{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T18:37:01Z","timestamp":1782239821885,"version":"3.54.5"},"publisher-location":"New York, NY","reference-count":99,"publisher":"Springer New York","isbn-type":[{"value":"9781493926862","type":"print"},{"value":"9781493926879","type":"electronic"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015]]},"DOI":"10.1007\/978-1-4939-2687-9_4","type":"book-chapter","created":{"date-parts":[[2015,5,16]],"date-time":"2015-05-16T04:49:29Z","timestamp":1431751769000},"page":"47-75","source":"Crossref","is-referenced-by-count":371,"title":["Annotation and Classification of CRISPR-Cas Systems"],"prefix":"10.1007","author":[{"given":"Kira S.","family":"Makarova","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene V.","family":"Koonin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","reference":[{"key":"4_CR1","doi-asserted-by":"publisher","first-page":"4360","DOI":"10.1093\/nar\/gkt157","volume":"41","author":"KS Makarova","year":"2013","unstructured":"Makarova KS, Wolf YI, Koonin EV (2013) Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res 41:4360\u20134377","journal-title":"Nucleic Acids Res"},{"key":"4_CR2","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1146\/annurev-food-022811-101134","volume":"3","author":"R Barrangou","year":"2012","unstructured":"Barrangou R, Horvath P (2012) CRISPR: new horizons in phage resistance and strain identification. Annu Rev Food Sci Technol 3:143\u2013162","journal-title":"Annu Rev Food Sci Technol"},{"key":"4_CR3","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1038\/nature10886","volume":"482","author":"B Wiedenheft","year":"2012","unstructured":"Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331\u2013338","journal-title":"Nature"},{"key":"4_CR4","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/j.tibs.2009.05.002","volume":"34","author":"J van der Oost","year":"2009","unstructured":"van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ (2009) CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 34:401\u2013407","journal-title":"Trends Biochem Sci"},{"key":"4_CR5","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/nrmicro2577","volume":"9","author":"KS Makarova","year":"2011","unstructured":"Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467\u2013477","journal-title":"Nat Rev Microbiol"},{"key":"4_CR6","doi-asserted-by":"publisher","first-page":"e60","DOI":"10.1371\/journal.pcbi.0010060","volume":"1","author":"DH Haft","year":"2005","unstructured":"Haft DH, Selengut J, Mongodin EF, Nelson KE (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR\/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1:e60","journal-title":"PLoS Comput Biol"},{"key":"4_CR7","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1745-6150-1-7","volume":"1","author":"KS Makarova","year":"2006","unstructured":"Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (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","journal-title":"Biol Direct"},{"key":"4_CR8","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1002\/wrna.1159","volume":"4","author":"R Barrangou","year":"2013","unstructured":"Barrangou R (2013) CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 4:267\u2013278","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"4_CR9","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1146\/annurev-genet-110711-155447","volume":"46","author":"ER Westra","year":"2012","unstructured":"Westra ER, Swarts DC, Staals RH, Jore MM, Brouns SJ, van der Oost J (2012) The CRISPRs, they are a-changin\u2019: how prokaryotes generate adaptive immunity. Annu Rev Genet 46:311\u2013339","journal-title":"Annu Rev Genet"},{"key":"4_CR10","doi-asserted-by":"publisher","first-page":"5569","DOI":"10.1093\/nar\/gks216","volume":"40","author":"I Yosef","year":"2012","unstructured":"Yosef I, Goren MG, Qimron U (2012) Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 40:5569\u20135576","journal-title":"Nucleic Acids Res"},{"key":"4_CR11","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1038\/nsmb.2820","volume":"21","author":"JK Nunez","year":"2014","unstructured":"Nunez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA (2014) Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol 