Applications of the versatile CRISPR-Cas systems

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

Volumn , Issue , 2013, Pages 267-286

  Horvath, Philippe ^a   Gasiunas, Giedrius ^b   Siksnys, Virginijus ^b   Barrangou, Rodolphe ^c  

^a DUPONT COMPANY   (United States)

^b VILNIUS UNIVERSITY   (Lithuania)

^c DuPont Nutrition and Health   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84940100856     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-34657-6     Document Type: Chapter

References (84)

1. Abadia E, Zhang J, dos Vultos T, Ritacco V, Kremer K, Aktas E, Matsumoto T, Refregier G, van Soolingen D, Gicquel B, Sola C (2010) Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method. Infect Genet Evol 10:1066-1074
2. Aklujkar M, Lovley DR (2010) Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus. BMC Evol Biol 10:230
3. Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047-1050
4. Anderson RE, Brazelton WJ, Baross JA (2011) Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. FEMS Microbiol Ecol 77:120-133
5. 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
6. Barrangou R (2012) RNA-mediated programmable DNA cleavage. Nat Biotechnol 30:836-838
7. Barrangou R, Horvath P (2012) CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol 3:143-162
8. 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
9. Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA (2012) Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 14:207-227
10. Bikard D, Hatoum-Aslan A, Mucida D, Marraffini LA (2012) CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12:177-186
11. 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
12. Borile C, Labarre M, Franz S, Sola C, Refrégier G (2011) Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis. BMC Bioinf 12:224
13. 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
14. Brudey K, Driscoll JR, Rigouts L et al (2006) Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 6:23
15. Brüggemann H, Lomholt HB, Tettelin H, Kilian M (2012) CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLoS ONE 7:e34171
16. Cady KC, O’Toole GA (2011) Non-identity-mediated CRISPR-bacteriophage interaction mediated via the Csy and Cas3 proteins. J Bacteriol 193:3433-3445
17. Cady KC, White AS, Hammond JH, Abendroth MD, Karthikeyan RS, Lalitha P, Zegans ME, O’Toole GA (2011) Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates. Microbiology 157:430-437
18. Cady KC, Bondy-Denomy J, Heussler GE, Davidson AR, O’Toole GA (2012) The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages. J Bacteriol 194:5728-5738
19. 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
20. 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
21. D’Auria G, Jiménez-Hernández N, Peris-Bondia F, Moya A, Latorre A (2010) Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics 11:181
22. Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, Ferguson-Noel N, Tsai P, Rodrigo A, Edwards SV (2012) Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum. PLoS Genet 8:e1002511
23. Delannoy S, Beutin L, Burgos Y, Fach P (2012) Specific detection of enteroaggregative hemorrhagic Escherichia coli O104:H4 strains using the CRISPR locus as target for a diagnostic real-time PCR. J Clin Microbiol 50:3485-3492
24. 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
25. Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJ (2010) Diversity of CRISPR loci in Escherichia coli. Microbiology 156:1351-1361
26. Djordjevic M, Djordjevic M, Severinov K (2012) CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs. Biol Direct 7:24
27. Erdmann S, Garrett RA (2012) Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol Microbiol 85:1044-1056
28. Fabre L, Zhang J, Guigon G, LeHello S, Guibert V, Accou-Demartin M, deRomans S, Lim C, Roux C, Passet V, Diancourt L, Guibourdenche M, Issenhuth-Jeanjean S, Achtman M, Brisse S, Sola C, Weill FX (2012) CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS ONE 7:e36995
