Viral diversity threshold for adaptive immunity in prokaryotes

mBio

Volumn 3, Issue 6, 2012, Pages

  Weinberger, Ariel D ^a   Wolf, Yuri I ^b   Lobkovsky, Alexander E ^b   Gilmore, Michael S ^a   Koonin, Eugene V ^b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

ADAPTIVE IMMUNITY; ARCHAEON; ARTICLE; BACTERIUM; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT ASSOCIATED GENE; COEVOLUTION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA STRUCTURE; ENVIRONMENTAL TEMPERATURE; EVOLUTIONARY ADAPTATION; GENE; GENETIC MODEL; GENETIC SELECTION; GENOMICS; IMMUNOLOGICAL MEMORY; INNATE IMMUNITY; MESOPHILE; MICROBIAL DIVERSITY; MUTATION RATE; NONHUMAN; PHASE TRANSITION; PLASMID; PRIORITY JOURNAL; PROKARYOTE; QUANTITATIVE ANALYSIS; STOCHASTIC MODEL; THERMOPHILE; VIRAL PROTOSPACER MUTATION; VIRUS CELL INTERACTION; VIRUS MUTATION;

ARCHAEA; BACTERIA (MICROORGANISMS); LAMARCKIA; PROKARYOTA;

EID: 84872139964     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00456-12     Document Type: Article

References (62)

