Diversity and evolution of class 2 CRISPR–Cas systems (original) (raw)
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I. & Koonin, E. V. 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. Direct1, 7 (2006). ArticlePubMedPubMed Central Google Scholar
Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science315, 1709–1712 (2007). ArticleCASPubMed Google Scholar
Barrangou, R. CRISPR–Cas systems and RNA-guided interference. Wiley Interdiscip. Rev. RNA4, 267–278 (2013). ArticleCASPubMed Google Scholar
Mohanraju, P. et al. Diverse evolutionary roots and mechanistic variations of the CRISPR–Cas systems. Science353, aad5147 (2016). ArticlePubMed Google Scholar
Van der Oost, J., Westra, E. R., Jackson, R. N. & Wiedenheft, B. Unravelling the structural and mechanistic basis of CRISPR–Cas systems. Nat. Rev. Microbiol.12, 479–492 (2014). ArticleCASPubMedPubMed Central Google Scholar
Makarova, K. S., Aravind, L., Wolf, Y. I. & Koonin, E. V. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR–Cas systems. Biol. Direct6, 38 (2011). ArticleCASPubMedPubMed Central Google Scholar
Makarova, K. S., Wolf, Y. I. & Koonin, E. V. The basic building blocks and evolution of CRISPR–Cas systems. Biochem. Soc. Trans.41, 1392–1400 (2013). ArticleCASPubMedPubMed Central Google Scholar
Takeuchi, N., Wolf, Y. I., Makarova, K. S. & Koonin, E. V. Nature and intensity of selection pressure on CRISPR-associated genes. J. Bacteriol.194, 1216–1225 (2012). ArticleCASPubMedPubMed Central Google Scholar
Bondy-Denomy, J. & Davidson, A. R. To acquire or resist: the complex biological effects of CRISPR–Cas systems. Trends Microbiol.22, 218–225 (2014). ArticleCASPubMed Google Scholar
Makarova, K. S. et al. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol.13, 722–736 (2015). This paper presents the latest classification of the CRISPR–Cas systems, prior to the application of the pipeline described here, along with computational approaches for the identification and quantitative comparison of CRISPR–casloci. CASPubMedPubMed Central Google Scholar
Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR–Cas systems. Mol. Cell60, 385–397 (2015). This paper presents the first instalment of the computational pipeline that is described in this article, using Cas1 as the seed, and experimental validation of the activity of subtype V-B. ArticleCASPubMedPubMed Central Google Scholar
Chylinski, K., Makarova, K. S., Charpentier, E. & Koonin, E. V. Classification and evolution of type II CRISPR–Cas systems. Nucleic Acids Res.42, 6091–6105 (2014). ArticleCASPubMedPubMed Central Google Scholar
Jore, M. M. et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat. Struct. Mol. Biol.18, 529–536 (2011). ArticleCASPubMed Google Scholar
Beloglazova, N. et al. CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli. Nucleic Acids Res.43, 530–543 (2015). ArticleCASPubMed Google Scholar
Jackson, R. N. et al. Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli. Science345, 1473–1479 (2014). ArticleCASPubMedPubMed Central Google Scholar
Rouillon, C. et al. Structure of the CRISPR interference complex CSM reveals key similarities with cascade. Mol. Cell52, 124–134 (2013). ArticleCASPubMedPubMed Central Google Scholar
Osawa, T., Inanaga, H., Sato, C. & Numata, T. Crystal structure of the CRISPR–Cas RNA silencing Cmr complex bound to a target analog. Mol. Cell58, 418–430 (2015). ArticleCASPubMed Google Scholar
Taylor, D. W. et al. Structural biology. Structures of the CRISPR–Cmr complex reveal mode of RNA target positioning. Science348, 581–585 (2015). ArticleCASPubMedPubMed Central Google Scholar
Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA109, E2579–E2586 (2012). ArticleCASPubMedPubMed Central Google Scholar
Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell156, 935–949 (2014). This paper reports the first structure of Cas9, which provides insight into the interaction of class 2 effectors with crRNA and target DNA. ArticleCASPubMedPubMed Central Google Scholar
Sternberg, S. H., LaFrance, B., Kaplan, M. & Doudna, J. A. Conformational control of DNA target cleavage by CRISPR–Cas9. Nature527, 110–113 (2015). ArticleCASPubMedPubMed Central Google Scholar
Sapranauskas, R. et al. The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res.39, 9275–9282 (2011). ArticleCASPubMedPubMed Central Google Scholar
Chylinski, K., Le Rhun, A. & Charpentier, E. The tracrRNA and Cas9 families of type II CRISPR–Cas immunity systems. RNA Biol.10, 726–737 (2013). ArticleCASPubMedPubMed Central Google Scholar
Briner, A. E. et al. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol. Cell56, 333–339 (2014). ArticleCASPubMed Google Scholar
Schunder, E., Rydzewski, K., Grunow, R. & Heuner, K. First indication for a functional CRISPR/Cas system in Francisella tularensis. Int. J. Med. Microbiol.303, 51–60 (2013). ArticleCASPubMed Google Scholar
Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR–Cas system. Cell163, 759–771 (2015). This work demonstrates the interference activity of Cpf1 and shows that Cpf1 is a single RNA-guided endonuclease that does not require tracrRNA. CASPubMedPubMed Central Google Scholar
Dong, D. et al. The crystal structure of Cpf1 in complex with CRISPR RNA. Nature532, 522–526 (2016). ArticleCASPubMed Google Scholar
Yamano, T. et al. Crystal structure of Cpf1 in complex with guide RNA and target DNA. Cell165, 949–962 (2016). Together with reference 39, this paper presents the structure of Cpf1 in complex with crRNA and target DNA, demonstrating that, despite similar overall shapes, the domain architectures of Cpf1 and Cas9 differ substantially. ArticleCASPubMedPubMed Central Google Scholar
Fonfara, I., Richter, H., Bratovic, M., Le Rhun, A. & Charpentier, E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature532, 517–521 (2016). This work demonstrates that Cpf1 is responsible not only for interference but also for pre-crRNA processing. ArticleCASPubMed Google Scholar
Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science353, aaf5573 (2016). This paper describes the first CRISPR–Cas system that exclusively cleaves RNA, and demonstrates the switch from specific to non-specific RNA cleavage following target recognition. ArticlePubMedPubMed Central Google Scholar
Pasternak, C. et al. ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB. Mol. Microbiol.88, 443–455 (2013). ArticleCASPubMed Google Scholar
Bao, W. & Jurka, J. Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements. Mob. DNA4, 12 (2013). ArticleCASPubMedPubMed Central Google Scholar
Kapitonov, V. V., Makarova, K. S. & Koonin, E. V. ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs. J. Bacteriol.198, 797–807 (2015). In this work, the direct evolutionary ancestors of Cas9 are identified. ArticlePubMed Google Scholar
Gomes-Filho, J. V. et al. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA Biol.12, 490–500 (2015). This work demonstrates that TnpB proteins bind to RNA, which is compatible with their role as ancestors of class 2 CRISPR–Cas effectors. ArticlePubMedPubMed Central Google Scholar
Westra, E. R., Buckling, A. & Fineran, P. C. CRISPR–Cas systems: beyond adaptive immunity. Nat. Rev. Microbiol.12, 317–326 (2014). ArticleCASPubMed Google Scholar
Anantharaman, V., Makarova, K. S., Burroughs, A. M., Koonin, E. V. & Aravind, L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol. Direct8, 15 (2013). ArticleCASPubMedPubMed Central Google Scholar
Makarova, K. S., Anantharaman, V., Grishin, N. V., Koonin, E. V. & Aravind, L. CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. Front. Genet.5, 102 (2014). ArticlePubMedPubMed Central Google Scholar
Makarova, K. S., Anantharaman, V., Aravind, L. & Koonin, E. V. Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol. Direct7, 40 (2012). ArticleCASPubMedPubMed Central Google Scholar
Iranzo, J., Lobkovsky, A. E., Wolf, Y. I. & Koonin, E. V. Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems. BMC Evol. Biol.15, 43 (2015). ArticlePubMedPubMed Central Google Scholar
East-Seletsky, A. et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature538, 270–273 (2016). This paper describes experiments that show that, similar to Cpf1, C2c2, the subtype VI-A effector, catalyses pre-crRNA processing. ArticleCASPubMedPubMed Central Google Scholar
Koonin, E. V., Dolja, V. V. & Krupovic, M. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology479–480, 2–25 (2015). ArticlePubMed Google Scholar
Sheppard, N. F., Glover, C. V., Terns, R. M. & Terns, M. P. The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease. RNA22, 216–224 (2016). ArticleCASPubMedPubMed Central Google Scholar
Niewoehner, O. & Jinek, M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA22, 318–329 (2016). ArticleCASPubMedPubMed Central Google Scholar
Curtis, T. P., Sloan, W. T. & Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA99, 10494–10499 (2002). ArticleCASPubMedPubMed Central Google Scholar
Curtis, T. P. et al. What is the extent of prokaryotic diversity? Philos. Trans. R. Soc. Lond. B Biol. Sci.361, 2023–2037 (2006). ArticlePubMedPubMed Central Google Scholar
Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G. & Hanage, W. P. The bacterial species challenge: making sense of genetic and ecological diversity. Science323, 741–746 (2009). ArticleCASPubMed Google Scholar
Quince, C., Curtis, T. P. & Sloan, W. T. The rational exploration of microbial diversity. ISME J.2, 997–1006 (2008). ArticleCASPubMed Google Scholar
Thakore, P. I., Black, J. B., Hilton, I. B. & Gersbach, C. A. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat. Methods13, 127–137 (2016). ArticleCASPubMedPubMed Central Google Scholar
Kim, Y. et al. Generation of knockout mice by Cpf1-mediated gene targeting. Nat. Biotechnol.34, 808–810 (2016). ArticleCASPubMed Google Scholar
Hur, J. K. et al. Targeted mutagenesis in mice by electroporation of Cpf1 ribonucleoproteins. Nat. Biotechnol.34, 807–808 (2016). ArticleCASPubMed Google Scholar
Kim, D. et al. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat. Biotechnol.34, 863–868 (2016). ArticleCASPubMed Google Scholar
Grissa, I., Vergnaud, G. & Pourcel, C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res.35, W52–W57 (2007). ArticlePubMedPubMed Central Google Scholar
Almendros, C., Guzman, N. M., Garcia-Martinez, J. & Mojica, F. J. Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR–Cas I-F systems. Nat. Microbiol.1, 16081 (2016). ArticleCASPubMed Google Scholar
Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res.41, 4360–4377 (2013). ArticleCASPubMedPubMed Central Google Scholar
Yang, H., Gao, P., Rajashankar, K. R. & Patel, D. J. PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR–Cas endonuclease. Cell167, 1814–1828.e12 (2016). ArticleCASPubMedPubMed Central Google Scholar
Liu, L. et al. Two distant catalytic sites are responsible for C2c2 RNase activities. Cell168, 121–134.e12. (2017). ArticleCASPubMed Google Scholar
Smargon, A. A. et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol. Cellhttp://dx.doi.org/10.1016/j.molcel.2016.12.023 (2017).