21:528\u2013534","journal-title":"Nat Struct Mol Biol"},{"key":"4_CR12","doi-asserted-by":"publisher","first-page":"e49549","DOI":"10.1371\/journal.pone.0049549","volume":"7","author":"C Richter","year":"2012","unstructured":"Richter C, Gristwood T, Clulow JS, Fineran PC (2012) In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR\/Cas System. PLoS One 7:e49549","journal-title":"PLoS One"},{"key":"4_CR13","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1038\/nature09886","volume":"471","author":"E Deltcheva","year":"2011","unstructured":"Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602\u2013607","journal-title":"Nature"},{"key":"4_CR14","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/j.molcel.2011.10.023","volume":"45","author":"CR Hale","year":"2012","unstructured":"Hale CR, Majumdar S, Elmore J, Pfister N, Compton M, Olson S, Resch AM, Glover CV III, Graveley BR, Terns RM, Terns MP (2012) Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol Cell 45:292\u2013302","journal-title":"Mol Cell"},{"key":"4_CR15","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1126\/science.1225829","volume":"337","author":"M Jinek","year":"2012","unstructured":"Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816\u2013821","journal-title":"Science"},{"key":"4_CR16","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1016\/j.molcel.2012.03.020","volume":"46","author":"DG Sashital","year":"2012","unstructured":"Sashital DG, Wiedenheft B, Doudna JA (2012) Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell 46:606\u2013615","journal-title":"Mol Cell"},{"key":"4_CR17","doi-asserted-by":"publisher","first-page":"1430","DOI":"10.1074\/mcp.M112.020263","volume":"11","author":"E van Duijn","year":"2012","unstructured":"van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, Heck AJ (2012) Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from escherichia coli and pseudomonas aeruginosa. Mol Cell Proteomics 11:1430\u20131441","journal-title":"Mol Cell Proteomics"},{"key":"4_CR18","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/j.molcel.2011.12.013","volume":"45","author":"J Zhang","year":"2012","unstructured":"Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, Naismith JH, Spagnolo L, White MF (2012) Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Mol Cell 45:303\u2013313","journal-title":"Mol Cell"},{"key":"4_CR19","doi-asserted-by":"publisher","first-page":"10092","DOI":"10.1073\/pnas.1102716108","volume":"108","author":"B Wiedenheft","year":"2011","unstructured":"Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, Doudna JA (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\u201310097","journal-title":"Proc Natl Acad Sci U S A"},{"key":"4_CR20","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1126\/science.1159689","volume":"321","author":"SJ Brouns","year":"2008","unstructured":"Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960\u2013964","journal-title":"Science"},{"key":"4_CR21","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1016\/j.molcel.2013.05.001","volume":"50","author":"Y Zhang","year":"2013","unstructured":"Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013) Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 50:488\u2013503","journal-title":"Mol Cell"},{"key":"4_CR22","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/j.molcel.2013.09.013","volume":"52","author":"RH Staals","year":"2013","unstructured":"Staals RH, Agari Y, Maki-Yonekura S, Zhu Y, Taylor DW, van Duijn E, Barendregt A, Vlot M, Koehorst JJ, Sakamoto K, Masuda A, Dohmae N, Schaap PJ, Doudna JA, Heck AJ, Yonekura K, van der Oost J, Shinkai A (2013) Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell 52:135\u2013145","journal-title":"Mol Cell"},{"key":"4_CR23","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.molcel.2013.09.008","volume":"52","author":"M Spilman","year":"2013","unstructured":"Spilman M, Cocozaki A, Hale C, Shao Y, Ramia N, Terns R, Terns M, Li H, Stagg S (2013) Structure of an RNA silencing complex of the CRISPR-Cas immune system. Mol Cell 52:146\u2013152","journal-title":"Mol Cell"},{"key":"4_CR24","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/1745-6150-6-38","volume":"6","author":"KS