1. Darwin C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London, UK.
2. Futuyma D. 2005. Evolution. Sinauer Associates, Sunderland, MA.
3. Lynch M. 2007. The origins of genome architecture. Sinauer Associates, Sunderland, MA.
4. Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8:610-618.
5. Carrasco P, de la Iglesia F, Elena SF. 2007. Distribution of fitness and virulence effects caused by single-nucleotide substitutions in tobacco etch virus. J. Virol. 81:12979-12984.
6. Peris JB, Davis P, Cuevas JM, Nebot MR, Sanjuán R. 2010. Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1. Genetics 185:603-609.
7. Estes S, Phillips PC, Denver DR, Thomas WK, Lynch M. 2004. Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans. Genetics 166:1269-1279.
8. Sanjuán R, Moya A, Elena SF. 2004. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl. Acad. Sci. U. S. A. 101:8396-8401.
9. Koonin EV, Wolf YI. 2009. Is evolution Darwinian or/and Lamarckian? Biol. Direct 4:42.
10. Koonin EV. 2011. The logic of chance: the nature and origin of biological evolution. FT Press, Upper Saddle River, NJ.
11. Weissman A. 1893. The germ-plasm. A theory of heredity. Charles Scribner's Sons, London, United Kingdom.
12. Wiedenheft B, Sternberg SH, Doudna JA. 2012. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331-338.
13. Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167-170.
14. Marraffini LA, Sontheimer EJ. 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 11:181-190.
15. Makarova KS, et al. 2011. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9:467-477.
16. Barrangou R, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712.
17. Marraffini LA, Sontheimer EJ. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843-1845.
18. Garneau JE, et al. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67-71.
19. Karginov FV, Hannon GJ. 2010. The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol. Cell 37:7-19.
20. Brouns SJ, et al. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960-964.
21. Jore MM, et al. 2011. Structural basis for CRISPR RNA-guided DNA recognition by cascade. Nat. Struct. Mol. Biol. 18:529-536.
22. Wiedenheft B, et al. 2011. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477:486-489.
23. Deltcheva E, et al. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602-607.
24. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. 2010. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329:1355-1358.
25. Al-Attar S, Westra ER, van der Oost J, Brouns SJ. 2011. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol. Chem. 392:277-289.
26. Westra ER, et al. 2012. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by cascade and Cas3. Mol. Cell 46:595-605.
27. Sashital DG, Wiedenheft B, Doudna JA. 2012. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46: 606-615
28. Deveau H, et al. 2008. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 190:1390-1400.
29. Andersson AF, Banfield JF. 2008. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320: 1047-1050.
30. Semenova E, et al. 2011. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc. Natl. Acad. Sci. U. S. A. 108:10098-10103.
31. Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D. 2009. Germ warfare in a microbial mat community: CRISPRs provide insights into the coevolution of host and viral genomes. PLoS One 4:e4169.
32. Horvath P, et al. 2008. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J. Bacteriol. 190:1401-1412.
33. Weinberger AD, et al. 2012. Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput. Biol. 8:e1002475.
34. Edwards RA, Rohwer F. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3:504-510.
35. Labrie SJ, Samson JE, Moineau S. 2010. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8:317-327.
36. Berezovsky IN, Shakhnovich EI. 2005. Physics and evolution of thermophilic adaptation. Proc. Natl. Acad. Sci. U. S. A. 102:12742-12747.
37. Zeldovich KB, Berezovsky IN, Shakhnovich EI. 2007. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput. Biol. 3:e5.
38. Zeldovich KB, Chen P, Shakhnovich EI. 2007. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc. Natl. Acad. Sci. U. S. A. 104:16152-16157.
39. Cherry JL. 2010. Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins. Mol. Biol. Evol. 27: 735-741.
40. Wylie CS, Shakhnovich EI. 2011. A biophysical protein folding model accounts for most mutational fitness effects in viruses. Proc. Natl. Acad. Sci. U. S. A. 108:9916-9921.
41. Grogan DW, Carver GT, Drake JW. 2001. Genetic fidelity under harsh conditions: analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Proc. Natl. Acad. Sci. U. S. A. 98: 7928-7933.
42. Drake JW. 2009. Avoiding dangerous missense: thermophiles display especially low mutation rates. PLoS Genet. 5:e1000520.
43. Mackwan RR, Carver GT, Kissling GE, Drake JW, Grogan DW. 2008. The rate and character of spontaneous mutation in Thermus thermophilus. Genetics 180:17-25.
44. Friedman R, Drake JW, Hughes AL. 2004. Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles. Genetics 167:1507-1512.
45. Makarova KS, Wolf YI, Snir S, Koonin EV. 2011. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J. Bacteriol. 193:6039-6056.
46. Edgar RC. 2007. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8:18.
47. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19:716-723.
48. He J, Deem MW. 2010. Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats). Phys. Rev. Lett. 105:128102.
49. Haerter JO, Trusina A, Sneppen K. 2011. Targeted bacterial immunity buffers phage diversity. J. Virol. 85:10554-10560.
50. Childs LM, Held NL, Young MJ, Whitaker RJ, Weitz JS. 2012. Multiscale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamrack and Darwin. Evolution 66:2015-2029.
51. Wilson GG, Murray NE. 1991. Restriction and modification systems. Annu. Rev. Genet. 25:585-627.
52. Marraffini LA, Sontheimer EJ. 2010. Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463:568-571.
53. Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. 2010. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 26:335-340.
54. Palmer KL, Kos VN, Gilmore MS. 2010. Horizontal gene transfer and the genomics of enterococcal antibiotic resistance. Curr. Opin. Microbiol. 13:632-639.
55. Palmer KL, Gilmore MS. 2010. Multidrug-resistant enterococci lack CRISPR-cas. mBio 1(4):e00227-10.
56. Hill TC, Walsh KA, Harris JA, Moffett BF. 2003. Using ecological diversity measures with bacterial communities. FEMS Microbiol. Ecol. 43:1-11.
57. Amitai G, Sorek R. Roles of CRISPR in regulation of physiological processes. In Barrangou R, van der Oost J (ed), CRISPR-Cas systems: RNAmediated adaptive immunity in Bacteria and Archaea, in press. Springer, Berlin, Germany.
58. Jorth P, Whiteley M. 2012. An evolutionary link between natural transformation and CRISPR adaptive immunity. mBio 3(5):e00309-e00312.
59. Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV. 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14:442-444.
60. Drake JW, Charlesworth B, Charlesworth D, Crow JF. 1998. Rates of spontaneous mutation. Genetics 148:1667-1686.
61. Kussell E, Leibler S. 2005. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309:2075-2078.
62. Kuo CH, Ochman H. 2009. Deletional bias across the three domains of life. Genome Biol. Evol. 1:145-152.