797
5. Bertani G. (1954). Studies on lysogenesis. III. Superinfection of lysogenic Shigella dysenteriae with temperate mutants of the carried phage. J Bacteriol 67: 696-707
6. Bobay L-M, Rocha EPC, Touchon M. (2013). The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol 30: 737-751
7. Bossi L, Fuentes JA, Mora G, Figueroa-Bossi N. (2003). Prophage contribution to bacterial population dynamics. J Bacteriol 185: 6467-6471
8. Boyce MS. (1984). Restitution of r-and K-selection as a model of density-dependent natural selection. Annu Rev Ecol Syst 15: 427-447
9. Bremer H, Dennis PP. (1996). Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhardt FC (ed), Escherichia Coli and Salmonella: Cellular and Molecular Biology. ASM Press: Washington, DC, pp 1553-1569
10. Brenner DJ, Krieg NR, Staley JT. (2005). In: George M Garrity (ed), The Proteobacteria, bergey's manual of systematic bacteriology, 2nd edn, vol. XXVI, Springer: New York, NY, USA, 304pp. 77
11. Brussow H, Canchaya C, Hardt WD. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68: 560-602
12. Canchaya C, Fournous G, Chibani-Chennoufi S, DillmannML, Brussow H. (2003a). Phage as agents of lateral gene transfer. Curr Opin Microbiol 6: 417-424
13. Canchaya C, Proux C, Fournoux G, Bruttin A, Brussow H. (2003b). Prophage genomics. Microbiol Mol Biol Rev 67: 238-276
14. Casjens S. (2003). Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 49: 277-300
15. Chrzanowski TH, Crotty RD, Hubbard GJ. (1988). Seasonal variation in cell volume of epilimnetic bacteria. Microb Ecol 16: 155-163
16. Cochran PK, Paul JH. (1998). Seasonal abundance of lysogenic bacteria in a subtropical estuary. Appl Environ Microbiol 64: 2308-2312
17. Cordero OX, Hogeweg P. (2009). The impact of long-distance horizontal gene transfer on prokaryotic genome size. Proc Natl Acad Sci USA 106: 21748-21753
18. Draper NR, Smith H. (1998). Applied Regression Analysis. John Wiley &Sons: New York
19. Eddy SR. (2011). Accelerated profile HMM searches. PLoS Comput Biol 7: e1002195
20. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR et al. (2008). The Pfam protein families database. Nucleic Acids Res 36: D281-D288
21. Fouts DE. (2006). Phage Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res 34: 5839-5851
22. Fuhrman JA. (1999). Marine viruses and their biogeochemical and ecological effects. Nature 399: 541-548
23. Galtier N, Tourasse N, Gouy M. (1999). A non-hyperthermophylic common ancestor to extant life forms. Science 283: 220-221
24. Gama JA, Reis AM, Domingues I,Mendes-Soares H, Matos AM, Dionisio F. (2013). Temperate bacterial viruses as double-edged swords in bacterial warfare. PLoS One 8: e59043
25. Ghosh D, Roy K, Williamson KE, White DC, Wommack KE, Sublette KL et al. (2008). Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA. Appl Environ Microbiol 74: 495-502
26. Goldberg GW, Jiang W, Bikard D, Marraffini LA. (2014). Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting. Nature 514: 633-637
27. Goldhill DH, Turner PE. (2014). The evolution of life history trade-offs in viruses. Curr Opin Virol 8: 79-84
28. Gophna U, Kristensen DM, Wolf YI, Popa O, Drevet C, Koonin EV. (2015). No evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME J 9: 2021-2027
29. Grissa I, Vergnaud G, Pourcel C. (2007). CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: W52-W57
30. Hatfull GF. (2010). Mycobacteriophages: genes and genomes. Annu Rev Microbiol 64: 331-356
31. Herskowitz I, Hagen D. (1980). The lysis-lysogeny decision of phage lambda: explicit programming and responsiveness. Annu Rev Genet 14: 399-445
32. Hyman P, Abedon ST. (2010). Bacteriophage host range and bacterial resistance. Adv Appl Microbiol 70: 217-248
33. Jiang SC, Paul JH. (1998). Gene transfer by transduction in the marine environment. Appl Environ Microbiol 64: 2780-2787
34. Koch AL. (2001). Oligotrophs versus copiotrophs. Bioessays 23: 657-661
35. Kourilsky P. (1973). Lysogenization by bacteriophage lambda. I. Multiple infection and the lysogenic response. Mol Gen Genet 122: 183-195
36. Labrie SJ, Samson JE, Moineau S. (2010). Bacteriophage resistance mechanisms. Nat Rev Microbiol 8: 317-327
37. Lieb M. (1953). Studies on lysogenization in Escherichia coli. Cold Spring Harb Symp Quant Biol 18: 71-73
38. Lwoff A. (1953). Lysogeny. Bacteriol Rev 17: 269-337
39. Maurice CF, Bouvier C, de Wit R, Bouvier T. (2013). Linking the lytic and lysogenic bacteriophage cycles to environmental conditions, host physiology and their variability in coastal lagoons. Environ Microbiol 15: 2463-2475
