CasPEDIA Database: a Functional Classification System for Class 2 CRISPR-Cas Enzymes

m-CAFEs researchers present new database for the collection, classification and utilization of CRISPR-Cas enzymes.

The Science

m-CAFEs researchers developed CasPEDIA, the Cas Protein Effector Database of Information and Assessment, a new database which provides summary information about the capabilities and limitations of Class 2 Cas technologies to facilitate tool selection and highlight opportunities for future biotechnological development. They also introduce CasID, a Cas enzyme classification scheme, to facilitate functional comparison between RNA-guided Class 2 Cas enzymes. The optimal selection of a CRISPR enzyme depends heavily on the intended application, and CasPEDIA allows for efficient comparison between enzymes by both their biochemical properties and their previously established uses. As a flexible database, CasPEDIA can be updated to accommodate the emergence of novel CRISPR-Cas enzymes and their applications.

The Impact

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. Integrating essential information about these proteins into a single database provides a new resource to facilitate adoption and innovation of these technologies.

Summary

m-CAFEs researchers present CasPEDIA, 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. 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.

Contact

CasPEDIA project
Innovative Genomics Institute
caspedia.contact@gmail.com

Funding

This work was supported by m-CAFEs Microbial Community Analysis & Functional Evaluation in Soils, a Science Focus Area led by Lawrence Berkeley National Laboratory based upon work supported by the US Department of Energy, Office of Science, Office of Biological & Environmental Research; the Swiss National Science Foundation Mobility Fellowship; the National Science Foundation Graduate Research Fellowship; the National Institutes of Health; the CIRM Training Program; the National Institutes of Health Ruth L. Kirschstein National Research Service Award F31 Pre-Doctoral Fellowship; the Siebel Scholarship from the Siebel Foundation; the Summer Undergraduate Research Fellowship from the Rose Hills Foundation; the U/SELECT Program at Utrecht University; the Jane Coffin Childs Fund for Medical Research Fellowship at HHMI; the Pediatric Scientist Development Program Fellowship; the Eunice Kennedy Shriver National Institute of Child Health and Human Development; the Monash Graduate Excellence Scholarship; the Snow Medical Fellowship and a National Health and Medical Research Council Investigator; the National Institutes of Health; the Edson Initiative for Dementia Care and Solutions; the European Regional Development Fund with the Central Project Management Agency, Lithuania; the Research Council of Lithuania (LMTLT); the European Molecular Biology Organization; the Helen Hay Whitney Foundation Fellowship; the National Institutes of Health; the Montana State University Agricultural Experimental Station (USDA NIFA); the Bioprotection Aotearoa and the Marsden Fund, Royal Society of New Zealand (Te Pūtea Rangahau a Marsden, Te Apārangi); the European Research Council; the Netherlands Organisation for Scientific Research; the National Institute of General Medical Sciences; and the Howard Hughes Medical Institute. Funding for open access charge: Howard Hughes Medical Institute.

Publication

Adler, B. A.*, Trinidad, M. I.* et al. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res. (2023). DOI: 10.1093/nar/gkad890