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CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.
Adler, Benjamin A; Trinidad, Marena I; Bellieny-Rabelo, Daniel; Zhang, Elaine; Karp, Hannah M; Skopintsev, Petr; Thornton, Brittney W; Weissman, Rachel F; Yoon, Peter H; Chen, LinXing; Hessler, Tomas; Eggers, Amy R; Colognori, David; Boger, Ron; Doherty, Erin E; Tsuchida, Connor A; Tran, Ryan V; Hofman, Laura; Shi, Honglue; Wasko, Kevin M; Zhou, Zehan; Xia, Chenglong; Al-Shimary, Muntathar J; Patel, Jaymin R; Thomas, Vienna C J X; Pattali, Rithu; Kan, Matthew J; Vardapetyan, Anna; Yang, Alana; Lahiri, Arushi; Maxwell, Micaela F; Murdock, Andrew G; Ramit, Glenn C; Henderson, Hope R; Calvert, Roland W; Bamert, Rebecca S; Knott, Gavin J; Lapinaite, Audrone; Pausch, Patrick; Cofsky, Joshua C; Sontheimer, Erik J; Wiedenheft, Blake; Fineran, Peter C; Brouns, Stan J J; Sashital, Dipali G; Thomas, Brian C; Brown, Christopher T; Goltsman, Daniela S A; Barrangou, Rodolphe; Siksnys, Virginius.
Afiliação
  • Adler BA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Trinidad MI; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Bellieny-Rabelo D; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Zhang E; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
  • Karp HM; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Skopintsev P; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Thornton BW; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Weissman RF; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
  • Yoon PH; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Chen L; Department of Chemistry, University of California, Berkeley, CA 94720, USA.
  • Hessler T; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Eggers AR; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Colognori D; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Boger R; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Doherty EE; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Tsuchida CA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Tran RV; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Hofman L; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Shi H; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Wasko KM; Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.
  • Zhou Z; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Xia C; Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.
  • Al-Shimary MJ; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
  • Patel JR; EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Thomas VCJX; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Pattali R; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Kan MJ; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Vardapetyan A; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Yang A; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Lahiri A; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Maxwell MF; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Murdock AG; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Ramit GC; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Henderson HR; University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
  • Calvert RW; Department of Chemistry, University of California, Berkeley, CA 94720, USA.
  • Bamert RS; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Knott GJ; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Lapinaite A; Graduate School of Life Sciences, Utrecht University, 3584 CS Utrecht, UT, The Netherlands.
  • Pausch P; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Cofsky JC; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
  • Sontheimer EJ; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Wiedenheft B; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Fineran PC; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Brouns SJJ; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Sashital DG; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Thomas BC; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
  • Brown CT; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Goltsman DSA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
  • Barrangou R; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
  • Siksnys V; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Nucleic Acids Res ; 52(D1): D590-D596, 2024 Jan 05.
Article em En | MEDLINE | ID: mdl-37889041
ABSTRACT
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.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Bases de Dados Genéticas / Endodesoxirribonucleases / Proteínas Associadas a CRISPR / Sistemas CRISPR-Cas Idioma: En Ano de publicação: 2024 Tipo de documento: Article
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Bases de Dados Genéticas / Endodesoxirribonucleases / Proteínas Associadas a CRISPR / Sistemas CRISPR-Cas Idioma: En Ano de publicação: 2024 Tipo de documento: Article