Makarova","year":"2011","unstructured":"Makarova KS, Aravind L, Wolf YI, Koonin EV (2011) Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 6:38","journal-title":"Biol Direct"},{"key":"4_CR25","doi-asserted-by":"publisher","first-page":"D205","DOI":"10.1093\/nar\/gkn845","volume":"37","author":"A Marchler-Bauer","year":"2009","unstructured":"Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH (2009) CDD: specific functional annotation with the conserved domain database. Nucleic Acids Res 37:D205\u2013D210","journal-title":"Nucleic Acids Res"},{"key":"4_CR26","doi-asserted-by":"publisher","first-page":"W244","DOI":"10.1093\/nar\/gki408","volume":"33","author":"J Soding","year":"2005","unstructured":"Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244\u2013W248","journal-title":"Nucleic Acids Res"},{"key":"4_CR27","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389\u20133402","journal-title":"Nucleic Acids Res"},{"key":"4_CR28","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/978-1-59745-514-5_9","volume":"395","author":"D Wheeler","year":"2007","unstructured":"Wheeler D, Bhagwat M (2007) BLAST QuickStart: example-driven web-based BLAST tutorial. Methods Mol Biol 395:149\u2013176","journal-title":"Methods Mol Biol"},{"key":"4_CR29","doi-asserted-by":"publisher","first-page":"6091","DOI":"10.1093\/nar\/gku241","volume":"42","author":"K Chylinski","year":"2014","unstructured":"Chylinski K, Makarova KS, Charpentier E, Koonin EV (2014) Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res 42:6091\u20136105","journal-title":"Nucleic Acids Res"},{"key":"4_CR30","doi-asserted-by":"publisher","first-page":"679","DOI":"10.4161\/rna.24022","volume":"10","author":"EV Koonin","year":"2013","unstructured":"Koonin EV, Makarova KS (2013) CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol 10:679\u2013686","journal-title":"RNA Biol"},{"key":"4_CR31","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1042\/BST20130038","volume":"41","author":"KS Makarova","year":"2013","unstructured":"Makarova KS, Wolf YI, Koonin EV (2013) The basic building blocks and evolution of CRISPR-CAS systems. Biochem Soc Trans 41:1392\u20131400","journal-title":"Biochem Soc Trans"},{"key":"4_CR32","doi-asserted-by":"publisher","first-page":"102","DOI":"10.3389\/fgene.2014.00102","volume":"5","author":"KS Makarova","year":"2014","unstructured":"Makarova KS, Anantharaman V, Grishin NV, Koonin EV, Aravind L (2014) CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. Front Genet 5:102","journal-title":"Front Genet"},{"key":"4_CR33","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1046\/j.1365-2958.2002.02839.x","volume":"43","author":"R Jansen","year":"2002","unstructured":"Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565\u20131575","journal-title":"Mol Microbiol"},{"key":"4_CR34","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1128\/JB.06521-11","volume":"194","author":"N Takeuchi","year":"2012","unstructured":"Takeuchi N, Wolf YI, Makarova KS, Koonin EV (2012) Nature and intensity of selection pressure on CRISPR-associated genes. J Bacteriol 194:1216\u20131225","journal-title":"J Bacteriol"},{"key":"4_CR35","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1016\/j.str.2009.03.019","volume":"17","author":"B Wiedenheft","year":"2009","unstructured":"Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA (2009) Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17:904\u2013912","journal-title":"Structure"},{"key":"4_CR36","doi-asserted-by":"publisher","first-page":"1928","DOI":"10.1016\/j.febslet.2009.04.047","volume":"583","author":"D Han","year":"2009","unstructured":"Han D, Lehmann K, Krauss G (2009) SSO1450\u2013a CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA. FEBS Lett 583:1928\u20131932","journal-title":"FEBS Lett"},{"key":"4_CR37","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1111\/j.1365-2958.2010.07465.x","volume":"79","author":"M Babu","year":"2011","unstructured":"Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF (2011) A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 79:484\u2013502","journal-title":"Mol Microbiol"},{"key":"4_CR38","doi-asserted-by":"publisher","first-page":"20361","DOI":"10.1074\/jbc.M803225200","volume":"283","author":"N