Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) coupled with CRISPR-associated (Cas) proteins (CRISPR/Cas) are the adaptive immune system of eubacteria and archaebacteria. This system provides protection of bacteria against invading foreign DNA, such as transposons, bacteriophages and plasmids. Three-stage processes in this system for immunity against foreign DNAs are defined as adaptation, expression and interference. Recent studies suggested a correlation between the interfering of the CRISPR/Cas locus, acquisition of antibiotic resistance and pathogenicity island. In this review article, we demonstrate and discuss the CRISPR/Cas system’s roles in interference with acquisition of antibiotic resistance and pathogenicity island in some eubacteria. Totally, these systems function as the adaptive immune system of bacteria against invading foreign DNA, blocking the acquisition of antibiotic resistance and virulence factor, detecting serotypes, indirect effects of CRISPR self-targeting, associating with physiological functions, associating with infections in humans at the transmission stage, interfering with natural transformation, a tool for genome editing in genome engineering, monitoring foodborne pathogens etc. These results showed that the CRISPR/Cas system might prevent the emergence of virulence both in vitro and in vivo. Moreover, this system was shown to be a strong selective pressure for the acquisition of antibiotic resistance and virulence factor in bacterial pathogens.
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References
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(5819):1709–1712
Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal Gene transfer in staphylococci by targeting DNA. Science 322(5909):1843–1845
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(3):653–663
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(5891):960–964
Sorek R, Kunin V, Hugenholtz P (2008) CRISPR—a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6(3):181–186
Al-Attar S, Westra ER, van der Oost J, Brouns SJ (2011) Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem 392(4):277–289
Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327(5962):167–170
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(1):7
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV (2011) Evolution and classification of the CRISPR–Cas systems. Nat Rev Microbiol 9(6):467–477
Deveau H, Garneau JE, Moineau S (2010) CRISPR/Cas system and its role in phage–bacteria interactions. Annu Rev Microbiol 64:475–493
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(8):401–407
Karginov FV, Hannon GJ (2010) The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 37(1):7–19
Garneau JE, Dupuis M-È, 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(7320):67–71
Sontheimer EJ, Marraffini LA (2010) Microbiology: slicer for DNA. Nature 468(7320):45–46
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(3):733–740
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(4):1390–1400
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329(5997):1355–1358
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471(7340):602–607
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(24):3489–3496
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(5):945–956
Wang R, Preamplume G, Terns MP, Terns RM, Li H (2011) Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 19(2):257–264
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(6):e60
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
Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005) Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121(7):1005–1016
Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM (2006) Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins 65(4):867–876
Marraffini LA, Sontheimer EJ (2010) Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 463(7280):568–571
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(6):904–912
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(29):20361–20371
Kleanthous C, Kühlmann 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 Mol Biol 6(3):243–252
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(1):157–169
Furuya EY, Lowy FD (2006) Antimicrobial-resistant bacteria in the community setting. Nat Rev Microbiol 4(1):36–45
