Function and Regulation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) / CRISPR Associated (Cas) Systems

Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous ‘innate’ mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific ‘adaptive’ immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.

[1]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[2]  Nick V Grishin,et al.  A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. , 2002, Nucleic acids research.

[3]  R. Terns,et al.  Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. , 2008, Genes & development.

[4]  L. Marraffini,et al.  CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea , 2010, Nature Reviews Genetics.

[5]  B. Graveley,et al.  RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex , 2009, Cell.

[6]  U. Qimron,et al.  High-temperature protein G is essential for activity of the Escherichia coli clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system , 2011, Proceedings of the National Academy of Sciences.

[7]  R. Terns,et al.  CRISPR-based adaptive immune systems. , 2011, Current opinion in microbiology.

[8]  Daniel Mucida,et al.  CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. , 2012, Cell host & microbe.

[9]  Konstantin Severinov,et al.  Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system , 2012, Nature Communications.

[10]  Chien-Chung Chen,et al.  LeuO-mediated Transcriptional Derepression* , 2003, Journal of Biological Chemistry.

[11]  C R Woese,et al.  Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1998, Nature.

[12]  E. Bolt,et al.  Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein. , 2011, The Biochemical journal.

[13]  M. DeLisa,et al.  Envelope stress is a trigger of CRISPR RNA‐mediated DNA silencing in Escherichia coli , 2011, Molecular Microbiology.

[14]  Stan J. J. Brouns,et al.  CRISPR Interference Directs Strand Specific Spacer Acquisition , 2012, PloS one.

[15]  R. Fleischmann,et al.  The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus , 1997, Nature.

[16]  Andrew Emili,et al.  A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair , 2011, Molecular microbiology.

[17]  Adi Stern,et al.  Self-targeting by CRISPR: gene regulation or autoimmunity? , 2010, Trends in genetics : TIG.

[18]  F. J. Mojica,et al.  Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria , 2000, Molecular microbiology.

[19]  R. Terns,et al.  Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. , 2008, RNA.

[20]  Stan J. J. Brouns,et al.  Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.

[21]  P. Glaser,et al.  The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome , 2012, Molecular microbiology.

[22]  Dipali G. Sashital,et al.  Mechanism of foreign DNA selection in a bacterial adaptive immune system. , 2012, Molecular cell.

[23]  J. Banfield,et al.  Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. , 2007, Environmental microbiology.

[24]  V. Kunin,et al.  Evolutionary conservation of sequence and secondary structures in CRISPR repeats , 2007, Genome Biology.

[25]  H. Nikaido,et al.  The BaeSR Two-Component Regulatory System Activates Transcription of the yegMNOB (mdtABCD) Transporter Gene Cluster in Escherichia coli and Increases Its Resistance to Novobiocin and Deoxycholate , 2002, Journal of bacteriology.

[26]  Yipeng Wang,et al.  Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella , 2006, Science.

[27]  J. García-Martínez,et al.  Short motif sequences determine the targets of the prokaryotic CRISPR defence system. , 2009, Microbiology.

[28]  L. Marraffini,et al.  Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site , 2011, Proceedings of the National Academy of Sciences.

[29]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[30]  A. Garza,et al.  Regulation of dev, an Operon That Includes Genes Essential for Myxococcus xanthus Development and CRISPR-Associated Genes and Repeats , 2007, Journal of bacteriology.

[31]  M. F. White,et al.  Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)* , 2011, The Journal of Biological Chemistry.

[32]  S. Ehrlich,et al.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. , 2005, Microbiology.

[33]  J. Fuhrman.  Marine viruses and their biogeochemical and ecological effects , 1999, Nature.

[34]  George A. O'Toole,et al.  The CRISPR/Cas Adaptive Immune System of Pseudomonas aeruginosa Mediates Resistance to Naturally Occurring and Engineered Phages , 2012, Journal of bacteriology.

[35]  R. Garrett,et al.  Genus-Specific Protein Binding to the Large Clusters of DNA Repeats (Short Regularly Spaced Repeats) Present in Sulfolobus Genomes , 2003, Journal of bacteriology.

[36]  L. Schouls,et al.  Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.

[37]  C. Dorman.  H-NS, the genome sentinel , 2007, Nature Reviews Microbiology.

[38]  Anders F. Andersson,et al.  Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities , 2008, Science.

