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EcoSal Plus

Domain 7:

Genetics and Genetic Tools

Mechanisms of Type I-E and I-F CRISPR-Cas Systems in

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • Authors: Chaoyou Xue1,2, and Dipali G. Sashital3
  • Editors: James M. Slauch4, Gregory Phillips5
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA; 2: Present address: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY; 3: Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA; 4: The School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL; 5: College of Veterinary Medicine, Iowa State University, Ames, IA
  • Received 25 June 2018 Accepted 02 January 2019 Published 06 February 2019
  • Address correspondence to Dipali Sashital, [email protected]
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  • Abstract:

    CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invasion by bacteriophages and other mobile genetic elements. Short fragments of invader DNA are stored as immunological memories within CRISPR (clustered regularly interspaced short palindromic repeat) arrays in the host chromosome. These arrays provide a template for RNA molecules that can guide CRISPR-associated (Cas) proteins to specifically neutralize viruses upon subsequent infection. Over the past 10 years, our understanding of CRISPR-Cas systems has benefited greatly from a number of model organisms. In particular, the study of several members of the Gram-negative family, especially and , have provided significant insights into the mechanisms of CRISPR-Cas immunity. In this review, we provide an overview of CRISPR-Cas systems present in members of the . We also detail the current mechanistic understanding of the type I-E and type I-F CRISPR-Cas systems that are commonly found in enterobacteria. Finally, we discuss how phages can escape or inactivate CRISPR-Cas systems and the measures bacteria can enact to counter these types of events.

  • Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018

References

1. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. 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.
2. Nakata A, Amemura M, Makino K. 1989. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J Bacteriol 171:3553–3556.
3. Mojica FJM, Díez-Villaseñor C, Soria E, Juez G. 2000. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 36:244–246. [PubMed]
4. Hermans PWM, van Soolingen D, Bik EM, de Haas PEW, Dale JW, van Embden JDA. 1991. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect Immun 59:2695–2705.
5. 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.
6. 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.
7. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174–182.
8. Jansen R, van Embden JD, Gaastra W, Schouls LM. 2002. Identification of a novel family of sequence repeats among prokaryotes. OMICS 6:23–33. [PubMed]
9. 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. [PubMed]
10. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 2006. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1:7. [PubMed]
11. 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.
12. 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. [PubMed]
13. Marraffini LA, Sontheimer EJ. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843–1845.
14. Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960–964. [PubMed]
15. 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.
16. Nuñez JK, Lee ASY, Engelman A, Doudna JA. 2015. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 519:193–198.
17. Jackson RN, Wiedenheft B. 2015. A conserved structural chassis for mounting versatile CRISPR RNA-guided immune responses. Mol Cell 58:722–728.
18. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945–956. [PubMed]
19. Westra ER, van Erp PBG, Künne T, Wong SP, Staals RHJ, Seegers CLC, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJJ, 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.
20. Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S. 2010. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67–71. [PubMed]
21. Koonin EV, Makarova KS, Zhang F. 2017. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 37:67–78. [PubMed]
22. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJM, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. 2015. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 13:722–736.
23. Murugan K, Babu K, Sundaresan R, Rajan R, Sashital DG. 2017. The revolution continues: newly discovered systems expand the CRISPR-Cas toolkit. Mol Cell 68:15–25. [PubMed]
24. Makarova KS, Zhang F, Koonin EV. 2017. SnapShot: class 1 CRISPR-Cas systems. Cell 168:946–946.e1. [PubMed]
25. Medina-Aparicio L, Dávila S, Rebollar-Flores JE, Calva E, Hernández-Lucas I. 2018. The CRISPR-Cas system in Enterobacteriaceae. Pathog Dis 76:fty002. [PubMed]
26. Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, Doudna JA. 2011. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A 108:10092–10097.
27. Richter C, Gristwood T, Clulow JS, Fineran PC. 2012. In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas system. PLoS One 7:e49549. [PubMed]
28. Mulepati S, Bailey S. 2013. In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target. J Biol Chem 288:22184–22192. [PubMed]
29. Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA. 2014. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A 111:6618–6623.
30. Rollins MF, Chowdhury S, Carter J, Golden SM, Wilkinson RA, Bondy-Denomy J, Lander GC, Wiedenheft B. 2017. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity. Proc Natl Acad Sci U S A 114:E5113–E5121. [PubMed]
31. Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. 2011. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J 30:1335–1342. [PubMed]
32. Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC. 2015. Surveillance and processing of foreign DNA by the Escherichia coli CRISPR-Cas system. Cell 163:854–865. [PubMed]
33. Xiao Y, Luo M, Dolan AE, Liao M, Ke A. 2018. Structure basis for RNA-guided DNA degradation by Cascade and Cas3. Science 361:eaat0839. [PubMed]
34. Pougach K, Semenova E, Bogdanova E, Datsenko KA, Djordjevic M, Wanner BL, Severinov K. 2010. Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol Microbiol 77:1367–1379.
35. Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJM. 2010. Diversity of CRISPR loci in Escherichia coli. Microbiology 156:1351–1361.
36. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA. 2014. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol 21:528–534.
37. 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 APL, Dickman MJ, Doudna JA, Boekema EJ, Heck AJR, van der Oost J, Brouns SJJ. 2011. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 18:529–536. [PubMed]
38. Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R. 2010. Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol 75:1495–1512.
39. Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N. 2006. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res 13:141–153. [PubMed]
40. Westra ER, Pul U, Heidrich N, Jore MM, Lundgren M, Stratmann T, Wurm R, Raine A, Mescher M, Van Heereveld L, Mastop M, Wagner EGH, Schnetz K, Van Der Oost J, Wagner R, Brouns SJJ. 2010. H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol Microbiol 77:1380–1393.
41. Majsec K, Bolt EL, Ivančić-Baće I. 2016. Cas3 is a limiting factor for CRISPR-Cas immunity in Escherichia coli cells lacking H-NS. BMC Microbiol 16:28. [PubMed]
42. Yang CD, Chen YH, Huang HY, Huang HD, Tseng CP. 2014. CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication. Mol Microbiol 92:1072–1091. [PubMed]
43. Sashital DG, Wiedenheft B, Doudna JA. 2012. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell 46:606–615. [PubMed]
44. Yosef I, Goren MG, Kiro R, Edgar R, Qimron U. 2011. High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system. Proc Natl Acad Sci U S A 108:20136–20141.
45. Swarts DC, Mosterd C, van Passel MWJ, Brouns SJJ. 2012. CRISPR interference directs strand specific spacer acquisition. PLoS One 7:e35888.
46. Fineran PC, Gerritzen MJH, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ. 2014. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A 111:E1629–E1638.
47. Xue C, Seetharam AS, Musharova O, Severinov K, Brouns SJ, Severin AJ, Sashital DG. 2015. CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Res 43:10831–10847.
48. Edgar R, Qimron U. 2010. The Escherichia coli CRISPR system protects from λ lysogenization, lysogens, and prophage induction. J Bacteriol 192:6291–6294.
49. Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJJ, Severinov K. 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.
50. 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. [PubMed]
51. Semenova E, Savitskaya E, Musharova O, Strotskaya A, Vorontsova D, Datsenko KA, Logacheva MD, Severinov K. 2016. Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex. Proc Natl Acad Sci U S A 113:7626–7631.