29. Fricke WF, Mammel MK, McDermott PF, Tartera C, White DG, Leclerc JE, Ravel J, Cebula TA (2011) Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPRmediated adaptive sublineage evolution. J Bacteriol 193:3556-3568
30. Garcia-Heredia I, Martin-Cuadrado AB, Mojica FJ, Santos F, Mira A, Antón J, Rodriguez-Valera F (2012) Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS ONE 7:e33802
31. Garneau JE, Dupuis MÈ, 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
32. Garrett RA, Shah SA, Vestergaard G, Deng L, Gudbergsdottir S, Kenchappa CS, Erdmann S, She Q (2011) CRISPR-based immune systems of the Sulfolobales: complexity and diversity. Biochem Soc Trans 39:51-57
33. Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109:E2579-E2586
34. Ginevra C, Jacotin N, Diancourt L, Guigon G, Arquilliere R, Meugnier H, Descours G, Vandenesch F, Etienne J, Lina G, Caro V, Jarraud S (2012) Legionella pneumophila sequence type 1/Paris pulsotype subtyping by spoligotyping. J Clin Microbiol 50:696-701
35. Godde JS, Bickerton A (2006) The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol 62:718-729
36. Groenen PM, Bunschoten AE, van Soolingen D, van Embden JD (1993) Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol 10:1057-1065
37. 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
38. Hale CR, Majumdar S, Elmore J, Pfister N, Compton M, Olson S, Resch AM, Glover CV 3rd, Graveley BR, Terns RM, Terns MP (2012) Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol Cell 45:292-302
39. 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
40. Held NL, Whitaker RJ (2009) Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol 11:457-466
41. Hoe N, Nakashima K, Grigsby D, Pan X, Dou SJ, Naidich S, Garcia M, Kahn E, Bergmire-Sweat D, Musser JM (1999) Rapid molecular genetic subtyping of serotype M1 group A Streptococcus strains. Emerg Infect Dis 5:254-263
42. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167-170
43. Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190:1401-1412
44. Horvath P, Coûté-Monvoisin AC, Romero DA, Boyaval P, Fremaux C, Barrangou R (2009) Comparative analysis of CRISPR loci in lactic acid bacteria genomes. Int J Food Microbiol 131:62-70
45. 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 337:816-821
46. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8:317-327
47. Liu F, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG (2011a) 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
48. Liu F, Kariyawasam S, Jayarao BM, Barrangou R, Gerner-Smidt P, Ribot EM, Knabel SJ, Dudley EG (2011b) 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
49. Lopez-Sanchez MJ, Sauvage E, Da Cunha V, Clermont D, Ratsima Hariniaina E, Gonzalez-Zorn B, Poyart C, Rosinski-Chupin I, Glaser P (2012) The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome. Mol Microbiol 85:1057-1071
50. Louwen R, Horst-Kreft D, de Boer AG, van der Graaf L, de Knegt G, Hamersma M, Heikema AP, Timms AR, Jacobs BC, Wagenaar JA, Endtz HP, van der Oost J, Wells JM, Nieuwenhuis EE, van Vliet AH, Willemsen PT, van Baarlen P, van Belkum A (2012) A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome. Eur J Clin Microbiol Infect Dis. doi:10.1007/s10096-012-1733-4
51. Magadán AH, Dupuis MÈ, Villion M, Moineau S (2012) Cleavage of Phage DNA by the Streptococcus thermophilus CRISPR3-Cas System. PLoS ONE 7:e40913
52. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843-1845
53. 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
54. McShan WM, Ferretti JJ, Karasawa T, Suvorov AN, Lin S, Qin B, Jia H, Kenton S, Najar F, Wu H, Scott J, Roe BA, Savic DJ (2008) Genome sequence of a nephritogenic and highly transformable M49 strain of Streptococcus pyogenes. J Bacteriol 190:7773-7785
55. Mills S, Griffin C, Coffey A, Meijer WC, Hafkamp B, Ross RP (2010) CRISPR analysis of bacteriophage-insensitive mutants (BIMs) of industrial Streptococcus thermophilus-implications for starter design. J Appl Microbiol 108:945-955
