Targeted bacterial immunity buffers phage diversity

Journal of Virology

Volumn 85, Issue 20, 2011, Pages 10554-10560

  Haerter, Jan O ^a   Trusina, Ala ^a   Sneppen, Kim ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE IMMUNITY; ARTICLE; BACTERIAL IMMUNITY; BACTERIOPHAGE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DEFENSE MECHANISM; DNA STRUCTURE; GENE LOCUS; MATHEMATICAL MODEL; MICROBIAL DIVERSITY; MOLECULAR EVOLUTION; PLASMID; PRIORITY JOURNAL; SPECIES COEXISTENCE; VIRUS;

BACTERIA; BACTERIOPHAGES; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; GENETIC VARIATION; MODELS, THEORETICAL;

BACTERIA (MICROORGANISMS);

EID: 80054971915     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.05222-11     Document Type: Article

References (42)

1. Abedon, S. T., et al. 2008. Bacteriophage ecology, population growth, evolution, and impact of bacterial viruses. Cambridge University Press, Cambridge, United Kingdom.
2. Alvarez, L. J., P. Thomen, T. Makushok, and D. Chatenay. 2006. Propagation of fluorescent viruses in growing plaques. Biotechnol. Bioeng. 96:615-621.
3. Andersson, A. F., and J. F. Banfield. 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320: 1047-1050.
4. Avlund, M., et al. 2009. Why do phage play dice? J. Virol. 83:11416-11420.
5. Bolotin, A., et al. 2004. Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat. Biotechnol. 22:1554.
6. Breitbart, M., and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13:278-284.
7. Brouns, S. J. J., et al. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960-964.
8. Drake, J. W., B. Charlesworth, D. Charlesworth, and J. F. Crow. 1998. Rates of spontaneous mutation. Genetics 148:1667-1686.
9. Ferenci, T., J. Brass, and W. Boos. 1980. The role of the periplasmic maltosebinding protein and the outer-membrane phage lambda receptor in maltodextrin transport of Escherichia coli. Biochem. Soc. Trans. 8:680-681.
10. Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22:403-434.
11. Hale, C., K. Kleppe, R. M. Terns, and M. P. Terns. 2008. Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA 14:2572-2579.
12. Hale, C. R., et al. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945-956.
13. He, J., and M. W. Deem. 2010. Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats). Phys. Rev. Lett. 105:128102.
14. Heilmann, S., K. Sneppen, and S. Krishna. 2010. Sustainability of virulence in a phage-bacteria ecosystem. J. Virol. 84:3016-3022.
15. Horvath, P., and R. Barrangou. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167-170.
16. Horvath, P., et al. 2008. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 190:1401.
17. Ishino, Y., H. Shinagawa, K. Makino, M. Amemura, and A. Nakata. 1987. Nucleotide sequence of the iap gene responsible for alkaline phosphatase isozyme conversion in Escherichia coli and identification of the gene product. J. Bacteriol. 169:5429-5433.
18. Jansen, R., J. D. Embden, W. Gaastra, and L. M. Schouls. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43:1565-1575.
19. Jessup, C. M., and S. E. Forde. 2008. Ecology and evolution in microbial systems: the generation and maintenance of diversity in phage-host interactions. Res. Microbiol. 159:382-389.
20. Karginov, F. V., and G. J. Hannon. 2010. The CRISPR system: small RNAguided defense in bacteria and archaea. Mol. Cell Rev. 37:7-19.
21. Kimura, M., Z.-J. Jia, N. Nakayama, and S. Asakawa. 2008. Ecology of viruses in soils: past, present, and future perspectives. Soil Sci. Plant Nutr. 54:1-32.
22. Lennon, J. T., S. A. Khatana, M. F. Marston, and J. B. Martiny. 2007. Is there a cost of virus resistance in marine cyanobacteria? ISME J. 1:300-312.
23. Levin, B. R. 2010. Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria. PLoS Genet. 6:e1001171.
24. Levin, B. R., F. M. Stewart, and L. Chao. 1977. Resource-limited growth, competition, and predation: a model and experimental studies with bacteria and bacteriophage. Am. Nat. 111:3-24.
25. Lillestol, R. K., et al. 2006. A putative viral defense mechanism in archaeal cells. Archaea 2:59-72.
26. Lillestol, R. K., et al. 2009. CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol. Microbiol. 72:259.
27. Marraffini, L. A. 2010. Impact of CRISPR immunity on the emergence of bacterial pathogens. Future Microbiol. 5:693-695.
28. Marraffini, L. A., and E. J. Sontheimer. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843-1845.
29. Marraffini, L. A., and E. J. Sontheimer. 2010. Self- versus non-self-discrimination during CRISPR RNA-directed immunity. Nature 463:568-571.
30. Marx, J. 2007. New bacterial defense against phage invaders identified. Science 315:1650-1651.
31. Pantastico-Caldas, M., K. Duncan, C. A. Istoc, and J. A. Bell. 1992. Population dynamics of bacteriophage and Bacillus subtilis in soil. Ecology 73: 1888-1902.
32. Prado, F., A. Sheih, J. West, and B. Kerr. 2009. Coevolutionary cycling of host sociality and pathogen virulence in contact networks. J. Theor. Biol. 261:561-569.
33. Rabinovitch, A., et al. 2003. Bacterial debris: an ecological mechanism for coexistence of bacteria and their viruses. J. Theor. Biol. 224:377-383.
34. Rohwer, F. 2003. Global phage diversity. Cell 113:141.
35. Rosvall, M., et al. 2006. Network models of phage-bacteria coevolution. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 74(Pt. 2):066105.
36. Sneppen, K., A. Trusina, M. H. Jensen, and S. Bornholdt. 2010. A minimal model for multiple epidemics and immunity spreading. PLoS One 5:e13326.
37. Sorek, R., V. Kunin, and P. Hugenholtz. 2008. CRISPR: a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6:181-186.
38. Tyson, G. W., and J. F. Banfield. 2008. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol. 10:200-207.
39. Vale, P., and T. J. Little. 2010. CRISPR-mediated phage resistance and the ghost of coevolution past. Proc. Biol. Sci. 277:2097-2103.
40. Weitz, J. S. 2006. Size and scaling of predator-prey dynamics. Ecol Lett. 9:548-557.
41. Weitz, J. S. 2008. Evolutionary ecology of bacterial viruses. Microbe 3:171-178.
42. Weitz, J. S., H. Hartman, and S. A. Levin. 2005. Coevolutionary arms races between bacteria and bacteriophage. Proc. Natl. Acad. Sci. U. S. A. 102: 9535-9540.