Evolution and classification of CRISPR-Cas systems and cas protein families

CRISPR-Cas Systems: RNA-Mediated Adaptive Immunity in Bacteria and Archaea

Volumn , Issue , 2013, Pages 61-91

  Makarova, Kira S ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84886650941     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-34657-6     Document Type: Chapter

References (70)

1. Anantharaman V, Iyer LM, Aravind L (2010) Presence of a classical RRM-fold palm domain in Thg1-type 30-50nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Biol Direct 5:43
2. Aravind L, Makarova KS, Koonin EV (2000) Survey and summary: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 28:3417-3432
3. Aravind L, Mazumder R, Vasudevan S, Koonin EV (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr Opin Struct Biol 12:392-399
4. Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF (2011) A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 79:484-502
5. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712
6. Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF (2008) A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem 283:20361-20371
7. Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin AF (2011) Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J 30:4616-4627
8. Bhaya D, Davison M, Barrangou R (2011) CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45:273-297
9. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960-964
10. Carte J, Wang R, Li H, Terns RM, Terns MP (2008) Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 22:3489-3496
11. Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H (2012) Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Structure 20:545-553
12. Csorba T, Pantaleo V, Burgyan J (2009) RNA silencing: an antiviral mechanism. Adv Virus Res 75:35-71
13. Daines DA, Jarisch J, Smith AL (2004) Identification and characterization of a nontypeable Haemophilus influenzae putative toxin-antitoxin locus. BMC Microbiol 4:30
14. Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E (2012) Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun 3:945
15. Fukuda E, Kaminska KH, Bujnicki JM, Kobayashi I (2008) Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases. Genome Biol 9:R163
16. Galperin MY (2006) Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol 188:4169-4182
17. Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67-71
18. Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM (2011) Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat Struct Mol Biol 18:688-692
19. Haft DH, Selengut J, Mongodin EF, Nelson KE (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1:e60
20. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP (2009) RNAguided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945-956
21. Han D, Krauss G (2009) Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2. FEBS Lett 583:771-776
22. Han D, Lehmann K, Krauss G (2009) SSO1450-a CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA. FEBS Lett 583:1928-1932
23. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) Sequence-and structurespecific RNA processing by a CRISPR endonuclease. Science 329:1355-1358
24. Iyer LM, Abhiman S, Aravind L (2008) A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases. Biol Direct 3:39
25. Jackman JE, Phizicky EM (2006) tRNAHis guanylyltransferase adds G-1 to the 50 end of tRNAHis by recognition of the anticodon, one of several features unexpectedly shared with tRNA synthetases. RNA 12:1007-1014
26. Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A (2007) Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. J Mol Biol 370:157-169
27. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816-821
28. Jore MM, Brouns SJ, van der Oost J (2011a) RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb Perspect Biol 4(6)
29. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ (2011b) Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 18:529-536
30. Kawano M, Aravind L, Storz G (2007) An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol 64:738-754
31. Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM (1999) Structural and mechanistic basis of immunity toward endonuclease colicins. Nat Struct Biol 6:243-252
32. Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29:3742-3756
33. Kojima KK, Kanehisa M (2008) Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. Mol Biol Evol 25:1395-1404
34. Kwon AR, Kim JH, Park SJ, Lee KY, Min YH, Im H, Lee I, Lee BJ (2012) Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity. Nucleic Acids Res 40:4216-4228
35. Lintner NG, Kerou M, Brumfield SK, Graham S, Liu H, Naismith JH, Sdano M, Peng N, She Q, Copie V, Young MJ, White MF, Lawrence CM (2011) Structural and functional characterization of an archaeal CASCADE complex for CRISPR-mediated viral defense. J Biol Chem 286:21643-21656
36. Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 30:482-496
37. Makarova KS, Aravind L, Wolf YI, Koonin EV (2011a) Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 6:38
38. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (2006) A putative RNAinterference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies wiTheukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1:7
39. Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineau S, Mojica FJM, Wolf YI, Yakunin AF, van der Oost J, Koonin EV (2011b) Evolution and classification of the CRISPR/Cas systems. Nat Rev Microbiol 9:467-477
40. Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV (2007) Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2:33
41. Makarova KS, Wolf YI, Koonin EV (2003) Potential genomic determinants of hyperthermophily. Trends Genet 19:172-176
42. Makarova KS, Wolf YI, Koonin EV (2009a) Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct 4:19
43. Makarova KS, Wolf YI, Snir S, Koonin EV (2011c) Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol 193:6039-6056
44. Makarova KS, Wolf YI, van der Oost J, Koonin EV (2009b) Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct 4:29
45. Marraffini LA, Sontheimer EJ (2009) Invasive DNA, chopped and in the CRISPR. Structure 17:786-788
46. Mulepati S, Bailey S (2011) Structural and biochemical analysis of the nuclease domain of the clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 3(CAS3). J Biol Chem 286(36):31896-31903
47. Pei J, Grishin NV (2001) GGDEF domain is homologous to adenylyl cyclase. Proteins 42:210-216
48. Rogozin IB, Makarova KS, Pavlov YI, Koonin EV (2008) A highly conserved family of inactivated archaeal B family DNA polymerases. Biol Direct 3:32
49. Sakamoto K, Agari Y, Agari K, Yokoyama S, Kuramitsu S, Shinkai A (2009) X-ray crystal structure of a CRISPR-associated RAMP module [corrected] Cmr5 protein [corrected] from Thermus thermophilus HB8. Proteins 75:528-532
50. Samai P, Smith P, Shuman S (2010) Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris. Acta Crystallogr Sect F: Struct Biol Cryst Commun 66:1552-1556
51. Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39(21):9275-9282
52. Sashital DG, Wiedenheft B, Doudna JA (2012) Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell 46:606-615
53. Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (2011) Cas3 is a singlestranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J 30(7):1335-1342.
54. Steitz TA (2004) The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase. Curr Opin Struct Biol 14:4-9
55. Steitz TA, Yin YW (2004) Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases. Philos Trans R Soc Lond B Biol Sci 359:17-23
56. Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV (2009) Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol Direct 4:11
57. Takeuchi N, Wolf YI, Makarova KS, Koonin EV (2012) Nature and intensity of selection pressure on CRISPR-associated genes. J Bacteriol 194:1216-1225
58. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 34:401-407
59. Van Melderen L, Saavedra De Bast M (2009) Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet 5:e1000437
60. Wang R, Preamplume G, Terns MP, Terns RM, Li H (2011) Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 19:257-264
61. Westra ER, van Erp PB, Kunne T, Wong SP, Staals RH, Seegers CL, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJ, van der Oost J (2012) CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by cascade and Cas3. Mol Cell 46:595-605
62. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E (2011a) Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477:486-489
63. Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331-338
64. Wiedenheft B, van Duijn E, Bultema J, Waghmare S, Zhou K, Barendregt A, Westphal W, Heck A, Boekema E, Dickman M, Doudna JA (2011b) RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci USA 108:10092-10097
65. Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA (2009) Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17:904-912
66. Yamaguchi Y, Inouye M (2009) mRNA interferases, sequence-specific endoribonucleases from the toxin-antitoxin systems. Prog Mol Biol Transl Sci 85:467-500
67. Yin YW, Steitz TA (2004) The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell 116:393-404
68. Yosef I, Goren MG, Qimron U (2012) Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 40:5569-5576
69. Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, Naismith JH, Spagnolo L, White MF (2012) Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell 45:303-313
70. Zhu X, Ye K (2012) Crystal structure of Cmr2 reveals a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. FEBS Lett 586(6):939-945