56. 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
57. Mojica FJ, 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
58. Mokrousov I, Limeschenko E, Vyazovaya A, Narvskaya O (2007) Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci. Biotechnol J 2:901-906
59. Mokrousov I, Vyazovaya A, Kolodkina V, Limeschenko E, Titov L, Narvskaya O (2009) Novel macroarray-based method of Corynebacterium diphtheriae genotyping: evaluation in a field study in Belarus. Eur J Clin Microbiol Infect Dis 28:701-703
60. Nozawa T, Furukawa N, Aikawa C, Watanabe T, Haobam B, Kurokawa K, Mauyama F, Nakagawa I (2011) CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS ONE 6:e19543
61. Palmer KL, Gilmore MS (2010) Multidrug-resistant enterococci lack CRISPR-cas. MBio 1:e00227-e00310
62. Palmer KL, Whiteley M (2011) DMS3-42: the secret to CRISPR-dependent biofilm inhibition in Pseudomonas aeruginosa. J Bacteriol 193:3431-3432
63. 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
64. 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
65. Price EP, Smith H, Huygens F, Giffard PM (2007) High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni. Appl Environ Microbiol 73:3431-3436
66. Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA (2011) Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res 21:126-136
67. Pride DT, Salzman J, Relman DA (2012) Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol 14:2564-2576
68. Rezzonico F, Smits TH, Duffy B (2011) Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora. Appl Environ Microbiol 77:3819-3829
69. Rho M, Wu YW, Tang H, Doak TG, Ye Y (2012) Diverse CRISPRs evolving in human microbiomes. PLoS Genet 8:e1002441
70. Riehm JM, Vergnaud G, Kiefer D, Damdindorj T, Dashdavaa O, Khurelsukh T, Zöller L, Wölfel R, Le Flèche P, Scholz HC (2012) Yersinia pestis lineages in Mongolia. PLoS ONE 7:e30624
71. 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 39:9275-9282
72. Schouls LM, Reulen S, Duim B, Wagenaar JA, Willems RJ, Dingle KE, Colles FM, Van Embden JD (2003) Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol 41:15-26
73. Snyder JC, Bateson MM, Lavin M, Young MJ (2010) Use of cellular CRISPR (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples. Appl Environ Microbiol 76:7251-7258
74. Stern A, Keren L, Wurtzel O, Amitai G, Sorek R (2010) Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet 26:335-340
75. Stern A, Mick E, Tirosh I, Sagy O, Sorek R (2012) CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res 22:1985-1994
76. Sturino JM, Klaenhammer TR (2006) Engineered bacteriophage-defence systems in bioprocessing. Nat Rev Microbiol 4:395-404
77. Swarts DC, Mosterd C, van Passel MW, Brouns SJ (2012) CRISPR interference directs strand specific spacer acquisition. PLoS ONE 7:e35888
78. Tasaki E, Hirayama J, Tazumi A, Hayashi K, Hara Y, Ueno H, Moore JE, Millar BC, Matsuda M (2012) Molecular identification and characterization of clustered regularly interspaced short palindromic repeats (CRISPRs) in a urease-positive thermophilic Campylobacter sp. (UPTC). World J Microbiol Biotechnol 28:713-720
79. Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10:200-207
80. van der Ploeg JR (2009) Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages. Microbiology 155:1966-1976
81. Vergnaud G, Li Y, Gorgé O, Cui Y, Song Y, Zhou D, Grissa I, Dentovskaya SV, Platonov ME, Rakin A, Balakhonov SV, Neubauer H, Pourcel C, Anisimov AP, Yang R (2007) Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA. Adv Exp Med Biol 603:327-338
82. 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
83. Zegans ME, Wagner JC, Cady KC, Murphy DM, Hammond JH, O’Toole GA (2009) Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J Bacteriol 191:210-219
84. Zhang J, Abadia E, Refregier G, Tafaj S, Boschiroli ML, Guillard B, Andremont A, Ruimy R, Sola C (2010) Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of ‘spoligotyping’ with new spacers and a microbead-based hybridization assay. J Med Microbiol 59:285-294