CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

被引：13

作者：

Adler, Benjamin A. ^{[1
,2
]}

Trinidad, Marena, I ^{[1
,3
]}

Bellieny-Rabelo, Daniel ^{[1
,2
]}

Zhang, Elaine ^{[1
,3
]}

Karp, Hannah M. ^{[1
,4
]}

Skopintsev, Petr ^{[1
,2
]}

Thornton, Brittney W. ^{[1
,5
]}

Weissman, Rachel F. ^{[1
,5
]}

Yoon, Peter H. ^{[1
,5
]}

Chen, Linxing ^{[1
,6
]}

Hessler, Tomas ^{[1
,6
,7
,8
]}

Eggers, Amy R. ^{[1
,5
]}

Colognori, David ^{[1
,5
]}

Boger, Ron ^{[1
,2
]}

Doherty, Erin E. ^{[1
,2
]}

Tsuchida, Connor A. ^{[1
,9
]}

Tran, Ryan, V ^{[4
]}

Hofman, Laura ^{[1
,2
,10
]}

Shi, Honglue ^{[1
,3
]}

Wasko, Kevin M. ^{[1
,5
]}

Zhou, Zehan ^{[1
,5
]}

Xia, Chenglong ^{[1
,2
]}

Al-Shimary, Muntathar J. ^{[1
,5
]}

Patel, Jaymin R. ^{[1
]}

Thomas, Vienna C. J. X. ^{[1
,4
]}

Pattali, Rithu ^{[1
,5
]}

Kan, Matthew J. ^{[1
,11
]}

Vardapetyan, Anna ^{[1
]}

Yang, Alana ^{[1
,5
]}

Lahiri, Arushi ^{[5
]}

Maxwell, Michaela F. ^{[12
]}

Murdock, Andrew G. ^{[1
]}

Ramit, Glenn C. ^{[1
]}

Henderson, Hope R. ^{[1
]}

Calvert, Roland W. ^{[13
]}

Bamert, Rebecca S. ^{[13
]}

Knott, Gavin J. ^{[13
]}

Lapinaite, Audrone ^{[14
,15
,16
]}

Pausch, Patrick ^{[17
]}

Cofsky, Joshua C. ^{[18
]}

Sontheimer, Erik J. ^{[19
,20
,21
]}

Wiedenheft, Blake ^{[22
]}

Fineran, Peter C. ^{[23
,24
,25
,26
]}

Brouns, Stan J. J. ^{[27
,28
]}

Sashital, Dipali G. ^{[29
]}

Thomas, Brian C. ^{[30
]}

Brown, Christopher T. ^{[30
]}

Goltsman, Daniela S. A. ^{[30
]}

Barrangou, Rodolphe ^{[1
,31
]}

Siksnys, Virginius ^{[32
]}

机构：

[1] Univ Calif Berkeley, Innovat Genom Inst, Berkeley, CA 94720 USA

[2] Univ Calif Berkeley, Calif Inst Quantitat Biosci QB3, Berkeley, CA 94720 USA

[3] Univ Calif Berkeley, Howard Hughes Med Inst, Berkeley, CA 94720 USA

[4] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA

[5] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[6] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA

[7] Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA

[8] Lawrence Berkeley Natl Lab, EGSB Div, Berkeley, CA 94720 USA

[9] Univ Calif Berkeley, Univ Calif Berkeley Univ Calif San Francisco Grad, Berkeley, CA 94720 USA

[10] Univ Utrecht, Grad Sch Life Sci, NL-3584 CS Utrecht, UT, Netherlands

[11] Univ Calif San Francisco, Dept Pediat, Div Allergy Immunol & Bone Marrow Transplantat, San Francisco, CA 94158 USA

[12] Hampton Univ, Dept Chem & Biochem, Hampton, VA 23668 USA

[13] Monash Univ, Monash Biomed Discovery Inst, Fac Med Nursing & Hlth Sci, Dept Biochem & Mol Biol, Clayton, Vic 3168, Australia

[14] Arizona State Univ, Sch Mol Sci, Tempe, AZ 85281 USA

[15] Arizona State Univ, Arizona State Univ Banner Neurodegenerat Dis Res C, Biodesign Inst, Tempe, AZ 85281 USA

[16] Arizona State Univ, Biodesign Inst, Ctr Mol Design & Biomimet, Tempe, AZ 85281 USA

[17] Vilnius Univ, LSC EMBL Partnership Inst Genome Editing Technol, Life Sci Ctr, LT-10257 Vilnius, Lithuania

[18] Harvard Med Sch, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA

[19] Univ Massachusetts, RNA Therapeut Inst, Chan Med Sch, Worcester, MA 01655 USA

[20] Univ Massachusetts, Program Mol Med, Chan Med Sch, Worcester, MA 01655 USA

[21] Univ Massachusetts, Li Weibo Inst Rare Dis Res, Chan Med Sch, Worcester, MA 01655 USA

[22] Montana State Univ, Dept Microbiol & Cell Biol, Bozeman, MT 59717 USA

[23] Univ Otago, Dept Microbiol & Immunol, Dunedin 9016, New Zealand

[24] Univ Otago, Genet Otago, Dunedin 9016, New Zealand

[25] Univ Otago, Bioprotect Aotearoa, Dunedin 9016, New Zealand

[26] Univ Otago, Maurice Wilkins Ctr Mol Biodiscovery, Dunedin 9016, New Zealand

[27] Delft Univ Technol, Dept Bionanosci, NL-2629 HZ Delft, Netherlands

[28] Kavli Inst Nanosci, NL-2629 HZ Delft, Netherlands

[29] Iowa State Univ, Roy J Carver Dept Biochem Biophys & Mol Biol, Ames, IA 50011 USA

[30] Metagenomi Inc, Emeryville, CA 94608 USA

[31] North Carolina State Univ, Dept Food Bioproc & Nutr Sci, Raleigh, NC 27606 USA

[32] Vilnius Univ, Inst Biotechnol, Life Sci Ctr, LT-10257 Vilnius, Lithuania

[33] Univ Melbourne, Parkville, Vic 3052, Australia

[34] Lawrence Berkeley Natl Lab, MBIB Div, Berkeley, CA 94720 USA

[35] Univ Calif San Francisco, Gladstone Inst, San Francisco, CA 94158 USA

来源：

NUCLEIC ACIDS RESEARCH | 2023年

关键词：

DNA; PHAGES;

D O I：

10.1093/nar/gkad890

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes. Graphical Abstract

引用

页码：D590 / D596

页数：7

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