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The basic building blocks and evolution of CRISPR–Cas systems

Makarova, Kira S., Wolf, Yuri I., Koonin, Eugene V.·2013·Biochemical Society Transactions
DOI 10.1042/bst20130038PMC PMC5898231
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Abstract

CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) is an adaptive immunity system in bacteria and archaea that functions via a distinct self/non-self recognition mechanism that involves unique spacers homologous with viral or plasmid DNA and integrated into the CRISPR loci. Most of the Cas proteins evolve under relaxed purifying selection and some underwent dramatic structural rearrangements during evolution. In many cases, CRISPR–Cas system components are replaced either by homologous or by analogous proteins or domains in some bacterial and archaeal lineages. However, recent advances in comparative sequence analysis, structural studies and experimental data suggest that, despite this remarkable evolutionary plasticity, all CRISPR–Cas systems employ the same architectural and functional principles, and given the conservation of the principal building blocks, share a common ancestry. We review recent advances in the understanding of the evolution and organization of CRISPR–Cas systems. Among other developments, we describe for the first time a group of archaeal cas1 gene homologues that are not associated with CRISPR–Cas loci and are predicted to be involved in functions other than adaptive immunity.

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  • The main difference between CRISPR-Cas classes is that the effector module of Class 1 systems is a complex of several proteins, while in Class 2 it is a single multidomain protein (Cas9, Cas12, or Cas13).

    “The main difference between the classes is that the effector module of Class 1 systems is represented by a complex of several proteins, while in Class 2 it is a single multidomain protein (Cas9, Cas12, or Cas13) [26-28].”

    From CRISPR–Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing (2022) · cites this paper as [26]

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Research works printed but not linked: 52