52. Musharova O, Klimuk E, Datsenko KA, Metlitskaya A, Logacheva M, Semenova E, Severinov K, Savitskaya E. 2017. Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation. Nucleic Acids Res 45:3297–3307.
53. Shmakov S, Savitskaya E, Semenova E, Logacheva MD, Datsenko KA, Severinov K. 2014. Pervasive generation of oppositely oriented spacers during CRISPR adaptation. Nucleic Acids Res 42:5907–5916.
54. Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R. 2018. Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in vitro. Nucleic Acids Res 46:4087–4098.
55. Ivančić-Baće I, Cass SD, Wearne SJ, Bolt EL. 2015. Different genome stability proteins underpin primed and naïve adaptation in E. coli CRISPR-Cas immunity. Nucleic Acids Res 43:10821–10830.
56. Przybilski R, Richter C, Gristwood T, Clulow JS, Vercoe RB, Fineran PC. 2011. Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum. RNA Biol 8:517–528.
57. Fagerlund RD, Wilkinson ME, Klykov O, Barendregt A, Pearce FG, Kieper SN, Maxwell HWR, Capolupo A, Heck AJR, Krause KL, Bostina M, Scheltema RA, Staals RHJ, Fineran PC. 2017. Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex. Proc Natl Acad Sci U S A 114:E5122–E5128.
58. van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, Heck AJ. 2012. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Mol Cell Proteomics 11:1430–1441.
59. Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S. 2017. Cryo-EM structures reveal mechanism and inhibition of DNA targeting by a CRISPR-Cas surveillance complex. Cell 171:414–426.e12. [PubMed]
60. Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B. 2017. Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex. Cell 169:47–57.e11. [PubMed]
61. Patterson AG, Chang JT, Taylor C, Fineran PC. 2015. Regulation of the type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference. Nucleic Acids Res 43:6038–6048.
62. Patterson AG, Yevstigneyeva MS, Fineran PC. 2017. Regulation of CRISPR-Cas adaptive immune systems. Curr Opin Microbiol 37:1–7. [PubMed]
63. Høyland-Kroghsbo NM, Paczkowski J, Mukherjee S, Broniewski J, Westra E, Bondy-Denomy J, Bassler BL. 2017. Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proc Natl Acad Sci U S A 114:131–135.
64. Patterson AG, Jackson SA, Taylor C, Evans GB, Salmond GPC, Przybilski R, Staals RHJ, Fineran PC. 2016. Quorum sensing controls adaptive immunity through the regulation of multiple CRISPR-Cas systems. Mol Cell 64:1102–1108.
65. Tyson GW, Banfield JF. 2008. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10:200–207.
66. Shariat N, Dudley EG. 2014. CRISPRs: molecular signatures used for pathogen subtyping. Appl Environ Microbiol 80:430–439.
67. Cui Y, Li Y, Gorgé O, Platonov ME, Yan Y, Guo Z, Pourcel C, Dentovskaya SV, Balakhonov SV, Wang X, Song Y, Anisimov AP, Vergnaud G, Yang R. 2008. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS One 3:e2652. [PubMed]
68. McGhee GC, Sundin GW. 2012. Erwinia amylovora CRISPR elements provide new tools for evaluating strain diversity and for microbial source tracking. PLoS One 7:e41706.
69. Liu F, Kariyawasam S, Jayarao BM, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG. 2011. Subtyping Salmonella enterica serovar Enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs). Appl Environ Microbiol 77:4520–4526.
70. Liu F, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG. 2011. Novel virulence gene and clustered regularly interspaced short palindromic repeat (CRISPR) multilocus sequence typing scheme for subtyping of the major serovars of Salmonella enterica subsp. enterica. Appl Environ Microbiol 77:1946–1956.
71. Delannoy S, Beutin L, Fach P. 2012. Use of clustered regularly interspaced short palindromic repeat sequence polymorphisms for specific detection of enterohemorrhagic Escherichia coli strains of serotypes O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 by real-time PCR. J Clin Microbiol 50:4035–4040.
72. Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley EG. 2015. Characterization and evolution of Salmonella CRISPR-Cas systems. Microbiology 161:374–386.
73. 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.
74. Medina-Aparicio L, Rebollar-Flores JE, Gallego-Hernández AL, Vázquez A, Olvera L, Gutiérrez-Ríos RM, Calva E, Hernández-Lucas I. 2011. The CRISPR/Cas immune system is an operon regulated by LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella enterica serovar Typhi. J Bacteriol 193:2396–2407.
75. Savitskaya E, Lopatina A, Medvedeva S, Kapustin M, Shmakov S, Tikhonov A, Artamonova II, Logacheva M, Severinov K. 2017. Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years. Mol Ecol 26:2019–2026.
76. Sampson TR, Weiss DS. 2013. Alternative roles for CRISPR/Cas systems in bacterial pathogenesis. PLoS Pathog 9:e1003621. [PubMed]
77. Sampson TR, Napier BA, Schroeder MR, Louwen R, Zhao J, Chin CY, Ratner HK, Llewellyn AC, Jones CL, Laroui H, Merlin D, Zhou P, Endtz HP, Weiss DS. 2014. A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion. Proc Natl Acad Sci U S A 111:11163–11168.
78. Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP. 2011. Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. Mol Microbiol 79:584–599. [PubMed]
79. Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS. 2013. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497:254–257.
80. Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. 2015. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res 43:10848–10860.
81. Richter C, Dy RL, McKenzie RE, Watson BNJ, Taylor C, Chang JT, McNeil MB, Staals RHJ, Fineran PC. 2014. Priming in the type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res 42:8516–8526.
82. Staals RHJ, Jackson SA, Biswas A, Brouns SJJ, Brown CM, Fineran PC. 2016. Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nat Commun 7:12853.
83. Levy A, Goren MG, Yosef I, Auster O, Manor M, Amitai G, Edgar R, Qimron U, Sorek R. 2015. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature 520:505–510.
84. Dillingham MS, Kowalczykowski SC. 2008. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol Mol Biol Rev 72:642–671.
85. George JW, Stohr BA, Tomso DJ, Kreuzer KN. 2001. The tight linkage between DNA replication and double-strand break repair in bacteriophage T4. Proc Natl Acad Sci U S A 98:8290–8297.
86. Kuzminov A. 2001. Single-strand interruptions in replicating chromosomes cause double-strand breaks. Proc Natl Acad Sci U S A 98:8241–8246.
87. Michel B, Flores M-J, Viguera E, Grompone G, Seigneur M, Bidnenko V. 2001. Rescue of arrested replication forks by homologous recombination. Proc Natl Acad Sci U S A 98:8181–8188.
88. Künne T, Kieper SN, Bannenberg JW, Vogel AIM, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJJ. 2016. Cas3-derived target DNA degradation fragments fuel primed CRISPR adaptation. Mol Cell 63:852–864.
