Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated sequence/structure evolutionary tracing approach to identify the ancestors of the RNA-targeting CRISPR-Cas13 system. We find that Cas13 likely evolved from AbiF, which is encoded by an abortive infection-linked gene that is stably associated with a conserved non-coding RNA (ncRNA). We further characterize a miniature Cas13, classified here as Cas13e, which serves as an evolutionary intermediate between AbiF and other known Cas13s. Despite this relationship, we show that their functions substantially differ. Whereas Cas13e is an RNA-guided RNA-targeting system, AbiF is a toxin-antitoxin (TA) system with an RNA antitoxin. We solve the structure of AbiF using cryoelectron microscopy (cryo-EM), revealing basic structural alterations that set Cas13s apart from AbiF. Finally, we map the key structural changes that enabled a non-guided TA system to evolve into an RNA-guided CRISPR system.

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Publication Details

Journal
Cell
Published
2025-02-18
DOI
https://doi.org/10.1016/j.cell.2025.01.034
Citations
29
Primary Topic
CRISPR and Genetic Engineering
Type
article
Field-Weighted Citation Impact
23.37

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article

Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

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29 citations
Cell
CRISPR and Genetic Engineering
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Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins

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article en
29 citations

Abstract

Despite ongoing efforts to study CRISPR systems, the evolutionary origins giving rise to reprogrammable RNA-guided mechanisms remain poorly understood. Here, we describe an integrated sequence/structure evolutionary tracing approach to identify the ancestors of the RNA-targeting CRISPR-Cas13 system. We find that Cas13 likely evolved from AbiF, which is encoded by an abortive infection-linked gene that is stably associated with a conserved non-coding RNA (ncRNA). We further characterize a miniature Cas13, classified here as Cas13e, which serves as an evolutionary intermediate between AbiF and other known Cas13s. Despite this relationship, we show that their functions substantially differ. Whereas Cas13e is an RNA-guided RNA-targeting system, AbiF is a toxin-antitoxin (TA) system with an RNA antitoxin. We solve the structure of AbiF using cryoelectron microscopy (cryo-EM), revealing basic structural alterations that set Cas13s apart from AbiF. Finally, we map the key structural changes that enabled a non-guided TA system to evolve into an RNA-guided CRISPR system.

CellVol. 188(7)
Broad Institute (US), National Institutes of Health (US), McGovern Institute for Brain Research (US), National Center for Biotechnology Information (US), Massachusetts Institute of Technology (US)
Howard Hughes Medical Institute, Helen Hay Whitney Foundation, Gruss-Lipper Family Foundation
Openalex Percentile: Top 0%
CRISPR and Genetic Engineering
23.37
DOIOpen Access PDFOpenAlex
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