Beloglazova","year":"2008","unstructured":"Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF (2008) A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem 283:20361\u201320371","journal-title":"J Biol Chem"},{"key":"4_CR39","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1016\/j.str.2012.06.016","volume":"20","author":"KH Nam","year":"2012","unstructured":"Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A (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\u20131584","journal-title":"Structure"},{"key":"4_CR40","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1038\/emboj.2011.41","volume":"30","author":"T Sinkunas","year":"2011","unstructured":"Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (2011) Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR\/Cas immune system. EMBO J 30:1335\u20131342","journal-title":"EMBO J"},{"key":"4_CR41","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1016\/j.febslet.2009.01.024","volume":"583","author":"D Han","year":"2009","unstructured":"Han D, Krauss G (2009) Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2. FEBS Lett 583:771\u2013776","journal-title":"FEBS Lett"},{"key":"4_CR42","doi-asserted-by":"publisher","first-page":"e47232","DOI":"10.1371\/journal.pone.0047232","volume":"7","author":"J Zhang","year":"2012","unstructured":"Zhang J, Kasciukovic T, White MF (2012) The CRISPR associated protein Cas4 Is a 5\u2032 to 3\u2032 DNA exonuclease with an iron-sulfur cluster. PLoS One 7:e47232","journal-title":"PLoS One"},{"key":"4_CR43","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1038\/nature10402","volume":"477","author":"B Wiedenheft","year":"2011","unstructured":"Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E (2011) Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477:486\u2013489","journal-title":"Nature"},{"key":"4_CR44","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1038\/nsmb.2019","volume":"18","author":"MM Jore","year":"2011","unstructured":"Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ (2011) Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 18:529\u2013536","journal-title":"Nat Struct Mol Biol"},{"key":"4_CR45","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.molcel.2013.08.020","volume":"52","author":"C Rouillon","year":"2013","unstructured":"Rouillon C, Zhou M, Zhang J, Politis A, Beilsten-Edmands V, Cannone G, Graham S, Robinson CV, Spagnolo L, White MF (2013) Structure of the CRISPR interference complex CSM reveals key similarities with cascade. Mol Cell 52:124\u2013134","journal-title":"Mol Cell"},{"key":"4_CR46","doi-asserted-by":"publisher","first-page":"3799","DOI":"10.1016\/j.jmb.2013.02.032","volume":"425","author":"Y Koo","year":"2013","unstructured":"Koo Y, Ka D, Kim EJ, Suh N, Bae E (2013) Conservation and variability in the structure and function of the Cas5d endoribonuclease in the CRISPR-mediated microbial immune system. J Mol Biol 425:3799\u20133810","journal-title":"J Mol Biol"},{"key":"4_CR47","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1016\/j.cell.2009.07.040","volume":"139","author":"CR Hale","year":"2009","unstructured":"Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP (2009) RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945\u2013956","journal-title":"Cell"},{"key":"4_CR48","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1093\/nar\/gkt922","volume":"42","author":"O Niewoehner","year":"2014","unstructured":"Niewoehner O, Jinek M, Doudna JA (2014) Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res 42:1341\u20131353","journal-title":"Nucleic Acids Res"},{"key":"4_CR49","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1042\/BJ20130269","volume":"452","author":"J Reeks","year":"2013","unstructured":"Reeks J, Sokolowski RD, Graham S, Liu H, Naismith JH, White MF (2013) Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing. Biochem J 452:223\u2013230","journal-title":"Biochem J"},{"key":"4_CR50","doi-asserted-by":"publisher","first-page":"700","DOI":"10.4161\/rna.23715","volume":"10","author":"H Richter","year":"2013","unstructured":"Richter H, Lange SJ, Backofen R, Randau L (2013) Comparative analysis of Cas6b processing and CRISPR RNA stability. RNA Biol 10:700\u2013707","journal-title":"RNA