89. Loeff L, Brouns SJJ, Joo C. 2018. Repetitive DNA reeling by the Cascade-Cas3 complex in nucleotide unwinding steps. Mol Cell 70:385–394.e3. [PubMed]
90. Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. 2018. Assembly and translocation of a CRISPR-Cas primed acquisition complex. Cell 175:934–946.e15. [PubMed]
91. Xue C, Whitis NR, Sashital DG. 2016. Conformational control of Cascade interference and priming activities in CRISPR immunity. Mol Cell 64:826–834.
92. Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA. 2015. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature 527:535–538.
93. Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y, Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y. 2015. Structural and mechanistic basis of PAM-dependent spacer acquisition in CRISPR-Cas systems. Cell 163:840–853. [PubMed]
94. Amitai G, Sorek R. 2016. CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol 14:67–76.
95. Moch C, Fromant M, Blanquet S, Plateau P. 2017. DNA binding specificities of Escherichia coli Cas1-Cas2 integrase drive its recruitment at the CRISPR locus. Nucleic Acids Res 45:2714–2723.
96. Mojica FJM, Díez-Villaseñor C, García-Martínez J, Almendros C. 2009. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155:733–740.
97. Rollins MF, Schuman JT, Paulus K, Bukhari HST, Wiedenheft B. 2015. Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa. Nucleic Acids Res 43:2216–2222.
98. Díez-Villaseñor C, Guzmán NM, Almendros C, García-Martínez J, Mojica FJM. 2013. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol 10:792–802.
99. Yosef I, Shitrit D, Goren MG, Burstein D, Pupko T, Qimron U. 2013. DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array. Proc Natl Acad Sci U S A 110:14396–14401.
100. Savitskaya E, Semenova E, Dedkov V, Metlitskaya A, Severinov K. 2013. High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli. RNA Biol 10:716–725.
101. Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL. 2016. Identifying and visualizing functional PAM diversity across CRISPR-Cas systems. Mol Cell 62:137–147.
102. Lee H, Zhou Y, Taylor DWDW, Sashital DGDG. 2018. Cas4-dependent prespacer processing ensures high-fidelity programming of CRISPR arrays. Mol Cell 70:48–59.e5.
103. Kieper SN, Almendros C, Behler J, McKenzie RE, Nobrega FL, Haagsma AC, Vink JNA, Hess WR, Brouns SJJ. 2018. Cas4 facilitates PAM-compatible spacer selection during CRISPR adaptation. Cell Reports 22:3377–3384.
104. Rollie C, Graham S, Rouillon C, White MF. 2018. Prespacer processing and specific integration in a type I-A CRISPR system. Nucleic Acids Res 46:1007–1020.
105. Shiimori M, Garrett SC, Graveley BR, Terns MP. 2018. Cas4 nucleases define the PAM, length, and orientation of DNA fragments integrated at CRISPR loci. Mol Cell 70:814–824.e6. [PubMed]
106. Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA. 2015. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 519:199–202. [PubMed]
107. Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna JA. 2016. CRISPR immunological memory requires a host factor for specificity. Mol Cell 62:824–833.
108. McGinn J, Marraffini LA. 2016. CRISPR-Cas systems optimize their immune response by specifying the site of spacer integration. Mol Cell 64:616–623. [PubMed]
109. Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA. 2017. Structures of the CRISPR genome integration complex. Science 357:1113–1118.
110. Arslan Z, Hermanns V, Wurm R, Wagner R, Pul Ü. 2014. Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system. Nucleic Acids Res 42:7884–7893.
111. Rollie C, Schneider S, Brinkmann AS, Bolt EL, White MF. 2015. Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition. eLife 4:e08716.
112. Yoganand KNR, Sivathanu R, Nimkar S, Anand B. 2017. Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system. Nucleic Acids Res 45:367–381.
113. Shipman SL, Nivala J, Macklis JD, Church GM. 2016. Molecular recordings by directed CRISPR spacer acquisition. Science 353:aaf1175. [PubMed]
114. Goren MG, Yosef I, Auster O, Qimron U. 2012. Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J Mol Biol 423:14–16.
115. Jackson SA, McKenzie RE, Fagerlund RD, Kieper SN, Fineran PC, Brouns SJJ. 2017. CRISPR-Cas: adapting to change. Science 356:eaal5056.
116. Wright AV, Doudna JA. 2016. Protecting genome integrity during CRISPR immune adaptation. Nat Struct Mol Biol 23:876–883.
117. Xiao Y, Ng S, Nam KH, Ke A. 2017. How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration. Nature 550:137–141.
118. 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. [PubMed]
119. 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.
120. Jackson RN, Golden SM, van Erp PBG, Carter J, Westra ER, Brouns SJJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B. 2014. Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science 345:1473–1479.
121. Mulepati S, Orr A, Bailey S. 2012. Crystal structure of the largest subunit of a bacterial RNA-guided immune complex and its role in DNA target binding. J Biol Chem 287:22445–22449.
122. Zhao H, Sheng G, Wang J, Wang M, Bunkoczi G, Gong W, Wei Z, Wang Y. 2014. Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli. Nature 515:147–150.
123. Xue C, Zhu Y, Zhang X, Shin Y-K, Sashital DG. 2017. Real-time observation of target search by the CRISPR surveillance complex Cascade. Cell Rep 21:3717–3727.
124. Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, Siksnys V, Seidel R. 2014. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci U S A 111:9798–9803.
125. Rutkauskas M, Sinkunas T, Songailiene I, Tikhomirova MS, Siksnys V, Seidel R. 2015. Directional R-loop formation by the CRISPR-Cas surveillance complex Cascade provides efficient off-target site rejection. Cell Rep 10:1534–1543.
126. van Erp PBG, Jackson RN, Carter J, Golden SM, Bailey S, Wiedenheft B. 2015. Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli. Nucleic Acids Res 43:8381–8391.
127. Hayes RP, Xiao Y, Ding F, van Erp PBG, Rajashankar K, Bailey S, Wiedenheft B, Ke A. 2016. Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature 530:499–503.
128. Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A. 2017. Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPR-Cas System. Cell 170:48–60.e11.
129. Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD Jr, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A. 2014. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nat Struct Mol Biol 21:771–777. [PubMed]
130. Gong B, Shin M, Sun J, Jung C-H, Bolt EL, van der Oost J, Kim J-S. 2014. Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3. Proc Natl Acad Sci U S A 111:16359–16364.
131. Sashital DG, Jinek M, Doudna JA. 2011. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol 18:680–687. [PubMed]
132. 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. [PubMed]
133. Cady KC, O’Toole GA. 2011. Non-identity targeting of Yersinia-subtype CRISPR-prophage interaction requires the Csy and Cas3 proteins. J Bacteriol 193:2433–2445. [PubMed]
