Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors

Basem Al-Shayeb; Petr Skopintsev; Katarzyna M Soczek; Elizabeth C Stahl; Zheng Li; Evan Groover; Dylan Smock; Amy R Eggers; Patrick Pausch; Brady F Cress; Carolyn J Huang; Brian Staskawicz; David F Savage; Steven E Jacobsen; Jillian F Banfield; Jennifer A Doudna

doi:10.1016/j.cell.2022.10.020

Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors

Cell. 2022 Nov 23;185(24):4574-4586.e16. doi: 10.1016/j.cell.2022.10.020.

Authors

Basem Al-Shayeb¹, Petr Skopintsev², Katarzyna M Soczek², Elizabeth C Stahl², Zheng Li³, Evan Groover⁴, Dylan Smock⁵, Amy R Eggers⁶, Patrick Pausch⁶, Brady F Cress⁵, Carolyn J Huang⁶, Brian Staskawicz⁴, David F Savage⁷, Steven E Jacobsen⁸, Jillian F Banfield⁹, Jennifer A Doudna¹⁰

Affiliations

¹ Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA.
² Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
³ Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA.
⁴ Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA.
⁵ Innovative Genomics Institute, University of California, Berkeley, CA, USA.
⁶ Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
⁷ Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
⁸ Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA; Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA.
⁹ Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia. Electronic address: jbanfield@berkeley.edu.
¹⁰ Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA. Electronic address: doudna@berkeley.edu.

PMID: 36423580
DOI: 10.1016/j.cell.2022.10.020

Abstract

CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells.

Keywords: CRISPR; CRISPR-Cas; anti-viral; enzyme; genome editing; genome editor; metagenomics; phage; structure; tool.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bacteriophages* / genetics
CRISPR-Cas Systems*
Cryoelectron Microscopy
DNA
Gene Editing
Genome
Humans
Mammals / genetics
RNA

Substances

DNA
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding