How bacteria control the CRISPR-Cas arsenal
Tài liệu tham khảo
Patterson, 2017, Regulation of CRISPR-Cas adaptive immune systems, Curr Opin Microbiol, 37, 1, 10.1016/j.mib.2017.02.004
Koonin, 2017, Evolutionary genomics of defense systems in archaea and bacteria, Annu Rev Microbiol, 71, 10.1146/annurev-micro-090816-093830
Suttle, 2007, Marine viruses—major players in the global ecosystem, Nat Rev Micro, 5, 801, 10.1038/nrmicro1750
Suttle, 2005, Viruses in the sea, Nature, 437, 356, 10.1038/nature04160
Chopin, 2005, Phage abortive infection in lactococci: variations on a theme, Curr Opin Microbiol, 8, 473, 10.1016/j.mib.2005.06.006
Depardieu, 2016, A eukaryotic-like serine/threonine kinase protects staphylococci against phages, Cell Host Microbe, 20, 471, 10.1016/j.chom.2016.08.010
Loenen, 2014, Highlights of the DNA cutters: a short history of the restriction enzymes, Nucleic Acids Res, 42, 3, 10.1093/nar/gkt990
Loenen, 2014, Type I restriction enzymes and their relatives, Nucleic Acids Resarch, 42, 20, 10.1093/nar/gkt847
Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140
Marraffini, 2015, CRISPR-Cas immunity in prokaryotes, Nature, 526, 55, 10.1038/nature15386
Koonin, 2017, Diversity, classification and evolution of CRISPR-Cas systems, Curr Opin Microbiol, 37, 67, 10.1016/j.mib.2017.05.008
Brouns, 2008, Small CRISPR RNAs guide antiviral defense in prokaryotes, Science, 321, 960, 10.1126/science.1159689
Haurwitz, 2010, Sequence- and structure-specific RNA processing by a CRISPR endonuclease, Science, 329, 1355, 10.1126/science.1192272
Hale, 2009, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040
Deltcheva, 2011, CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III, Nature, 471, 602, 10.1038/nature09886
Carte, 2008, Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes, Genes Dev, 22, 3489, 10.1101/gad.1742908
Jiang, 2015, CRISPR-Cas: new tools for genetic manipulations from bacterial immunity systems, Annu Rev Microbiol, 69, 209, 10.1146/annurev-micro-091014-104441
Sternberg, 2015, Expanding the biologist's toolkit with CRISPR-Cas9, Mol Cell, 58, 568, 10.1016/j.molcel.2015.02.032
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
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
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
Huo, 2014, Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation, Nat Struct Mol Biol, 21, 771, 10.1038/nsmb.2875
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
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
Zhang, 2012, The CRISPR associated protein Cas4 is a 5″ to 3″ DNA exonuclease with an iron-sulfur cluster, PLoS ONE, 7, e47232, 10.1371/journal.pone.0047232
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
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
Samai, 2015, Co-transcriptional DNA and RNA cleavage during type III CRISPR-Cas immunity, Cell, 161, 1164, 10.1016/j.cell.2015.04.027
Tamulaitis, 2014, Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus, Mol Cell, 10.1016/j.molcel.2014.09.027
Osawa, 2015, Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog, Mol Cell, 58, 418, 10.1016/j.molcel.2015.03.018
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 USA, 109, E2579, 10.1073/pnas.1208507109
Kazlauskiene, 2016, Spatiotemporal control of type III-A CRISPR-Cas immunity: coupling DNA degradation with the target RNA recognition, Mol Cell, 62, 295, 10.1016/j.molcel.2016.03.024
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
Fonfara, 2016, The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA, Nature, 532, 517, 10.1038/nature17945
Abudayyeh, 2016, C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science, 353, aaf5573, 10.1126/science.aaf5573
East-Seletsky, 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 538, 270, 10.1038/nature19802
Makarova, 2015, An updated evolutionary classification of CRISPR-Cas systems, Nat Rev Micro, 13, 722, 10.1038/nrmicro3569
Yosef, 2012, Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli, Nucleic Acids Res, 40, 5569, 10.1093/nar/gks216
Levy, 2015, CRISPR adaptation biases explain preference for acquisition of foreign, DNA, 520, 505
Modell, 2017, CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity, Nature, 544, 101, 10.1038/nature21719
Nuñez, 2016, CRISPR immunological memory requires a host factor for specificity, Mol Cell, 62, 824, 10.1016/j.molcel.2016.04.027
Wright, 2017, Structures of the CRISPR genome integration complex, Science, 64, eaao0679
Fagerlund, 2017, Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex, Proc Natl Acad Sci USA, 114, E5122, 10.1073/pnas.1618421114
Nuñez, 2015, Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity, Nature, 519, 193, 10.1038/nature14237
Datsenko, 2012, Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system, Nat Commun, 3, 945, 10.1038/ncomms1937
Richter, 2014, Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer, Nucleic Acids Res, 42, 8516, 10.1093/nar/gku527
Staals, 2016, Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system, Nat Commun, 7, 12853, 10.1038/ncomms12853
Künne, 2016, Cas3-derived target DNA degradation fragments fuel primed CRISPR adaptation, Mol Cell, 63, 852, 10.1016/j.molcel.2016.07.011
Heler, 2015, Cas9 specifies functional viral targets during CRISPR-Cas adaptation, Nature, 519, 199, 10.1038/nature14245
Wei, 2015, Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation, Genes Dev, 29, 356, 10.1101/gad.257550.114