[39]  U. Qimron,et al.  Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. , 2012, Journal of molecular biology.

[40]  Ibtissem Grissa,et al.  The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats , 2007, BMC Bioinformatics.

[41]  Stan J. J. Brouns,et al.  H‐NS‐mediated repression of CRISPR‐based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO , 2010, Molecular microbiology.

[42]  Peter C. Fineran,et al.  Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum , 2011, RNA biology.

[43]  J. García-Martínez,et al.  Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements , 2005, Journal of Molecular Evolution.

[44]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[45]  M. DeLisa,et al.  Double-stranded Endonuclease Activity in Bacillus halodurans Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas2 Protein* , 2012, The Journal of Biological Chemistry.

[46]  S. Shuman,et al.  Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris. , 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

[47]  E. Koonin,et al.  A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats* , 2008, Journal of Biological Chemistry.

[48]  Philippe Horvath,et al.  The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli , 2011, Nucleic acids research.

[49]  N. Grishin,et al.  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 , 2006, Biology Direct.

[50]  J. S. Godde,et al.  The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes , 2006, Journal of Molecular Evolution.

[51]  S. Encarnación,et al.  The LysR-Type Transcriptional Regulator LeuO Controls Expression of Several Genes in Salmonella enterica Serovar Typhi , 2007, Journal of bacteriology.

[52]  J. Doudna,et al.  RNA-guided genetic silencing systems in bacteria and archaea , 2012, Nature.

[53]  Laura S. Frost,et al.  Mobile genetic elements: the agents of open source evolution , 2005, Nature Reviews Microbiology.

[54]  Erik J. Sontheimer,et al.  Self vs. non-self discrimination during CRISPR RNA-directed immunity , 2009, Nature.

[55]  K. Zhou,et al.  Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. , 2009, Structure.

[56]  F. Rodríguez-Valera,et al.  Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning , 1995, Molecular microbiology.

[57]  R. Gutiérrez-Ríos,et al.  The CRISPR/Cas Immune System Is an Operon Regulated by LeuO, H-NS, and Leucine-Responsive Regulatory Protein in Salmonella enterica Serovar Typhi , 2011, Journal of bacteriology.

[58]  R. Garrett,et al.  Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus , 2011, Nucleic acids research.

[59]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[60]  R. Terns,et al.  Binding and cleavage of CRISPR RNA by Cas6. , 2010, RNA.

[61]  Jennifer A. Doudna,et al.  Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease , 2010, Science.

[62]  Stan J. J. Brouns,et al.  The rise and fall of CRISPRs – dynamics of spacer acquisition and loss , 2012, Molecular microbiology.

[63]  Ruud Jansen,et al.  Genetic Variation and Evolutionary Origin of the Direct Repeat Locus of Mycobacterium tuberculosis Complex Bacteria , 2000, Journal of bacteriology.

[64]  A. MacMillan,et al.  Recognition and maturation of effector RNAs in a CRISPR interference pathway , 2011, Nature Structural &Molecular Biology.

[65]  S. Yokoyama,et al.  Transcription Activation Mediated by a Cyclic AMP Receptor Protein from Thermus thermophilus HB8 , 2007, Journal of bacteriology.

[66]  Dipali G. Sashital,et al.  An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3 , 2011, Nature Structural &Molecular Biology.

[67]  P. Groenen,et al.  Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method , 1993, Molecular microbiology.

[68]  Philippe Horvath,et al.  The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA , 2010, Nature.

[69]  Marko Djordjevic,et al.  Transcription, processing and function of CRISPR cassettes in Escherichia coli , 2010, Molecular microbiology.

[70]  Albert J R Heck,et al.  RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions , 2011, Proceedings of the National Academy of Sciences.

[71]  G. Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[72]  Samuel H Sternberg,et al.  Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. , 2012, RNA.

[73]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

[74]  Rolf Backofen,et al.  Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis , 2012, Nucleic acids research.

[75]  U. Qimron,et al.  Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli , 2012, Nucleic acids research.

[76]  T. Mizuno,et al.  LeuO Expression in Response to Starvation for Branched-chain Amino Acids* , 2001, The Journal of Biological Chemistry.

[77]  D. Relman,et al.  Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome , 2011, The ISME Journal.

