CRISPR associated diversity within a population of Sulfolobus islandicus

PLoS ONE

Volumn 5, Issue 9, 2010, Pages

  Held, Nicole L ^a   Herrera, Alfa ^a   Quiroz, Hinsby Cadillo ^a   Whitaker, Rachel J ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; GENE SEQUENCE; GENETIC MARKER; GENETIC PARAMETERS; GENETIC VARIABILITY; GENOTYPE; HOST RESISTANCE; MICROBIAL IMMUNITY; MICROBIAL POPULATION DYNAMICS; MOLECULAR CLONING; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RUSSIAN FEDERATION; SULFOLOBUS; SULFOLOBUS ISLANDICUS; THERMAL SPRING;

BASE SEQUENCE; BIODIVERSITY; DNA, INTERGENIC; HOT SPRINGS; INVERTED REPEAT SEQUENCES; MOLECULAR SEQUENCE DATA; PHYLOGENY; RUSSIA; SULFOLOBUS;

SULFOLOBUS ISLANDICUS;

EID: 77958590947     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012988     Document Type: Article

References (50)

1. Lenski RE, Levin BR (1985) Constraints on the coevolution of bacteria and virulent phage: A model, some experiments, and predictions for natural communities. Am Nat 125: 585-602.
2. Thingstad TF (2000) Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr 45: 1320-1328.
3. Bohannan BJM, Lenski RE (1997) Effect of resource enrichment on a chemostat community of bacteria and bacteriophage. Ecology 78: 2303-2315.
4. Yoshida T, Ellner SP, Jones LE, Bohannan BJM, Lenski RE, et al. (2007) Cryptic population dynamics: Rapid evolution masks trophic interactions. PLoS Biol 5: 1868-1879.
5. Abrams PA, Matsuda H (1997) Prey adaptation as a cause of predator-prey cycles. Evolution 51: 1742-1750.
6. Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pašić L, Thingstad TF, et al. (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7: 828-836.
7. Bohannan BJM, Lenski RE (1999) Effect of prey heterogeneity on the response of a model food chain to resource enrichment. Am Nat 153: 73-82.
8. Middelboe M (2000) Bacterial growth rate and marine virus-host dynamics. Microb Ecol 40: 114-124.
9. Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, et al. (2010) Viral and microbial community dynamics in four aquatic environments. ISME J 4: 739-751.
10. Weitz JS, Hartman H, Levin SA (2005) Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci USA 102: 9535-9540.
11. 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.
12. Middelboe M, Holmfeldt K, Riemann L, Nybroe O, Haaber J (2009) Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. Environ Microbiol 11: 1971-1982.
13. Lennon JT, Khatana SAM, Marston MF, Martiny JBH (2007) Is there a cost of virus resistance in marine cyanobacteria? ISME J 1: 300-312.
14. Brockhurst MA, Rainey PB, Buckling A (2004) The effect of spatial heterogeneity and parasites on the evolution of host diversity. Proc R Soc Lond B Biol Sci 271: 107-111.
15. Hutchinson GE (1961) The paradox of the plankton. Am Nat 95: 137-145.
16. Holmfeldt K, Middelboe M, Nybroe O, Riemann L (2007) Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Applied and Environmental Microbiology 73: 6730-6739.
17. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, et al. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
18. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in Staphylococci by Targeting DNA. Science 322: 1843-1845.
19. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151: 2551-2561.
20. Mojica FJM, Di{dotless}́ez-Villasenñor C, Garci{dotless}́a-Marti{dotless}́nez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60: 174-182.
21. Pourcel C, Salvignol G, Vergnaud G (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151: 653-663.
22. Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, et al. (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190: 1390-1400.
23. Pancer Z, Cooper MD (2006) The evolution of adaptive immunity. Annu Rev Immunol 24: 497-518.
24. Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H, et al. (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190: 1401-1412.
25. Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10: 200-207.
26. Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D (2009) Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE 4: e4169.
27. Banfield JF, Young M (2009) Variety-the splice of life-in microbial communities. Science 326: 1198-1199.
28. Whitaker RJ, Grogan DW, Taylor JW (2005) Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol Biol Evol 22: 2354-2361.
29. Smith JM, Smith NH, O'Rourke M, Spratt BG (1993) How clonal are bacteria? Proc Natl Acad Sci USA 90: 4384-4388.
30. Didelot X, Falush D (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251-1266.
31. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11: 265-270.
32. Held NL, Whitaker RJ (2009) Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol 11: 457-466.
33. Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA 106: 8605-8610.
34. van Embden JDA, van Gorkom T, Kremer K, Jansen R, van der Zeijst BAM, et al. (2000) Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. Journal of Bacteriology 182: 2393-2401.
35. Lillestol RK, Shah SA, Brugger K, Redder P, Phan H, et al. (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 72: 259-272.
36. Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320: 1047-1050.
37. Schrag SJ, Mittler JE (1996) Host-parasite coexistence: The role of spatial refuges in stabilizing bacteria-phage interactions. Am Nat 148: 348-377.
38. Brockhurst MA, Buckling A, Rainey PB (2005) The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa. Proc R Soc Lond B Biol Sci 272: 1385-1391.
39. Gerrish PJ, Lenski RE (1998) The fate of competing beneficial mutations in an asexual population. Genetica 103: 127-144.
40. Lythgoe KA, Chao L (2003) Mechanisms of coexistence of a bacteria and a bacteriophage in a spatially homogeneous environment. Ecol Lett 6: 326-334.
41. Bize A, Karlsson EA, Ekefjärd K, Quax TEF, Pina M, et al. (2009) A unique virus release mechanism in the Archaea. Proc Natl Acad Sci USA 106: 11306-11311.
42. Prangishvili D, Garrett RA (2005) Viruses of hyperthermophilic Crenarchaea. Trends Microbiol 13: 535-542.
43. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
44. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
45. Maddison WP, Maddison DR (2005) MacClade: Anlaysis of Phylogeny and Character Evolution.Version 4.08. Sunderland Massachusetts: Sinauer Associates.
46. Swofford DL (2003) PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods).Version 4. SunderlandMassachusetts: Sinauer Associates.
47. Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17: 368-376.
48. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
49. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.
50. Grissa I, Vergnaud G, Pourcel C (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. Bmc Bioinformatics 8: 172.