Diversity, classification and evolution of CRISPR-Cas systems

Sorek, 2013, CRISPR-mediated adaptive immune systems in bacteria and archaea, Annu. Rev. Biochem., 82, 237, 10.1146/annurev-biochem-072911-172315

Wright, 2016, Biology and applications of CRISPR systems: harnessing nature’s toolbox for genome engineering, Cell, 164, 29, 10.1016/j.cell.2015.12.035

Komor, 2017, CRISPR-based technologies for the manipulation of eukaryotic genomes, Cell, 168, 20, 10.1016/j.cell.2016.10.044

Mohanraju, 2016, Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems, Science, 353, 10.1126/science.aad5147

Pingoud, 2014, Type II restriction endonucleases—a historical perspective and more, Nucleic Acids Res., 42, 7489, 10.1093/nar/gku447

Takeuchi, 2012, Nature and intensity of selection pressure on CRISPR-associated genes, J. Bacteriol., 194, 216, 10.1128/JB.06521-11

Makarova, 2011, Evolution and classification of the CRISPR-Cas systems, Nat. Rev. Microbiol., 9, 467, 10.1038/nrmicro2577

Makarova, 2015, An updated evolutionary classification of CRISPR-Cas systems, Nat. Rev. Microbiol., 13, 722, 10.1038/nrmicro3569

Bondy-Denomy, 2013, Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system, Nature, 493, 429, 10.1038/nature11723

Bondy-Denomy, 2015, Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins, Nature, 526, 136, 10.1038/nature15254

Pawluk, 2016, Naturally occurring off-switches for CRISPR-Cas9, Cell, 167, 1829, 10.1016/j.cell.2016.11.017

Pawluk, 2016, Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species, Nat. Microbiol., 1, 16085, 10.1038/nmicrobiol.2016.85

Makarova, 2013, The basic building blocks and evolution of CRISPR-cas systems, Biochem. Soc. Trans., 41, 1392, 10.1042/BST20130038

Amitai, 2016, CRISPR-Cas adaptation: insights into the mechanism of action, Nat. Rev. Microbiol., 14, 67, 10.1038/nrmicro.2015.14

Makarova, 2011, Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems, Biol. Direct., 6, 10.1186/1745-6150-6-38

Zhao, 2014, Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli, Nature, 515, 147, 10.1038/nature13733

van der Oost, 2014, Unravelling the structural and mechanistic basis of CRISPR-Cas systems, Nat. Rev. Microbiol., 12, 479, 10.1038/nrmicro3279

Jackson, 2014, Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli, Science, 345, 1473, 10.1126/science.1256328

Jackson, 2015, A conserved structural chassis for mounting versatile CRISPR RNA-guided immune responses, Mol. Cell., 58, 722, 10.1016/j.molcel.2015.05.023

Hochstrasser, 2014, CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference, Proc. Natl. Acad. Sci. U. S. A., 111, 6618, 10.1073/pnas.1405079111

Hochstrasser, 2016, DNA Targeting by a minimal CRISPR RNA-guided cascade, Mol. Cell., 63, 840, 10.1016/j.molcel.2016.07.027

Staals, 2013, Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus, Mol. Cell., 52, 135, 10.1016/j.molcel.2013.09.013

Staals, 2014, RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus, Mol. Cell., 56, 518, 10.1016/j.molcel.2014.10.005

Hatoum-Aslan, 2013, A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs, J. Biol. Chem., 288, 27888, 10.1074/jbc.M113.499244

Kuznedelov, 2016, Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation, Nucleic Acids Res., 44, 10849, 10.1093/nar/gkw914

Luo, 2016, The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers, Nucleic Acids Res., 44, 7385

Charpentier, 2015, Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity, FEMS Microbiol. Rev., 39, 428, 10.1093/femsre/fuv023

Niewoehner, 2016, Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6, RNA, 22, 318, 10.1261/rna.054098.115

Zetsche, 2015, Cpf1 is a single RNA-guided endonuclease of a Class 2 CRISPR-Cas system, Cell, 163, 759, 10.1016/j.cell.2015.09.038

Shmakov, 2015, Discovery and functional characterization of diverse Class 2 CRISPR-Cas systems, Mol. Cell., 60, 385, 10.1016/j.molcel.2015.10.008

Shmakov, 2017, Diversity and evolution of class 2 CRISPR-Cas systems, Nat. Rev. Microbiol., 10.1038/nrmicro.2016.184

Abudayyeh, 2016, C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science, 353, 10.1126/science.aaf5573

Smargon, 2017, Cab is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx 28, Mol. Cell., 65, 618, 10.1016/j.molcel.2016.12.023