134. Haurwitz RE, Sternberg SH, Doudna JA. 2012. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J 31:2824–2832. [PubMed]
135. Sternberg SH, Haurwitz RE, Doudna JA. 2012. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 18:661–672. [PubMed]
136. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna JA, Nogales E. 2011. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477:486–489. [PubMed]
137. Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M, Datsenko KA, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin AF, Severinov K, Semenova E. 2016. Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Nucleic Acids Res 44:10849–10861. [PubMed]
138. Luo ML, Jackson RN, Denny SR, Tokmina-Lukaszewska M, Maksimchuk KR, Lin W, Bothner B, Wiedenheft B, Beisel CL. 2016. The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers. Nucleic Acids Res 44:7385–7394. [PubMed]
139. Mulepati S, Héroux A, Bailey S. 2014. Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target. Science 345:1479–1484. [PubMed]
140. van Erp PBG, Patterson A, Kant R, Berry L, Golden SM, Forsman BL, Carter J, Jackson RN, Bothner B, Wiedenheft B. 2018. Conformational dynamics of DNA binding and Cas3 recruitment by the CRISPR RNA-guided Cascade complex. ACS Chem Biol 13:481–490. [PubMed]
141. Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJJ. 2013. Type I-E CRISPR-Cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet 9:e1003742. [PubMed]
142. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. 2014. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507:62–67. [PubMed]
143. Singh D, Sternberg SH, Fei J, Doudna JA, Ha T. 2016. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun 7:12778. [PubMed]
144. Singh D, Mallon J, Poddar A, Wang Y, Tippana R, Yang O, Bailey S, Ha T. 2018. Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). Proc Natl Acad Sci U S A 115:5444–5449. [PubMed]
145. Jackson RN, Lavin M, Carter J, Wiedenheft B. 2014. Fitting CRISPR-associated Cas3 into the helicase family tree. Curr Opin Struct Biol 24:106–114. [PubMed]
146. Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, Romero DA, Horvath P, Moineau S. 2008. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190:1390–1400. [PubMed]
147. van Houte S, Ekroth AKE, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, Westra ER. 2016. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature 532:385–388. [PubMed]
148. Paez-Espino D, Sharon I, Morovic W, Stahl B, Thomas BC, Barrangou R, Banfield JF. 2015. CRISPR immunity drives rapid phage genome evolution in Streptococcus thermophilus. MBio 6:e00262-15. [PubMed]
149. Tao P, Wu X, Rao V. 2018. Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9. Sci Adv 4:eaar4134. [PubMed]
150. Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR. 2013. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493:429–432. [PubMed]
151. Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, Wiedenheft B, Maxwell KL, Davidson AR. 2015. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature 526:136–139.
152. Borges AL, Davidson AR, Bondy-Denomy J. 2017. The discovery, mechanisms, and evolutionary impact of anti-CRISPRs. Annu Rev Virol 4:37–59.
153. Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M. 2017. Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. Sci Rep 7:10392.
154. Semenova E, Kuznedelov K, Datsenko KA, Boudry PM, Savitskaya EE, Medvedeva S, Beloglazova N, Logacheva M, Yakunin AF, Severinov K. 2015. The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I-E CRISPR-Cas system. Nucleic Acids Res 43:6049–6061.
155. Fu BX, Wainberg M, Kundaje A, Fire AZ. 2017. High-throughput characterization of cascade type I-E CRISPR guide efficacy reveals unexpected PAM diversity and target sequence preferences. Genetics 206:1727–1738.
156. Cooper LA, Stringer AM, Wade JT. 2018. Determining the specificity of Cascade binding, interference, and primed adaptation in vivo in the Escherichia coli type I-E CRISPR-Cas system. MBio 9:e02100-17.
157. Caliando BJ, Voigt CA. 2015. Targeted DNA degradation using a CRISPR device stably carried in the host genome. Nat Commun 6:6989.
158. Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C. 2015. Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol Cell 58:60–70.
159. Jung C, Hawkins JA, Jones SK Jr, Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. 2017. Massively parallel biophysical analysis of CRISPR-Cas complexes on next generation sequencing chips. Cell 170:35–47.e13.
160. Pawluk A, Bondy-Denomy J, Cheung VHW, Maxwell KL, Davidson AR. 2014. A new group of phage anti-CRISPR genes inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. MBio 5:e00896.
161. Pawluk A, Staals RHJJ, Taylor C, Watson BNJJ, Saha S, Fineran PC, Maxwell KL, Davidson AR. 2016. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat Microbiol 1:16085.
162. Pawluk A, Amrani N, Zhang Y, Garcia B, Hidalgo-Reyes Y, Lee J, Edraki A, Shah M, Sontheimer EJ, Maxwell KL, Davidson AR. 2016. Naturally occurring off-switches for CRISPR-Cas9. Cell 167:1829–1838.e9.
163. Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. 2017. Inhibition of CRISPR-Cas9 with bacteriophage proteins. Cell 168:150–158.e10.
164. He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X. 2018. Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 3:461–469. [PubMed]
165. Guo T, Han W, She Q. 2018. Tolerance of Sulfolobus SMV1 virus to the immunity of I-A and III-B CRISPR-Cas systems in Sulfolobus islandicus. RNA Biol. Epub ahead of print. doi:10.1080/15476286.2018.1460993.
166. Wang X, Yao D, Xu JG, Li AR, Xu J, Fu P, Zhou Y, Zhu Y. 2016. Structural basis of Cas3 inhibition by the bacteriophage protein AcrF3. Nat Struct Mol Biol 23:868–870.
167. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. 2017. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv 3:e1701620. [PubMed]
168. Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA. 2017. A broad-spectrum inhibitor of CRISPR-Cas9. Cell 170:1224–1233.e15.
169. Kim I, Jeong M, Ka D, Han M, Kim NK, Bae E, Suh JY. 2018. Solution structure and dynamics of anti-CRISPR AcrIIA4, the Cas9 inhibitor. Sci Rep 8:3883. [PubMed]
170. Yang H, Patel DJ. 2017. Inhibition mechanism of an anti-CRISPR suppressor AcrIIA4 targeting SpyCas9. Mol Cell 67:117–127.e5.
171. Dong D, Guo M, Wang S, Zhu Y, Wang S, Xiong Z, Yang J, Xu Z, Huang Z. 2017. Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein. Nature 546:436–439.
172. Borges AL, Zhang JY, Rollins MF, Osuna BA, Wiedenheft B, Bondy-Denomy J. 2018. Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity. Cell 174:917–925.e10.
173. Landsberger M, Gandon S, Meaden S, Rollie C, Chevallereau A, Chabas H, Buckling A, Westra ER, van Houte S. 2018. Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity. Cell 174:908–916.e12. [PubMed]
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/content/journal/ecosalplus/10.1128/ecosalplus.ESP-0008-2018
2019-02-06
2020-11-24