Biol"},{"key":"4_CR51","doi-asserted-by":"publisher","first-page":"3489","DOI":"10.1101\/gad.1742908","volume":"22","author":"J Carte","year":"2008","unstructured":"Carte J, Wang R, Li H, Terns RM, Terns MP (2008) Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 22:3489\u20133496","journal-title":"Genes Dev"},{"key":"4_CR52","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1126\/science.1192272","volume":"329","author":"RE Haurwitz","year":"2010","unstructured":"Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329:1355\u20131358","journal-title":"Science"},{"key":"4_CR53","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.str.2012.01.018","volume":"20","author":"AI Cocozaki","year":"2012","unstructured":"Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H (2012) Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Structure 20:545\u2013553","journal-title":"Structure"},{"key":"4_CR54","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1042\/BJ20130316","volume":"453","author":"J Reeks","year":"2013","unstructured":"Reeks J, Naismith JH, White MF (2013) CRISPR interference: a structural perspective. Biochem J 453:155\u2013166","journal-title":"Biochem J"},{"key":"4_CR55","doi-asserted-by":"publisher","first-page":"762","DOI":"10.4161\/rna.23854","volume":"10","author":"J Reeks","year":"2013","unstructured":"Reeks J, Graham S, Anderson L, Liu H, White MF, Naismith JH (2013) Structure of the archaeal Cascade subunit Csa5: relating the small subunits of CRISPR effector complexes. RNA Biol 10:762\u2013769","journal-title":"RNA Biol"},{"key":"4_CR56","doi-asserted-by":"publisher","first-page":"1709","DOI":"10.1126\/science.1138140","volume":"315","author":"R Barrangou","year":"2007","unstructured":"Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709\u20131712","journal-title":"Science"},{"key":"4_CR57","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/nature09523","volume":"468","author":"JE Garneau","year":"2010","unstructured":"Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S (2010) The CRISPR\/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67\u201371","journal-title":"Nature"},{"key":"4_CR58","doi-asserted-by":"publisher","first-page":"9275","DOI":"10.1093\/nar\/gkr606","volume":"39","author":"R Sapranauskas","year":"2011","unstructured":"Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (2011) The Streptococcus thermophilus CRISPR\/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39:9275\u20139282","journal-title":"Nucleic Acids Res"},{"key":"4_CR59","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1016\/j.cell.2014.02.001","volume":"156","author":"H Nishimasu","year":"2014","unstructured":"Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O (2014) Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156:935\u2013949","journal-title":"Cell"},{"key":"4_CR60","doi-asserted-by":"publisher","first-page":"1247997","DOI":"10.1126\/science.1247997","volume":"343","author":"M Jinek","year":"2014","unstructured":"Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343:1247997","journal-title":"Science"},{"key":"4_CR61","doi-asserted-by":"publisher","first-page":"31896","DOI":"10.1074\/jbc.M111.270017","volume":"286","author":"S Mulepati","year":"2011","unstructured":"Mulepati S, Bailey S (2011) Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3). J Biol Chem 286:31896\u201331903","journal-title":"J Biol Chem"},{"key":"4_CR62","doi-asserted-by":"publisher","first-page":"4616","DOI":"10.1038\/emboj.2011.377","volume":"30","author":"N Beloglazova","year":"2011","unstructured":"Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin AF (2011) Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J 30:4616\u20134627","journal-title":"EMBO J"},{"key":"4_CR63","doi-asserted-by":"publisher","first-page":"2941","DOI":"10.1021\/bi035535u","volume":"43","author":"A Chakrabarti","year":"2004","unstructured":"Chakrabarti A, Desai P, Wickstrom E (2004) Transposon Tn7 protein TnsD binding to Escherichia coli attTn7 DNA and its eukaryotic orthologs. Biochemistry 43:2941\u20132946","journal-title":"Biochemistry"},{"key":"4_CR64","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1111\/j.1365-2958.1995.mmi_17061189.x","volume":"17","author":"GY