Burstein, 2017, New CRISPR-Cas systems from uncultivated microbes, Nature, 542, 237, 10.1038/nature21059

Jinek, 2014, Structures of Cas9 endonucleases reveal RNA-mediated conformational activation, Science, 343, 1247997, 10.1126/science.1247997

Nishimasu, 2015, Crystal Structure of Staphylococcus aureus Cas9, Cell, 162, 1113, 10.1016/j.cell.2015.08.007

Nishimasu, 2014, Crystal structure of Cas9 in complex with guide RNA and target DNA, Cell, 156, 935, 10.1016/j.cell.2014.02.001

Hirano, 2016, Structure and Engineering of Francisella novicida Cas9, Cell, 164, 950, 10.1016/j.cell.2016.01.039

Dong, 2016, The crystal structure of Cpf1 in complex with CRISPR RNA, Nature, 532, 522, 10.1038/nature17944

Yamano, 2016, Crystal structure of Cpf1 in complex with guide RNA and target DNA, Cell, 165, 949, 10.1016/j.cell.2016.04.003

Gao, 2016, Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition, Cell Res., 26, 901, 10.1038/cr.2016.88

Swarts, 2017, Structural basis for guide RNA processing and seed-dependent DNA targeting by CRISPR-Cas12a, Mol. Cell., 66, 221, 10.1016/j.molcel.2017.03.016

Liu, 2017, C2c1-sgRNA complex structure reveals RNA-guided DNA cleavage mechanism, Mol. Cell., 65, 310, 10.1016/j.molcel.2016.11.040

Yang, 2016, PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease, Cell, 167, 1814, 10.1016/j.cell.2016.11.053

Lewis, 2017, Building the Class 2 CRISPR-Cas Arsenal, Mol. Cell., 65, 377, 10.1016/j.molcel.2017.01.024

Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829

Gasiunas, 2012, Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria, Proc. Natl. Acad. Sci. U. S. A., 109, E2579, 10.1073/pnas.1208507109

Jiang, 2016, Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage, Science, 351, 867, 10.1126/science.aad8282

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

Hale, 2014, Target RNA capture and cleavage by the Cmr type III-B CRISPR-Cas effector complex, Genes. Dev., 28, 2432, 10.1101/gad.250712.114

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

Samai, 2015, Co-transcriptional DNA and RNA cleavage during Type III CRISPR-Cas immunity, Cell, 161, 1164, 10.1016/j.cell.2015.04.027

Liu, 2017, Two distant catalytic sites are responsible for C2c2 RNase activities, Cell, 168, 121, 10.1016/j.cell.2016.12.031

Koonin, 2017, Coupling immunity and programmed cell suicide in prokaryotes: life-or-death choices, Bioessays, 39, 1, 10.1002/bies.201600186

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

Zhang, 2013, Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis, Mol. Cell., 50, 488, 10.1016/j.molcel.2013.05.001

Fonfara, 2016, The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA, Nature, 532, 517, 10.1038/nature17945

East-Seletsky, 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 538, 270, 10.1038/nature19802

Zetsche, 2017, Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array, Nat. Biotechnol., 35, 31, 10.1038/nbt.3737

Krupovic, 2016, Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Curr. Opin. Microbiol., 31, 25, 10.1016/j.mib.2016.01.006

Krupovic, 2014, Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biol., 12, 36, 10.1186/1741-7007-12-36

Hickman, 2015, The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications, Nucleic Acids Res., 43, 10576, 10.1093/nar/gkv1180

Beguin, 2016, Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems, Nucleic Acids Res., 44, 10367

Koonin, 2015, Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nat. Rev. Genet., 16, 184, 10.1038/nrg3859

Krupovic, 2017, Casposons: the mobile elements that gave rise to the adaptation module of CRISPR-Cas systems, Curr. Opin. Microbiol., 38, 36, 10.1016/j.mib.2017.04.004

Swarts, 2014, The evolutionary journey of Argonaute proteins, Nat. Struct. Mol. Biol., 21, 743, 10.1038/nsmb.2879

Pasternak, 2013, ISDra2 transposition in Deinococcus radiodurans is downregulated by TnpB, Mol. Microbiol., 88, 443, 10.1111/mmi.12194

Chylinski, 2014, Classification and evolution of type II CRISPR-Cas systems, Nucleic Acids Res., 42, 6091, 10.1093/nar/gku241

Kapitonov, 2015, ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs, J. Bacteriol., 198, 797, 10.1128/JB.00783-15

Jiang, 2016, Degradation of phage transcripts by CRISPR-associated RNases enables type III CRISPR-Cas immunity, Cell, 164, 710, 10.1016/j.cell.2015.12.053

Silas, 2016, Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Ca fusion protein, Science, 351, 10.1126/science.aad4234