Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9

Kazuki Kato, Sae Okazaki, Soumya Kannan, Han Altae-Tran, F. Esra Demircioglu, Yukari Isayama, Junichiro Ishikawa, Masahiro Fukuda, Rhiannon K. Macrae, Tomohiro Nishizawa, Kira S. Makarova, Eugene V. Koonin, Feng Zhang () and Hiroshi Nishimasu ()
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Kazuki Kato: The University of Tokyo
Sae Okazaki: The University of Tokyo
Soumya Kannan: Massachusetts Institute of Technology
Han Altae-Tran: Massachusetts Institute of Technology
F. Esra Demircioglu: Massachusetts Institute of Technology
Yukari Isayama: The University of Tokyo
Junichiro Ishikawa: The University of Tokyo
Masahiro Fukuda: The University of Tokyo, Meguro
Rhiannon K. Macrae: Massachusetts Institute of Technology
Tomohiro Nishizawa: Yokohama City University
Kira S. Makarova: National Institutes of Health
Eugene V. Koonin: National Institutes of Health
Feng Zhang: Massachusetts Institute of Technology
Hiroshi Nishimasu: The University of Tokyo

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: Abstract Transposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. IscB associates with its cognate ωRNA to form a ribonucleoprotein complex that cleaves double-stranded DNA targets complementary to an ωRNA guide segment. Although IscB shares the RuvC and HNH endonuclease domains with Cas9, it is much smaller than Cas9, mainly due to the lack of the α-helical nucleic-acid recognition lobe. Here, we report the cryo-electron microscopy structure of an IscB protein from the human gut metagenome (OgeuIscB) in complex with its cognate ωRNA and a target DNA, at 2.6-Å resolution. This high-resolution structure reveals the detailed architecture of the IscB–ωRNA ribonucleoprotein complex, and shows how the small IscB protein assembles with the ωRNA and mediates RNA-guided DNA cleavage. The large ωRNA scaffold structurally and functionally compensates for the recognition lobe of Cas9, and participates in the recognition of the guide RNA–target DNA heteroduplex. These findings provide insights into the mechanism of the programmable DNA cleavage by the IscB–ωRNA complex and the evolution of the type II CRISPR-Cas9 effector complexes.

Date: 2022
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DOI: 10.1038/s41467-022-34378-3

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