Kholodii","year":"1995","unstructured":"Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV, Nikiforov VG (1995) Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol Microbiol 17:1189\u20131200","journal-title":"Mol Microbiol"},{"key":"4_CR65","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.sbi.2014.01.001","volume":"24","author":"RN Jackson","year":"2014","unstructured":"Jackson RN, Lavin M, Carter J, Wiedenheft B (2014) Fitting CRISPR-associated Cas3 into the helicase family tree. Curr Opin Struct Biol 24:106\u2013114","journal-title":"Curr Opin Struct Biol"},{"key":"4_CR66","doi-asserted-by":"publisher","first-page":"726","DOI":"10.4161\/rna.24321","volume":"10","author":"K Chylinski","year":"2013","unstructured":"Chylinski K, Le Rhun A, Charpentier E (2013) The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol 10:726\u2013737","journal-title":"RNA Biol"},{"key":"4_CR67","doi-asserted-by":"publisher","first-page":"2577","DOI":"10.1093\/nar\/gkt1074","volume":"42","author":"I Fonfara","year":"2014","unstructured":"Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lecrivain AL, Bzdrenga J, Koonin EV, Charpentier E (2014) Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res 42:2577\u20132590","journal-title":"Nucleic Acids Res"},{"key":"4_CR68","doi-asserted-by":"publisher","first-page":"30759","DOI":"10.1074\/jbc.M111.256263","volume":"286","author":"KH Nam","year":"2011","unstructured":"Nam KH, Kurinov I, Ke A (2011) Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2\u2009+\u2009-dependent double-stranded DNA binding activity. J Biol Chem 286:30759\u201330768","journal-title":"J Biol Chem"},{"key":"4_CR69","doi-asserted-by":"publisher","first-page":"e33401","DOI":"10.1371\/journal.pone.0033401","volume":"7","author":"Y Koo","year":"2012","unstructured":"Koo Y, Jung DK, Bae E (2012) Crystal structure of Streptococcus pyogenes Csn2 reveals calcium-dependent conformational changes in its tertiary and quaternary structure. PLoS One 7:e33401","journal-title":"PLoS One"},{"key":"4_CR70","doi-asserted-by":"publisher","first-page":"6347","DOI":"10.1093\/nar\/gkt315","volume":"41","author":"Z Arslan","year":"2013","unstructured":"Arslan Z, Wurm R, Brener O, Ellinger P, Nagel-Steger L, Oesterhelt F, Schmitt L, Willbold D, Wagner R, Gohlke H, Smits SH, Pul U (2013) Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucleic Acids Res 41:6347\u20136359","journal-title":"Nucleic Acids Res"},{"key":"4_CR71","doi-asserted-by":"publisher","first-page":"2573","DOI":"10.1002\/prot.24138","volume":"80","author":"KH Lee","year":"2012","unstructured":"Lee KH, Lee SG, Eun Lee K, Jeon H, Robinson H, Oh BH (2012) Identification, structural, and biochemical characterization of a group of large Csn2 proteins involved in CRISPR-mediated bacterial immunity. Proteins 80:2573\u20132582","journal-title":"Proteins"},{"key":"4_CR72","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.jgg.2013.03.013","volume":"40","author":"C Wei","year":"2013","unstructured":"Wei C, Liu J, Yu Z, Zhang B, Gao G, Jiao R (2013) TALEN or Cas9 - rapid, efficient and specific choices for genome modifications. J Genet Genomics 40:281\u2013289","journal-title":"J Genet Genomics"},{"key":"4_CR73","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1126\/science.341.6148.833","volume":"341","author":"E Pennisi","year":"2013","unstructured":"Pennisi E (2013) The CRISPR craze. Science 341:833\u2013836","journal-title":"Science"},{"key":"4_CR74","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/1745-6150-5-43","volume":"5","author":"V Anantharaman","year":"2010","unstructured":"Anantharaman V, Iyer LM, Aravind L (2010) Presence of a classical RRM-fold palm domain in Thg1-type 3\u2032-5\u2032 nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains. Biol Direct 5:43","journal-title":"Biol Direct"},{"key":"4_CR75","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1002\/1097-0134(20010201)42:2<210::AID-PROT80>3.0.CO;2-8","volume":"42","author":"J Pei","year":"2001","unstructured":"Pei J, Grishin NV (2001) GGDEF domain is homologous to adenylyl cyclase. Proteins 42:210\u2013216","journal-title":"Proteins"},{"key":"4_CR76","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1093\/nar\/30.2.482","volume":"30","author":"KS