40. McDaniel L, Paul JH. (2005). Effect of nutrient addition and environmental factors on prophage induction in natural populations of marine synechococcus species. Appl Environ Microbiol 71: 842-850
41. McGrath S, Fitzgerald GF, van Sinderen D. (2002). Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. Mol Microbiol 43: 509-520
42. McNair K, Bailey BA, Edwards RA. (2012). PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28: 614-618
43. Menouni R, Champ S, Espinosa L, Boudvillain M, Ansaldi M. (2013). Transcription termination controls prophage maintenance in Escherichia coli genomes. Proc Natl Acad Sci USA 110: 14414-14419
44. Middelboe M. (2000). Bacterial growth rate and marine virus-host dynamics. Microb Ecol 40: 114-124
45. Modi SR, Lee HH, Spina CS, Collins JJ. (2013). Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499: 219-222
46. Oliveira PH, Touchon M, Rocha EPC. (2014). The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res 42: 10618-10631
47. Paradis E, Claude J, Strimmer K. (2004). APE: analyses of phylogenetics and evolution in R596 language. Bioinformatics 20: 289-290
48. Pirofski LA, Casadevall A. (2012). Q and A: What is a pathogen? A question that begs the point. BMC Biol 10: 6
49. Pradeep Ram AS, Sime-Ngando T. (2010). Resources drive trade-off between viral lifestyles in the plankton: evidence from freshwater microbial microcosms. Environ Microbiol 12: 467-479
50. Ptashne M. (1992). Genetic Switch: Phage Lambda and Higher Organisms, 2nd edn, Blackwell: Cambridge, MA
51. Roux S, Hallam SJ, Woyke T, Sullivan MB. (2015). Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4: 1-20
52. Shan J, Korbsrisate S, Withatanung P, Adler NL, Clokie MR, Galyov EE. (2014). Temperature dependent bacteriophages of a tropical bacterial pathogen. Front Microbiol 5: 599
53. Smillie C, Garcillan-Barcia MP, Francia MV, Rocha EP, de la Cruz F. (2010). Mobility of plasmids. Microbiol Mol Biol Rev 74: 434-452
54. Spearman C. (1904). The proof and measurement of association between two things. Am J Psychol 15: 72-101
55. St-Pierre F, Endy D. (2008). Determination of cell fate selection during phage lambda infection. Proc Natl Acad Sci USA 105: 20705-20710
56. Stearns SC. (1977). The evolution of life history traits: a critique of the theory and a review of the data. Annu Rev Ecol Syst 8: 145-171
57. Stewart FM, Levin BR. (1984). The population biology of bacterial viruses: why be temperate? Theor Popul Biol 26: 93-117
58. Torrella F, Morita RY. (1981). Microcultural study of bacterial size changes and microcolony and ultramicrocolony formation by heterotrophic bacteria in seawater. Appl Environ Microbiol 41: 518-527
59. Touchon M, Charpentier S, Clermont O, Rocha EPC, Denamur E, Branger C. (2011). CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J Bacteriol 193: 2460-2467
60. Touchon M, Rocha EP. (2007). Causes of insertion sequences abundance in prokaryotic genomes. Mol Biol Evol 24: 969-981
61. Touchon M, Rocha EP. (2010). The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS ONE 5: e11126
62. Vieira-Silva S, Rocha EPC. (2010). The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet 6: e1000808
63. Vieira-Silva S, Touchon M, Abby SS, Rocha EP. (2011). Investment in rapid growth shapes the evolutionary rates of essential proteins. Proc Natl Acad Sci USA 108: 20030-20035
64. Volkmer B, Heinemann M. (2011). Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling. PLoS One 6: e23126
65. Wagner PL, Waldor MK. (2002). Bacteriophage control of bacterial virulence. Infect Immun 70: 3985-3993
66. Waldor MK, Friedman DI. (2005). Phage regulatory circuits and virulence gene expression. Curr Opin Microbiol 8: 459-465
67. Wang X, Kim Y, Ma Q, Hong SH, Pokusaeva K, Sturino JM et al. (2010). Cryptic prophages help bacteria cope with adverse environments. Nat Commun 1: 147
68. Weinbauer MG. (2004). Ecology of prokaryotic viruses. FEMS Microbiol Rev 28: 127-181
69. Westra ER, Buckling A, Fineran PC. (2014). CRISPR-Cas systems: beyond adaptive immunity. Nat Rev Microbiol 12: 317-326
70. Wilcoxon F. (1945). Individual comparisons by ranking methods. Biometrics Bull 1: 80-83
71. Wilhelm SW, Suttle CA. (1999). Viruses and nutrient cycles in the sea viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49: 781-788
72. Williamson SJ, Houchin LA, McDaniel L, Paul JH. (2002). Seasonal variation in lysogeny as depicted by prophage induction in Tampa Bay, Florida. Appl Environ Microbiol 68: 4307-4314
73. Winter C, Bouvier T, Weinbauer MG, Thingstad TF. (2010). Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited. Microbiol Mol Biol Rev 74: 42-57
74. Zeldovich KB, Berezovsky IN, Shakhnovich EI. (2007). Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 3: e5