CRISPR and Genetic Engineering
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An updated evolutionary classification of CRISPR–Cas systems is presented and an exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution is explored.
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The known diversity of CRISPR-Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR-Cas systems. The updated CRISPR-Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR-Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR-Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR-Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.
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@article{Makarova2025updated,
title = {An updated evolutionary classification of CRISPR–Cas systems including rare variants},
author = {Kira S. Makarova and Sergey Shmakov and Yuri I. Wolf and Pascal Mutz and Han Altae-Tran and Chase L. Beisel and Stan J. J. Brouns and Emmanuelle Charpentier and David R. Cheng and Jennifer A. Doudna and Daniel H. Haft and Philippe Horvath and Sylvain Moineau and Francisco J. M. Mojica and Patrick Pausch and Rafael Pinilla‐Redondo and Shiraz A. Shah and Virginijus Šikšnys and Michael P. Terns and Jesse Tordoff and Česlovas Venclovas and Malcolm F. White and Alexander F. Yakunin and Feng Zhang and Roger A. Garrett and Rolf Backofen and John van der Oost and Rodolphe Barrangou and Eugene V Koonin},
journal = {Nature Microbiology},
year = {2025},
doi = {10.1038/s41564-025-02180-8},
url = {https://doi.org/10.1038/s41564-025-02180-8}
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