Bikard D, Hatoum-Aslan A, Mucida D, Marraffini Luciano A (2012) CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 12(2):177–186
Palmer KL, Gilmore MS (2010) Multidrug-resistant enterococci lack CRISPR-cas. MBio 1(4):e00227-10
Avery OT, MacLeod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79(2):137–158
Griffith F (1928) The significance of pneumococcal types. J Hyg (Lond) 27(2):113–159
Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331(6016):430–434
Edgar R, Qimron U (2010) The Escherichia coli CRISPR system protects from λ lysogenization, lysogens, and prophage induction. J Bacteriol 192(23):6291–6294
Gudbergsdottir S, Deng L, Chen Z, Jensen JV, Jensen LR, She Q, Garrett RA (2011) Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol Microbiol 79(1):35–49
Weigel LM, Clewell DB, Gill SR, Clark NC, McDougal LK, Flannagan SE, Kolonay JF, Shetty J, Killgore GE, Tenover FC (2003) Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science 302(5650):1569–1571
Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, Sensabaugh GF, Perdreau-Remington F (2006) Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367(9512):731–739
Gill SR, Fouts DE, Archer GL, Mongodin EF, DeBoy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM (2005) Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol 187(7):2426–2438
Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJ (2010) Diversity of CRISPR loci in Escherichia coli. Microbiology 156(5):1351–1361
Touchon M, Rocha EP (2010) The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One 5(6):e11126
Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, Denamur E, Branger C (2012) Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology 158(12):2997–3004
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(50):20136–20141
Kutter E (2009) Phage host range and efficiency of plating. In: Clokie MRJ, Kropinski AM (eds) Bacteriophages: methods and protocols. Isolation, characterization, and interactions, vol 1. Humana Press, Totowa, pp 141–149
Toro M, Cao G, Ju W, Allard M, Barrangou R, Zhao S, Brown E, Meng J (2014) Association of clustered regularly interspaced short palindromic repeat (CRISPR) elements with specific serotypes and virulence potential of Shiga toxin-producing Escherichia coli. Appl Environ Microbiol 80(4):1411–1420
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(12):4035–4040
Delannoy S, Beutin L, Burgos Y, Fach P (2012) Specific detection of enteroaggregative hemorrhagic Escherichia coli O104:H4 strains by use of the CRISPR locus as a target for a diagnostic real-time PCR. J Clin Microbiol 50(11):3485–3492
Yin S, Jensen MA, Bai J, DebRoy C, Barrangou R, Dudley EG (2013) The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition. Appl Environ Microbiol 79(18):5710–5720
Vaca-Pacheco S, Paniagua-Contreras GL, García-González O, de la Garza M (1999) The clinically isolated FIZ15 bacteriophage causes lysogenic conversion in Pseudomonas aeruginosa PAO1. Curr Microbiol 38(4):239–243
Newton GJ, Daniels C, Burrows LL, Kropinski AM, Clarke AJ, Lam JS (2001) Three-component-mediated serotype conversion in Pseudomonas aeruginosa by bacteriophage D3. Mol Microbiol 39(5):1237–1247
McLeod SM, Kimsey HH, Davis BM, Waldor MK (2005) CTXφ and Vibrio cholerae: exploring a newly recognized type of phage–host cell relationship. Mol Microbiol 57(2):347–356
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(1):210–219
Heussler GE, Cady KC, Koeppen K, Bhuju S, Stanton BA, O’Toole GA (2015) Clustered regularly interspaced short palindromic repeat-dependent, biofilm-specific death of Pseudomonas aeruginosa mediated by increased expression of phage-related genes. MBio 6(3):e00129-15
Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR (2013) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493(7432):429–432
Pawluk A, Staals RH, Taylor C, Watson BN, 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
Pawluk A, Bondy-Denomy J, Cheung VH, 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(2):e00896-14
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(7571):136–139
Wiedenheft B (2013) In defense of phage: viral suppressors of CRISPR-mediated adaptive immunity in bacteria. RNA Biol 10(5):886–890
Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJ, 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(6203):1473–1479
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(6203):1479–1484