Makarova","year":"2002","unstructured":"Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res 30:482\u2013496","journal-title":"Nucleic Acids Res"},{"key":"4_CR77","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1016\/j.febslet.2012.02.036","volume":"586","author":"X Zhu","year":"2012","unstructured":"Zhu X, Ye K (2012) Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. FEBS Lett 586:939\u2013945","journal-title":"FEBS Lett"},{"key":"4_CR78","doi-asserted-by":"publisher","first-page":"779","DOI":"10.4161\/rna.23928","volume":"10","author":"L Nickel","year":"2013","unstructured":"Nickel L, Weidenbach K, Jager D, Backofen R, Lange SJ, Heidrich N, Schmitz RA (2013) Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III. RNA Biol 10:779\u2013791","journal-title":"RNA Biol"},{"key":"4_CR79","doi-asserted-by":"publisher","first-page":"1843","DOI":"10.1126\/science.1165771","volume":"322","author":"LA Marraffini","year":"2008","unstructured":"Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843\u20131845","journal-title":"Science"},{"key":"4_CR80","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1042\/BST0370547","volume":"37","author":"MF White","year":"2009","unstructured":"White MF (2009) Structure, function and evolution of the XPD family of iron-sulfur-containing 5\u2032\u2009\u2192\u20093\u2032 DNA helicases. Biochem Soc Trans 37:547\u2013551","journal-title":"Biochem Soc Trans"},{"key":"4_CR81","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1007\/s00792-014-0672-7","volume":"18","author":"KS Makarova","year":"2014","unstructured":"Makarova KS, Wolf YI, Forterre P, Prangishvili D, Krupovic M, Koonin EV (2014) Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles 18:877\u2013893","journal-title":"Extremophiles"},{"key":"4_CR82","doi-asserted-by":"publisher","first-page":"6039","DOI":"10.1128\/JB.05535-11","volume":"193","author":"KS Makarova","year":"2011","unstructured":"Makarova KS, Wolf YI, Snir S, Koonin EV (2011) Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol 193:6039\u20136056","journal-title":"J Bacteriol"},{"key":"4_CR83","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1038\/ncomms1937","volume":"3","author":"KA Datsenko","year":"2012","unstructured":"Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E (2012) Molecular memory of prior infections activates the CRISPR\/Cas adaptive bacterial immunity system. Nat Commun 3:945","journal-title":"Nat Commun"},{"key":"4_CR84","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1016\/j.bbrc.2013.10.122","volume":"441","author":"TY Kim","year":"2013","unstructured":"Kim TY, Shin M, Huynh Thi Yen L, Kim JS (2013) Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity. Biochem Biophys Res Commun 441:720\u2013725","journal-title":"Biochem Biophys Res Commun"},{"key":"4_CR85","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/1741-7007-12-36","volume":"12","author":"M Krupovic","year":"2014","unstructured":"Krupovic M, Makarova KS, Forterre P, Prangishvili D, Koonin EV (2014) Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity. BMC Biol 12:36","journal-title":"BMC Biol"},{"key":"4_CR86","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/1745-6150-7-40","volume":"7","author":"KS Makarova","year":"2012","unstructured":"Makarova KS, Anantharaman V, Aravind L, Koonin EV (2012) Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol Direct 7:40","journal-title":"Biol Direct"},{"key":"4_CR87","doi-asserted-by":"publisher","first-page":"21643","DOI":"10.1074\/jbc.M111.238485","volume":"286","author":"NG Lintner","year":"2011","unstructured":"Lintner NG, Kerou M, Brumfield SK, Graham S, Liu H, Naismith JH, Sdano M, Peng N, She Q, Copie V, Young MJ, White MF, Lawrence CM (2011) Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE). J Biol Chem 286:21643\u201321656","journal-title":"J Biol Chem"},{"key":"4_CR88","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1016\/j.str.2013.01.002","volume":"21","author":"Y Shao","year":"2013","unstructured":"Shao Y, Cocozaki AI, Ramia NF, Terns RM, Terns MP, Li H (2013) Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex. Structure 21:376\u2013384","journal-title":"Structure"},{"key":"4_CR89","doi-asserted-by":"publisher","first-page":"pii: a003657","DOI":"10.1101\/cshperspect.a003657","volume":"4","author":"MM Jore","year":"2012","unstructured":"Jore MM, Brouns SJ, van der Oost J (2012) RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb Perspect Biol 4:pii: a003657","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"4_CR90","doi-asserted-by":"publisher","first-page":"1670","DOI":"10.4161\/rna.26500","volume":"10","author":"A Hrle","year":"2013","unstructured":"Hrle A, Su AA, Ebert J, Benda C, Randau L, Conti E (2013) Structure and RNA-binding properties of the type III-A CRISPR-associated protein Csm3. RNA Biol 10:1670\u20131678","journal-title":"RNA Biol"},{"key":"4_CR91","doi-asserted-by":"publisher","first-page":"3811","DOI":"10.1016\/j.jmb.2013.03.042","volume":"425","author":"T Osawa","year":"2013","unstructured":"Osawa T, Inanaga H, Numata T (2013) Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. J Mol Biol 425:3811\u20133823","journal-title":"J Mol Biol"},{"key":"4_CR92","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1016\/j.celrep.2013.07.049","volume":"4","author":"TE Quax","year":"2013","unstructured":"Quax TE, Wolf YI, Koehorst JJ, Wurtzel O, van der Oost R, Ran W, Blombach F, Makarova KS, Brouns SJ, Forster AC, Wagner EG, Sorek R, Koonin EV, van der Oost J (2013) Differential translation tunes uneven production of operon-encoded proteins. Cell Rep 4:938\u2013944","journal-title":"Cell Rep"},{"key":"4_CR93","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.sbi.2004.01.006","volume":"14","author":"TA Steitz","year":"2004","unstructured":"Steitz TA (2004) The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase. Curr Opin Struct Biol 14:4\u20139","journal-title":"Curr Opin Struct Biol"},{"key":"4_CR94","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1745-6150-8-15","volume":"8","author":"V Anantharaman","year":"2013","unstructured":"Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L (2013) Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct 8:15","journal-title":"Biol Direct"},{"key":"4_CR95","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1006\/jmbi.1995.0343","volume":"249","author":"M Penner","year":"1995","unstructured":"Penner M, Morad I, Snyder L, Kaufmann G (1995) Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems. J Mol Biol 249:857\u2013868","journal-title":"J Mol Biol"},{"key":"4_CR96","doi-asserted-by":"publisher","first-page":"7620","DOI":"10.1093\/nar\/gkr397","volume":"39","author":"C Wang","year":"2011","unstructured":"Wang C, Villion M, Semper C, Coros C, Moineau S, Zimmerly S (2011) A reverse transcriptase-related protein mediates phage resistance and polymerizes untemplated DNA in vitro. Nucleic Acids Res 39:7620\u20137629","journal-title":"Nucleic Acids Res"},{"key":"4_CR97","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1002\/prot.24183","volume":"81","author":"YK Kim","year":"2013","unstructured":"Kim YK, Kim YG, Oh BH (2013) Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus. Proteins 81:261\u2013270","journal-title":"Proteins"},{"key":"4_CR98","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1016\/j.jmb.2010.11.019","volume":"405","author":"NG Lintner","year":"2011","unstructured":"Lintner NG, Frankel KA, Tsutakawa SE, Alsbury DL, Copie V, Young MJ, Tainer JA, Lawrence CM (2011) The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR\/Cas system. J Mol Biol 405:939\u2013955","journal-title":"J Mol Biol"},{"key":"4_CR99","doi-asserted-by":"publisher","first-page":"852","DOI":"10.4161\/rna.24160","volume":"10","author":"S Hein","year":"2013","unstructured":"Hein S, Scholz I, Voss B, Hess WR (2013) Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. RNA Biol 10:852\u2013864","journal-title":"RNA Biol"}],"container-title":["Methods in Molecular Biology","CRISPR"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-2687-9_4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T07:52:18Z","timestamp":1676015538000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-4939-2687-9_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9781493926862","9781493926879"],"references-count":99,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-2687-9_4","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015]]}}}