Abstract:

CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invasion by bacteriophages and other mobile genetic elements. Short fragments of invader DNA are stored as immunological memories within CRISPR (clustered regularly interspaced short palindromic repeat) arrays in the host chromosome. These arrays provide a template for RNA molecules that can guide CRISPR-associated (Cas) proteins to specifically neutralize viruses upon subsequent infection. Over the past 10 years, our understanding of CRISPR-Cas systems has benefited greatly from a number of model organisms. In particular, the study of several members of the Gram-negative family, especially and , have provided significant insights into the mechanisms of CRISPR-Cas immunity. In this review, we provide an overview of CRISPR-Cas systems present in members of the . We also detail the current mechanistic understanding of the type I-E and type I-F CRISPR-Cas systems that are commonly found in enterobacteria. Finally, we discuss how phages can escape or inactivate CRISPR-Cas systems and the measures bacteria can enact to counter these types of events.

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Mechanisms of Type I-E and I-F CRISPR-Cas Systems in
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Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
/content/ecosalplus/10.1128/ecosalplus.ESP-0008-2018.fig1
Figure 1
CRISPR-Cas operons contain CRISPR arrays and CRISPR-associated () genes. In the adaptation stage, short DNA fragments generated from phage DNA are captured by the adaptation complex. Following trimming of excess DNA, the adaptation complex integrates these fragments into the CRISPR array. During the expression and maturation stage, the CRISPR array is transcribed into long pre-CRISPR RNAs (pre-crRNAs). The pre-crRNAs are cleaved within the repeat regions to generate mature crRNAs. Each crRNA assembles with Cas proteins to form a surveillance complex. During the interference stage, the surveillance complex recognizes the target by complementary base-pairing with the crRNA sequence. Target binding triggers recruitment of a nuclease, which catalyzes degradation of the target nucleic acid.
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Figure 1

CRISPR-Cas operons contain CRISPR arrays and CRISPR-associated () genes. In the adaptation stage, short DNA fragments generated from phage DNA are captured by the adaptation complex. Following trimming of excess DNA, the adaptation complex integrates these fragments into the CRISPR array. During the expression and maturation stage, the CRISPR array is transcribed into long pre-CRISPR RNAs (pre-crRNAs). The pre-crRNAs are cleaved within the repeat regions to generate mature crRNAs. Each crRNA assembles with Cas proteins to form a surveillance complex. During the interference stage, the surveillance complex recognizes the target by complementary base-pairing with the crRNA sequence. Target binding triggers recruitment of a nuclease, which catalyzes degradation of the target nucleic acid.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Figure 2
Type I-E CRISPR-Cas operon of K-12. Promoters are shown as arrows. Repressors of the and promoters are indicated. Type I-F CRISPR-Cas operon of . CRISPR 1 is expressed on the minus strand. Activator of the promoter, which controls expression of all genes, is indicated.
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Figure 2

Type I-E CRISPR-Cas operon of K-12. Promoters are shown as arrows. Repressors of the and promoters are indicated. Type I-F CRISPR-Cas operon of . CRISPR 1 is expressed on the minus strand. Activator of the promoter, which controls expression of all genes, is indicated.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Figure 3
During naive adaptation, RecBCD products serve as substrates for the Cas1-Cas2 adaptation complex (gold). The abundance of Chi sites (magenta) prevents accumulation of DNA fragments from the host genome, while the lack of Chi sites in foreign DNA leads to a larger pool from this source. Replication forks are common sites for DSBs, which are initiation sites for RecBCD degradation sites. Higher-copy foreign DNA contains more replication forks and therefore leads to more DSBs and RecBCD recruitment. Phage DNA is often injected in a linear form, and these ends are subject to degradation by RecBCD. Also shown are two potential mechanisms for primed adaptation: During interference-dependent primed adaptation, the surveillance complex (light blue) directs Cas3 (dark blue) degradation of the foreign DNA. Cas3 products create a DNA fragment pool that provides prespacer substrates for Cas1-Cas2. During interference-independent primed adaptation, both Cas3 and Cas1-Cas2 (or Cas1-Cas2/3) are recruited to the target-bound surveillance complex. The Cas3 helicase domain extrudes a DNA loop as the priming complex searches for prespacer substrates and excises them through the nuclease activity of either Cas1, Cas3, or both subunits.
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Figure 3

During naive adaptation, RecBCD products serve as substrates for the Cas1-Cas2 adaptation complex (gold). The abundance of Chi sites (magenta) prevents accumulation of DNA fragments from the host genome, while the lack of Chi sites in foreign DNA leads to a larger pool from this source. Replication forks are common sites for DSBs, which are initiation sites for RecBCD degradation sites. Higher-copy foreign DNA contains more replication forks and therefore leads to more DSBs and RecBCD recruitment. Phage DNA is often injected in a linear form, and these ends are subject to degradation by RecBCD. Also shown are two potential mechanisms for primed adaptation: During interference-dependent primed adaptation, the surveillance complex (light blue) directs Cas3 (dark blue) degradation of the foreign DNA. Cas3 products create a DNA fragment pool that provides prespacer substrates for Cas1-Cas2. During interference-independent primed adaptation, both Cas3 and Cas1-Cas2 (or Cas1-Cas2/3) are recruited to the target-bound surveillance complex. The Cas3 helicase domain extrudes a DNA loop as the priming complex searches for prespacer substrates and excises them through the nuclease activity of either Cas1, Cas3, or both subunits.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Figure 4
Schematic illustration of Cas1-Cas2 bound to a 23-bp duplex with splayed ends. Individual subunits of Cas1 are shown in orange or gold, individual subunits of Cas2 are shown in light or dark blue, DNA substrate is shown in gray, and PAM is shown in yellow. The 3′-overhangs, one of which contains the PAM, are located in the Cas1 active sites, suggesting that trimming of these ends may be carried out by Cas1. The 5′-overhangs are exposed and may be trimmed by another factor. The trimmed product is a prespacer containing a 23-bp duplex with 5-nt 3′-overhangs containing exposed 3′-hydroxyl groups. Structure of the Cas1-Cas2 complex bound to an untrimmed substrate (PDB number 5DQZ) ( 93 ). Colors are as in panel A. Close-up of Cas1 active site recognition of the 5′-CTT-3′ PAM (yellow) region of the untrimmed prespacer. Hydrogen-bonding interactions are shown with dashed lines. The boxed region shows the scissile phosphate, which is coordinated by the catalytic histidine and aspartate residues of the HD domain. Following cleavage, only the cytosine is retained as the last nucleotide of the trimmed substrate.
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Figure 4

