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

Area of Science:

• Molecular Biology
• Biotechnology
• Genomics

Background:

• CRISPR-Cas enzymes provide RNA-guided bacterial immunity and are foundational to genome editing technologies.
• Class 2 CRISPR-associated enzymes (Cas9, Cas12, Cas13) have broad applications in research, medicine, and agriculture.
• The vast genetic and biochemical diversity of these enzymes presents challenges for researchers aiming to harness their functions.

Purpose of the Study:

• To introduce CasPEDIA, a curated encyclopedia of Cas effector proteins.
• To provide a standardized classification and comprehensive information resource for diverse Cas enzymes.
• To facilitate the selection and application of suitable Cas enzymes for biotechnological purposes.

Main Methods:

• Development of CasPEDIA, a web-based database (http://caspedia.org).
• Curated integration of hundreds of Cas enzymes from Cas9, Cas12, and Cas13 families, plus related IscB and TnpB proteins.
• Standardized annotation workflow for nuclease activity, target requirements, and guide-RNA constraints.
• Implementation of a functional classification scheme (CasID) alongside phylogenetic classification.

Main Results:

• CasPEDIA offers enzymatic classification for hundreds of Cas enzymes across 27 phylogenetic groups.
• Enzymes are annotated with nuclease activity, target specificity, and guide-RNA design parameters.
• The CasID system allows searching by enzymatic function and sequence similarity, complementing existing phylogenetic nomenclature.

Conclusions:

• CasPEDIA serves as a comprehensive data portal for Cas enzyme properties.
• The database contextualizes enzymatic characteristics, aiding researchers in biotechnological development.
• CasPEDIA empowers users to leverage the diverse nucleic-acid targeting capabilities of Class 2 CRISPR-Cas enzymes.