Carte, 2010, Binding and cleavage of CRISPR RNA by Cas6, RNA, 16, 2181, 10.1261/rna.2230110
Garside, 2012, Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases, RNA, 18, 2020, 10.1261/rna.033100.112
East-Seletsky, 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 10.1038/nature19802
Hochstrasser, 2014, CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference, Proc Natl Acad Sci USA, 111, 6618, 10.1073/pnas.1405079111
Xue, 2016, Conformational control of cascade interference and priming activities in CRISPR immunity, Mol Cell, 64, 826, 10.1016/j.molcel.2016.09.033
Xiao, 2017, Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPR-Cas system, Cell, 170, 48, 10.1016/j.cell.2017.06.012
Rollins, 2017, Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity, Proc Natl Acad Sci USA, 23
Sternberg, 2014, DNA interrogation by the CRISPR RNA-guided endonuclease Cas9, Nature, 507, 62, 10.1038/nature13011
Jinek, 2014, Structures of Cas9 endonucleases reveal RNA-mediated conformational activation, Science, 343, 1247997, 10.1126/science.1247997
Nishimasu, 2014, Crystal structure of Cas9 in complex with guide RNA and target DNA, Cell, 156, 935, 10.1016/j.cell.2014.02.001
Jiang, 2015, A Cas9–guide RNA complex preorganized for target DNA recognition, Science, 348, 1477, 10.1126/science.aab1452
Rauch, 2017, Inhibition of CRISPR-Cas9 with bacteriophage proteins, Cell, 168, 150, 10.1016/j.cell.2016.12.009
Dong, 2017, Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein, Nature, 10.1038/nature22377
Szczelkun, 2014, Direct observation of R-loop formation by single RNA-guided Cas9 and cascade effector complexes, Proc Natl Acad Sci USA, 111, 9798, 10.1073/pnas.1402597111
Anders, 2014, Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease, Nature, 10.1038/nature13579
Sternberg, 2015, Conformational control of DNA target cleavage by CRISPR-Cas9, Nature, 527, 110, 10.1038/nature15544
Jiang, 2016, Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage, Science, 351, 867, 10.1126/science.aad8282
Chen, 2017, Enhanced proofreading governs CRISPR-Cas9 targeting accuracy, Nature, 10.1038/nature24268
Dagdas, 2017, A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9, Sci Adv, 3, eaao0027, 10.1126/sciadv.aao0027
Harrington, 2017, A broad-spectrum inhibitor of CRISPR-Cas9, Cell, 10.1016/j.cell.2017.07.037
Hale, 2009, RNA-Guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040
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
Marraffini, 2010, Self versus non-self discrimination during CRISPR RNA-directed immunity, Nature, 463, 568, 10.1038/nature08703
Kazlauskiene, 2017, A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems, Science, 357, eaao0100, 10.1126/science.aao0100
Niewoehner, 2017, Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers, Nature, 10.1038/nature23467
Makarova, 2014, CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems, Front Genet, 5, 102, 10.3389/fgene.2014.00102
Bertani, 1953, Host controlled variation in bacterial viruses, J Bacteriol, 65, 113, 10.1128/JB.65.2.113-121.1953
Luria, 1952, A nonhereditary, host-induced variation of bacterial viruses, J Bacteriol, 64, 557, 10.1128/JB.64.4.557-569.1952
Arber, 1962, Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda, J Mol Biol, 5, 18, 10.1016/S0022-2836(62)80058-8
Arber, 1962, Host specificity of DNA produced by Escherichia coli: I. Host controlled modification of bacteriophage λ, J Mol Biol, 5, 18, 10.1016/S0022-2836(62)80058-8
Tock, 2005, The biology of restriction and anti-restriction, Curr Opin Microbiol, 8, 466, 10.1016/j.mib.2005.06.003
Bickle, 1993, Biology of DNA restriction, Microbiol Rev, 57, 434, 10.1128/MR.57.2.434-450.1993
Kennaway, 2012, Structure and operation of the DNA-translocating type I DNA restriction enzymes, Genes Dev, 26, 92, 10.1101/gad.179085.111
Weiserova, 1993, Cloning, production and characterisation of wild type and mutant forms of the R. EcoK endonucleases, Nucleic Acids Res, 21, 373, 10.1093/nar/21.3.373
Dryden, 1993, Purification and characterization of the methyltransferase from the type 1 restriction and modification system of Escherichia coli K12, J Biol Chem, 268, 13228, 10.1016/S0021-9258(19)38641-7
Keatch, 2004, Alleviation of restriction by DNA condensation and non-specific DNA binding ligands, Nucleic Acids Res, 32, 5841, 10.1093/nar/gkh918
Keatch, 2005, StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI, Nucleic Acids Res, 33, 6540, 10.1093/nar/gki951
Blakely, 2006, Control of the endonuclease activity of type I restriction-modification systems is required to maintain chromosome integrity following homologous recombination, Mol Microbiol, 60, 883, 10.1111/j.1365-2958.2006.05144.x
Makovets, 1999, Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes, Proc Natl Acad Sci USA, 96, 9757, 10.1073/pnas.96.17.9757
Simons, 2014, ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation, Nucleic Acids Res, 42, 12082, 10.1093/nar/gku851
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
Chowdhury, 2017, Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex, Cell, 169, 47, 10.1016/j.cell.2017.03.012
Borges, 2017, The discovery, mechanisms, and evolutionary impact of anti-CRISPRs, Annu Rev Virol, 4, 10.1146/annurev-virology-101416-041616
Carter, 2017, The interfaces of genetic conflict are hot spots for innovation, Cell, 168, 9, 10.1016/j.cell.2016.12.007