Schematic illustration of Cas1-Cas2 bound to a 23-bp duplex with splayed ends. Individual subunits of Cas1 are shown in orange or gold, individual subunits of Cas2 are shown in light or dark blue, DNA substrate is shown in gray, and PAM is shown in yellow. The 3′-overhangs, one of which contains the PAM, are located in the Cas1 active sites, suggesting that trimming of these ends may be carried out by Cas1. The 5′-overhangs are exposed and may be trimmed by another factor. The trimmed product is a prespacer containing a 23-bp duplex with 5-nt 3′-overhangs containing exposed 3′-hydroxyl groups. Structure of the Cas1-Cas2 complex bound to an untrimmed substrate (PDB number 5DQZ) ( 93 ). Colors are as in panel A. Close-up of Cas1 active site recognition of the 5′-CTT-3′ PAM (yellow) region of the untrimmed prespacer. Hydrogen-bonding interactions are shown with dashed lines. The boxed region shows the scissile phosphate, which is coordinated by the catalytic histidine and aspartate residues of the HD domain. Following cleavage, only the cytosine is retained as the last nucleotide of the trimmed substrate.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Figure 5
Schematic overview of the integration process in . A 3′-OH group of the prespacer attacks the backbone at the leader-proximal end of the first repeat within the CRISPR array, forming a half-site intermediate. The end of the prespacer containing the cytosine from the PAM attacks at the leader-distal end of the opposite strand of the repeat, forming a full-site intermediate. The single-stranded repeats on either end of the integrated spacer are filled by DNA polymerase I, and the nicks are ligated to create an intact CRISPR array. Schematic of leader-proximal and leader-distal integration by Cas1-Cas2 (colored as in Fig. 4 ). Cas1-Cas2 senses the sequence-dependent deformation of the repeat to facilitate integration at the correct sites within the repeat. Cryo-EM structure of Cas1-Cas2 bound to a half-site intermediate containing the IHF-bound leader (PDB number 5WFE) ( 109 ). IHF (dark and light green subunits) binds positions -9 to -35 of the leader (pink) and bends the DNA by ∼180°. This bending brings the upstream binding element (UBS, turquoise) into proximity of the leader-proximal Cas1 dimer, an interaction that ensures integration at the leader-proximal repeat.
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Figure 5

Schematic overview of the integration process in . A 3′-OH group of the prespacer attacks the backbone at the leader-proximal end of the first repeat within the CRISPR array, forming a half-site intermediate. The end of the prespacer containing the cytosine from the PAM attacks at the leader-distal end of the opposite strand of the repeat, forming a full-site intermediate. The single-stranded repeats on either end of the integrated spacer are filled by DNA polymerase I, and the nicks are ligated to create an intact CRISPR array. Schematic of leader-proximal and leader-distal integration by Cas1-Cas2 (colored as in Fig. 4 ). Cas1-Cas2 senses the sequence-dependent deformation of the repeat to facilitate integration at the correct sites within the repeat. Cryo-EM structure of Cas1-Cas2 bound to a half-site intermediate containing the IHF-bound leader (PDB number 5WFE) ( 109 ). IHF (dark and light green subunits) binds positions -9 to -35 of the leader (pink) and bends the DNA by ∼180°. This bending brings the upstream binding element (UBS, turquoise) into proximity of the leader-proximal Cas1 dimer, an interaction that ensures integration at the leader-proximal repeat.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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/content/ecosalplus/10.1128/ecosalplus.ESP-0008-2018.fig6
Figure 6
The product of transcription of the CRISPR is a pre-crRNA containing stem-loops within the repeats. Cas6 endoribonucleases (pink) recognize the stem-loops and cleave at the base to form mature crRNAs. Cas6 subunits remain bound to the stem-loop at the 3′-end of the crRNA following cleavage. Six Cas7 subunits (blue) assemble along the length of the crRNA spacer (red), and the Cas5 subunit (purple) caps the Cas7 backbone by specifically recognizing the 5′-repeat-derived handle. In type I-E Cascade, two subtype-specific subunits, Cse2 (orange), assemble on the belly of the complex. The Cas8 subunit (green) caps the complex on the Cas5 end. Schematic of assembled Cascade and Csy complex. Subunits are colored as in panel B, except for Cas8e (panel C) and Cas8f (panel D), which are shown with a green outline. Structures of fully assembled Cascade (PDB ID 4TVX) and Csy (PDB ID 6B45) complex ( 59 , 120 ).
ecosalplus/8/2/ESP-0008-2018_fig_006_thmb.gif
ecosalplus/8/2/ESP-0008-2018_fig_006.gif
Image of Figure 6
Figure 6

The product of transcription of the CRISPR is a pre-crRNA containing stem-loops within the repeats. Cas6 endoribonucleases (pink) recognize the stem-loops and cleave at the base to form mature crRNAs. Cas6 subunits remain bound to the stem-loop at the 3′-end of the crRNA following cleavage. Six Cas7 subunits (blue) assemble along the length of the crRNA spacer (red), and the Cas5 subunit (purple) caps the Cas7 backbone by specifically recognizing the 5′-repeat-derived handle. In type I-E Cascade, two subtype-specific subunits, Cse2 (orange), assemble on the belly of the complex. The Cas8 subunit (green) caps the complex on the Cas5 end. Schematic of assembled Cascade and Csy complex. Subunits are colored as in panel B, except for Cas8e (panel C) and Cas8f (panel D), which are shown with a green outline. Structures of fully assembled Cascade (PDB ID 4TVX) and Csy (PDB ID 6B45) complex ( 59 , 120 ).

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Figure 7
Overview of target search by Cascade. Nonspecific interactions at sites with no PAM or PAMs adjacent to nonmatching sequences result in rapid dissociation. At PAM sites, Cascade can initiate unwinding to enable crRNA strand invasion. At partially matching targets, R-loops can form directionally away from the PAM until a mismatch is encountered. Depending on the location and thermodynamic barrier of the mismatch, the R-loop can stall, it can continue to form, or Cascade can dissociate. At a perfect target, complete R-loop formation leads to Cascade locking and a highly stable interaction. Structure of Cascade bound to dsDNA (PDB number 5H9F, colored as in Fig. 6 ) ( 127 ). The Cas11 subunits move down along the belly during R-loop locking. The nontarget strand is stabilized through interactions with Cas8e. Close-up of Cas8e-PAM and Cascade-dsDNA interactions. A glutamine residue acts as a wedge to facilitate DNA unwinding. The PAM is read through minor-groove interactions with Cas8e. Lys-rich loops in Cas7 and Cas7 subunits act as an electrostatic vise to hold the dsDNA during unwinding. The Cas8e CTD four-helix bundle moves toward the N-terminal domain during R-loop locking. Structure of the Csy complex bound to dsDNA (PDB number 6B44, colored as in Fig. 6 ) ( 59 ). The Cas7 backbone elongates by ∼20 Å upon DNA binding. Close-up of Cas8f-PAM and Csy-dsDNA interactions. A lysine residue acts as a wedge to facilitate DNA unwinding. The PAM is read through minor-groove interactions with Cas8f. Several positive residues in Cas7, Cas8f, and Cas5 stabilize interactions with the dsDNA. The Cas8f hook elongates to accommodate the dsDNA.
ecosalplus/8/2/ESP-0008-2018_fig_007_thmb.gif
ecosalplus/8/2/ESP-0008-2018_fig_007.gif
Image of Figure 7
Figure 7