  1. Makarova, 2013, Comparative genomics of defense systems in archaea and bacteria, Nucleic Acids Res., 41, 4360, 10.1093/nar/gkt157 · DOI
  2. Roberts, 2003, A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes, Nucleic Acids Res., 31, 1805, 10.1093/nar/gkg274 · DOI · Paper page
  3. Xu, 2010, A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella, Nucleic Acids Res., 38, 7133, 10.1093/nar/gkq610 · DOI
  4. Barrangou, 2012, CRISPR: new horizons in phage resistance and strain identification, Annu. Rev. Food Sci. Technol., 3, 143, 10.1146/annurev-food-022811-101134 · DOI
  5. van der Oost, 2009, CRISPR-based adaptive and heritable immunity in prokaryotes, Trends Biochem. Sci., 34, 401, 10.1016/j.tibs.2009.05.002 · DOI
  6. Makarova, 2011, Evolution and classification of the CRISPR–Cas systems, Nat. Rev. Microbiol., 9, 467, 10.1038/nrmicro2577 · DOI · Paper page
  7. Koonin, 2009, Is evolution Darwinian or/and Lamarckian?, Biol. Direct, 4, 42, 10.1186/1745-6150-4-42 · DOI
  8. Jansen, 2002, Identification of genes that are associated with DNA repeats in prokaryotes, Mol. Microbiol., 43, 1565, 10.1046/j.1365-2958.2002.02839.x · DOI · Paper page
  9. Haft, 2005, A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes, PLoS Comput. Biol., 1, e60, 10.1371/journal.pcbi.0010060 · DOI
  10. Mojica, 2005, Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements, J. Mol. Evol., 60, 174, 10.1007/s00239-004-0046-3 · DOI · Paper page
  11. Bolotin, 2005, Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin, Microbiology, 151, 2551, 10.1099/mic.0.28048-0 · DOI
  12. Makarova, 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, 10.1186/1745-6150-1-7 · DOI · Paper page
  13. Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
  14. Carroll, 2012, A CRISPR approach to gene targeting, Mol. Ther., 20, 1658, 10.1038/mt.2012.171 · DOI
  15. Qi, 2012, RNA processing enables predictable programming of gene expression, Nat. Biotechnol., 30, 1002, 10.1038/nbt.2355 · DOI
  16. Yosef, 2012, Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli, Nucleic Acids Res., 40, 5569, 10.1093/nar/gks216 · DOI · Paper page
  17. Hale, 2012, Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs, Mol. Cell, 45, 292, 10.1016/j.molcel.2011.10.023 · DOI
  18. Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829 · DOI · Paper page
  19. Sashital, 2012, Mechanism of foreign DNA selection in a bacterial adaptive immune system, Mol. Cell, 46, 606, 10.1016/j.molcel.2012.03.020 · DOI
  20. van Duijn, 2012, Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced short-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa, Mol. Cell. Proteomics, 11, 1430, 10.1074/mcp.M112.020263 · DOI
  21. Zhang, 2012, Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity, Mol. Cell, 45, 303, 10.1016/j.molcel.2011.12.013 · DOI
  22. Wiedenheft, 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, 10.1073/pnas.1102716108 · DOI
  23. Barrangou, 2013, CRISPR–Cas systems and RNA-guided interference, Wiley Interdiscip. Rev.: RNA, 4, 267, 10.1002/wrna.1159 · DOI
  24. Westra, 2012, The CRISPRs, they are a-changin’: how prokaryotes generate adaptive immunity, Annu. Rev. Genet., 46, 311, 10.1146/annurev-genet-110711-155447 · DOI
  25. Makarova, 2012, Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes, Biol. Direct, 7, 40, 10.1186/1745-6150-7-40 · DOI
  26. Koonin, 2013, CRISPR–Cas: evolution of an RNA-based adaptive immunity system in prokaryotes, RNA Biol., 10, 679, 10.4161/rna.24022 · DOI
  27. Wiedenheft, 2009, Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense, Structure, 17, 904, 10.1016/j.str.2009.03.019 · DOI · Paper page
  28. Makarova, 2011, Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR–Cas systems, Biol. Direct, 6, 38, 10.1186/1745-6150-6-38 · DOI
  29. Beloglazova, 2008, A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats, J. Biol. Chem., 283, 20361, 10.1074/jbc.M803225200 · DOI
  30. Samai, 2010, Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris, Acta Crystallogr., Sect. F: Struct. Biol. Crystal. Commun., 66, 1552, 10.1107/S1744309110039801 · DOI
  31. Nam, 2012, Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein, J. Biol. Chem., 287, 35943, 10.1074/jbc.M112.382598 · DOI
  32. Haurwitz, 2010, Sequence- and structure-specific RNA processing by a CRISPR endonuclease, Science, 329, 1355, 10.1126/science.1192272 · DOI
  33. Deng, 2012, Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus, Nucleic Acids Res., 40, 2470, 10.1093/nar/gkr1111 · DOI
  34. Hale, 2009, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040 · DOI · Paper page
  35. Nam, 2012, Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR–Cas system, Structure, 20, 1574, 10.1016/j.str.2012.06.016 · DOI
  36. Brouns, 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689 · DOI · Paper page
  37. Wiedenheft, 2011, Structures of the RNA-guided surveillance complex from a bacterial immune system, Nature, 477, 486, 10.1038/nature10402 · DOI
  38. Sinkunas, 2011, Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system, EMBO J., 30, 1335, 10.1038/emboj.2011.41 · DOI
  39. Beloglazova, 2011, Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference, EMBO J., 30, 4616, 10.1038/emboj.2011.377 · DOI
  40. Mulepati, 2011, Structural and biochemical analysis of the nuclease domain of the clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 3 (CAS3), J. Biol. Chem., 286, 31896, 10.1074/jbc.M111.270017 · DOI
  41. Yutin, 2012, Phylogenomics of prokaryotic ribosomal proteins, PLoS ONE, 7, e36972, 10.1371/journal.pone.0036972 · DOI
  42. Babu, 2011, A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair, Mol. Microbiol., 79, 484, 10.1111/j.1365-2958.2010.07465.x · DOI · Paper page
  43. Shao, 2013, Structure of the cmr2-cmr3 subcomplex of the cmr RNA silencing complex, Structure, 21, 376, 10.1016/j.str.2013.01.002 · DOI
  44. Reeks, 2013, Structure of the archaeal Cascade subunit Csa5: relating the small subunits of CRISPR effector complexes, RNA Biol., 10, 762, 10.4161/rna.23854 · DOI
  45. Zhu, 2012, Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR–Cas systems, FEBS Lett., 586, 939, 10.1016/j.febslet.2012.02.036 · DOI
  46. Kim, 2013, Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus, Proteins, 81, 261, 10.1002/prot.24183 · DOI
  47. Lintner, 2010, The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system, J. Mol. Biol., 405, 939, 10.1016/j.jmb.2010.11.019 · DOI
  48. Anantharaman, 2013, Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing, Biol. Direct, 8, 15, 10.1186/1745-6150-8-15 · DOI
  49. Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 · DOI · Paper page
  50. Wheeler, 2007, BLAST QuickStart: example-driven web-based BLAST tutorial, Methods Mol. Biol., 395, 149, 10.1007/978-1-59745-514-5_9 · DOI
  51. Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 · DOI · Paper page
  52. Price, 2010, FastTree 2–approximately maximum-likelihood trees for large alignments, PLoS ONE, 5, e9490, 10.1371/journal.pone.0009490 · DOI · Paper page

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Metadata

Authors
Makarova, K. S., Wolf, Y. I., & Koonin, E. V.
Affiliations
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, U.S.A.
Venue
Biochemical Society Transactions
Publisher
Portland Press Ltd.
Published
2013-11-20
Volume
41
Issue
6
Pages
1392-1400
ISSN
  • 0300-5127
  • 1470-8752
DOI
10.1042/bst20130038
PMC
PMC5898231
Cited by
169
References
3
Language
en

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