[78]  Daniel H. Haft,et al.  A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes , 2005, PLoS Comput. Biol..

[79]  R. Garrett,et al.  A putative viral defence mechanism in archaeal cells. , 2006, Archaea.

[80]  B. Tjaden,et al.  Characterization of the CRISPR/Cas Subtype I-A System of the Hyperthermophilic Crenarchaeon Thermoproteus tenax , 2012, Journal of bacteriology.

[81]  R. Hendrix,et al.  Effect of bacteriophage lambda infection on synthesis of groE protein and other Escherichia coli proteins , 1982, Journal of bacteriology.

[82]  A. Savchenko,et al.  Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference , 2011, The EMBO journal.

[83]  Mark A. Ragan,et al.  The complete genome of the crenarchaeon Sulfolobus solfataricus P2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Albert J R Heck,et al.  Structural basis for CRISPR RNA-guided DNA recognition by Cascade , 2011, Nature Structural &Molecular Biology.

[85]  S. Kuramitsu,et al.  Transcription profile of Thermus thermophilus CRISPR systems after phage infection. , 2010, Journal of molecular biology.

[86]  Sylvain Moineau,et al.  Bacteriophage resistance mechanisms , 2010, Nature Reviews Microbiology.

[87]  K. Makino,et al.  Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product , 1987, Journal of bacteriology.

[88]  Avital Brodt,et al.  CRISPR loci reveal networks of gene exchange in archaea , 2011, Biology Direct.

[89]  R. Terns,et al.  Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. , 2011, Structure.

[90]  L. Schouls,et al.  Identification of a novel family of sequence repeats among prokaryotes. , 2002, Omics : a journal of integrative biology.

[91]  Philippe Horvath,et al.  Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus , 2007, Journal of bacteriology.

[92]  J. Doudna,et al.  Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA , 2012, The EMBO journal.

[93]  G. Krauss,et al.  SSO1450 – A CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA , 2009, FEBS letters.

[94]  Hongwei Wang,et al.  Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. , 2012, Structure.

[95]  K. Makino,et al.  Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome , 1989, Journal of bacteriology.

[96]  J. Vogel,et al.  CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III , 2011, Nature.

[97]  Peter C. Fineran,et al.  Biotechnological exploitation of bacteriophage research. , 2007, Trends in biotechnology.

[98]  Konstantin Severinov,et al.  CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. , 2012, Molecular cell.

[99]  Joshua R. Elmore,et al.  Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. , 2012, Molecular cell.

[100]  Jennifer A. Doudna,et al.  Structures of the RNA-guided surveillance complex from a bacterial immune system , 2011, Nature.

[101]  Konstantin Severinov,et al.  Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence , 2011, Proceedings of the National Academy of Sciences.

[102]  Rolf Wagner,et al.  Identification and characterization of E. coli CRISPR‐cas promoters and their silencing by H‐NS , 2010, Molecular microbiology.

[103]  Alex van Belkum,et al.  Short-Sequence DNA Repeats in Prokaryotic Genomes , 1998, Microbiology and Molecular Biology Reviews.

[104]  Graham F Hatfull,et al.  Bacteriophage genomics. , 2008, Current opinion in microbiology.

[105]  Philippe Horvath,et al.  Cas3 is a single‐stranded DNA nuclease and ATP‐dependent helicase in the CRISPR/Cas immune system , 2011, The EMBO journal.

[106]  César Díez-Villaseñor,et al.  The on–off switch of CRISPR immunity against phages in Escherichia coli , 2010, Molecular microbiology.

[107]  J. Hinton.  H-NS mediates the silencing of laterally acquired genes in bacteria (vol 2, pg 746, 2006) , 2007 .

[108]  R. Garrett,et al.  Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms , 2012, Molecular microbiology.

[109]  J. Banfield,et al.  Phage-Induced Expression of CRISPR-Associated Proteins Is Revealed by Shotgun Proteomics in Streptococcus thermophilus , 2012, PloS one.

[110]  T. Raivio,et al.  Two-component signaling and gram negative envelope stress response systems. , 2008, Advances in experimental medicine and biology.

[111]  Jing Zhang,et al.  Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. , 2012, Molecular cell.

[112]  E. Koonin,et al.  Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world , 2008, Nucleic acids research.

[113]  Philippe Horvath,et al.  Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus , 2007, Journal of bacteriology.