Overview of target search by Cascade. Nonspecific interactions at sites with no PAM or PAMs adjacent to nonmatching sequences result in rapid dissociation. At PAM sites, Cascade can initiate unwinding to enable crRNA strand invasion. At partially matching targets, R-loops can form directionally away from the PAM until a mismatch is encountered. Depending on the location and thermodynamic barrier of the mismatch, the R-loop can stall, it can continue to form, or Cascade can dissociate. At a perfect target, complete R-loop formation leads to Cascade locking and a highly stable interaction. Structure of Cascade bound to dsDNA (PDB number 5H9F, colored as in Fig. 6 ) ( 127 ). The Cas11 subunits move down along the belly during R-loop locking. The nontarget strand is stabilized through interactions with Cas8e. Close-up of Cas8e-PAM and Cascade-dsDNA interactions. A glutamine residue acts as a wedge to facilitate DNA unwinding. The PAM is read through minor-groove interactions with Cas8e. Lys-rich loops in Cas7 and Cas7 subunits act as an electrostatic vise to hold the dsDNA during unwinding. The Cas8e CTD four-helix bundle moves toward the N-terminal domain during R-loop locking. Structure of the Csy complex bound to dsDNA (PDB number 6B44, colored as in Fig. 6 ) ( 59 ). The Cas7 backbone elongates by ∼20 Å upon DNA binding. Close-up of Cas8f-PAM and Csy-dsDNA interactions. A lysine residue acts as a wedge to facilitate DNA unwinding. The PAM is read through minor-groove interactions with Cas8f. Several positive residues in Cas7, Cas8f, and Cas5 stabilize interactions with the dsDNA. The Cas8f hook elongates to accommodate the dsDNA.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Figure 8
Structure of type I-E Cascade-dsDNA following Cas3 recruitment (PDB number 6C66) ( 33 ). Cascade and DNA are colored as in Fig. 6 and 7 ; Cas3 is shown in cyan (helicase and C-terminal domains) and dark blue (HD nuclease domain). Cas3 senses the conformation of Cas8e following R-loop locking. Comparison of Cas8e structure in the locked (PDB number 6C66, green) and unlocked (PDB number 5U07, gray) conformations ( 33 , 128 ). Prior to R-loop locking and movement of the CTD, a loop and helix of the Cas8e CTD would cause steric clashes with the Cas3 nuclease domain. Also shown is a schematic of Cas3 DNA reeling and degradation: Following its recruitment to the R-loop, Cas3 nicks the nontarget strand. The nicked strand is loaded into the Cas3 helicase domain, stabilizing the Cas3-Cascade interaction. The Cas3 helicase domain reels the nontarget strand, while the target strand is extruded and forms an ssDNA loop. The HD nuclease domain can nick the nontarget strand intermittently, creating products that could serve as prespacer substrates for Cas1-Cas2 ( Fig. 3E ), or it can release the DNA and repeat the reeling motion. In type I-F systems, two Cas2/3 molecules may be recruited to the Csy complex, allowing for bidirectional degradation of both strands of the DNA.
ecosalplus/8/2/ESP-0008-2018_fig_008_thmb.gif
ecosalplus/8/2/ESP-0008-2018_fig_008.gif
Image of Figure 8
Figure 8

Structure of type I-E Cascade-dsDNA following Cas3 recruitment (PDB number 6C66) ( 33 ). Cascade and DNA are colored as in Fig. 6 and 7 ; Cas3 is shown in cyan (helicase and C-terminal domains) and dark blue (HD nuclease domain). Cas3 senses the conformation of Cas8e following R-loop locking. Comparison of Cas8e structure in the locked (PDB number 6C66, green) and unlocked (PDB number 5U07, gray) conformations ( 33 , 128 ). Prior to R-loop locking and movement of the CTD, a loop and helix of the Cas8e CTD would cause steric clashes with the Cas3 nuclease domain. Also shown is a schematic of Cas3 DNA reeling and degradation: Following its recruitment to the R-loop, Cas3 nicks the nontarget strand. The nicked strand is loaded into the Cas3 helicase domain, stabilizing the Cas3-Cascade interaction. The Cas3 helicase domain reels the nontarget strand, while the target strand is extruded and forms an ssDNA loop. The HD nuclease domain can nick the nontarget strand intermittently, creating products that could serve as prespacer substrates for Cas1-Cas2 ( Fig. 3E ), or it can release the DNA and repeat the reeling motion. In type I-F systems, two Cas2/3 molecules may be recruited to the Csy complex, allowing for bidirectional degradation of both strands of the DNA.

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
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Tables

Mechanisms of Type I-E and I-F CRISPR-Cas Systems in
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Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018
/content/ecosalplus/10.1128/ecosalplus.ESP-0008-2018.T1
Table 1
Cas proteins of type I-E and I-F CRISPR-Cas systems
Generic image for table
Table 1

Cas proteins of type I-E and I-F CRISPR-Cas systems

Citation: Xue C, Sashital D. 2019. Mechanisms of Type I-E and I-F CRISPR-Cas Systems in , EcoSal Plus 2019; doi:10.1128/ecosalplus.ESP-0008-2018

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