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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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Substrate Generation for Endonucleases of CRISPR/Cas Systems
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Diversity and evolution of class 2 CRISPR-Cas systems.

Sergey Shmakov1,2, Aaron Smargon3,4, David Scott3

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Summary

Researchers discovered six new CRISPR-Cas subtypes using a computational pipeline. These novel class 2 CRISPR-Cas systems offer versatile genome editing and regulation tools, expanding the CRISPR toolbox.

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Area of Science:

  • * Molecular Biology
  • * Genomics
  • * Bioinformatics

Background:

  • * Class 2 CRISPR-Cas systems utilize single multidomain proteins (e.g., Cas9, Cpf1) for genome manipulation.
  • * Existing CRISPR-Cas systems are crucial tools in molecular biology and biotechnology.
  • * Understanding the diversity of these systems is key to expanding their applications.

Purpose of the Study:

  • * To discover novel class 2 CRISPR-Cas variants through computational analysis.
  • * To provide a comprehensive census of class 2 CRISPR-Cas systems in microbial genomes.
  • * To propose an updated classification and nomenclature for CRISPR-Cas systems.

Main Methods:

  • * Development of a computational pipeline for identifying class 2 CRISPR-Cas variants.
  • * Analysis of complete and draft bacterial and archaeal genomes.
  • * Evolutionary analysis to infer origins from mobile genetic elements.

Main Results:

  • * Identification of six novel CRISPR-Cas subtypes within class 2.
  • * Comprehensive census of class 2 CRISPR-Cas types and subtypes across diverse microbial genomes.
  • * Elucidation of evolutionary pathways suggesting independent origins from mobile genetic elements.

Conclusions:

  • * The discovery of new class 2 CRISPR-Cas systems significantly expands the repertoire of genome editing tools.
  • * These novel systems possess diverse properties, enabling potential advancements in genome editing and regulation.
  • * An amended classification and nomenclature are proposed to better organize the CRISPR-Cas landscape.