Latifi A, Winson MK, Foglino M, Bycroft BW, Stewart GS, Lazdunski A, Williams P (1995) Multiple homologues of LuxR and LuxI control expression of virulence determinants and secondary metabolites through quorum sensing in Pseudomonas aeruginosa PAO1. Mol Microbiol 17(2):333–343
Gambello MJ, Kaye S, Iglewski BH (1993) LasR of Pseudomonas aeruginosa is a transcriptional activator of the alkaline protease gene (apr) and an enhancer of exotoxin a expression. Infect Immun 61(4):1180–1184
Seed PC, Passador L, Iglewski BH (1995) Activation of the Pseudomonas aeruginosa lasI gene by LasR and the Pseudomonas autoinducer PAI: an autoinduction regulatory hierarchy. J Bacteriol 177(3):654–659
Pesci EC, Pearson JP, Seed PC, Iglewski BH (1997) Regulation of las and rhl quorum sensing in Pseudomonas aeruginosa. J Bacteriol 179(10):3127–3132
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(1):131–135
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(21):5728–5738
van Houte S, Ekroth AK, 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(7599):385–388
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(25):10092–10097
Gunderson FF, Cianciotto NP (2013) The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae. MBio 4(2):e00074-13
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(1):181
Faucher SP, Shuman HA (2011) Small regulatory RNA and Legionella pneumophila. Front Microbiol 2:98
Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 50(4):488–503
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
Hou Z, Zhang Y, Propson NE, Howden SE, Chu L-F, Sontheimer EJ, Thomson JA (2013) Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A 110(39):15644–15649
Lee CM, Cradick TJ, Bao G (2016) The Neisseria meningitidis CRISPR-Cas9 system enables specific genome editing in mammalian cells. Mol Ther 24(3):645–654
Box AM, McGuffie MJ, O’Hara BJ, Seed KD (2016) Functional analysis of bacteriophage immunity through a type I-E CRISPR-Cas system in Vibrio cholerae and its application in bacteriophage genome engineering. J Bacteriol 198(3):578–590
Sun H, Li Y, Shi X, Lin Y, Qiu Y, Zhang J, Liu Y, Jiang M, Zhang Z, Chen Q, Sun Q, Hu Q (2015) Association of CRISPR/Cas evolution with Vibrio parahaemolyticus virulence factors and genotypes. Foodborne Pathog Dis 12(1):68–73
Sampson TR, Saroj SD, Llewellyn AC, Tzeng Y-L, Weiss DS (2013) A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 497(7448):254–257
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 EES, van Vliet AHM, Willemsen PTJ, van Baarlen P, van Belkum A (2013) A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain–Barré syndrome. Eur J Clin Microbiol Infect Dis 32(2):207–226
Labbate M, Orata FD, Petty NK, Jayatilleke ND, King WL, Kirchberger PC, Allen C, Mann G, Mutreja A, Thomson NR, Boucher Y, Charles IG (2016) A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules. Sci Rep 6:36891
Aliprantis AO, Yang R-B, Mark MR, Suggett S, Devaux B, Radolf JD, Klimpel GR, Godowski P, Zychlinsky A (1999) Cell activation and apoptosis by bacterial lipoproteins through toll-like receptor-2. Science 285(5428):736–739
Brightbill HD, Libraty DH, Krutzik SR, Yang R-B, Belisle JT, Bleharski JR, Maitland M, Norgard MV, Plevy SE, Smale ST, Brennan PJ, Bloom BR, Godowski PJ, Modlin RL (1999) Host defense mechanisms triggered by microbial lipoproteins through toll-like receptors. Science 285(5428):732–736
van Doorn PA, Ruts L, Jacobs BC (2008) Clinical features, pathogenesis, and treatment of Guillain–Barré syndrome. Lancet Neurol 7(10):939–950
van Belkum A, van den Braak N, Godschalk P, Ang W, Jacobs B, Gilbert M, Wakarchuk W, Verbrugh H, Endtz H (2001) A Campylobacter jejuni gene associated with immune-mediated neuropathy. Nat Med 7(7):752–753
Godschalk PC, Heikema AP, Gilbert M, Komagamine T, Ang CW, Glerum J, Brochu D, Li J, Yuki N, Jacobs BC, van Belkum A, Endtz HP (2004) The crucial role of Campylobacter jejuni genes in anti-ganglioside antibody induction in Guillain–Barré syndrome. J Clin Invest 114(11):1659–1665
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Gholizadeh, P., Aghazadeh, M., Asgharzadeh, M. et al. Suppressing the CRISPR/Cas adaptive immune system in bacterial infections. Eur J Clin Microbiol Infect Dis 36, 2043–2051 (2017). https://doi.org/10.1007/s10096-017-3036-2
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DOI: https://doi.org/10.1007/s10096-017-3036-2