Cryo-EM structure of the transposon-associated TnpB enzyme

Ryoya Nakagawa, Hisato Hirano, Satoshi N. Omura, Suchita Nety, Soumya Kannan, Han Altae-Tran, Xiao Yao, Yuriko Sakaguchi, Takayuki Ohira, Wen Y. Wu, Hiroshi Nakayama, Yutaro Shuto, Tatsuki Tanaka, Fumiya K. Sano, Tsukasa Kusakizako, Yoshiaki Kise, Yuzuru Itoh, Naoshi Dohmae, John Oost, Tsutomu Suzuki, Feng Zhang and Osamu Nureki ()
Additional contact information
Ryoya Nakagawa: The University of Tokyo
Hisato Hirano: The University of Tokyo
Satoshi N. Omura: The University of Tokyo
Suchita Nety: Broad Institute of MIT and Harvard
Soumya Kannan: Broad Institute of MIT and Harvard
Han Altae-Tran: Broad Institute of MIT and Harvard
Xiao Yao: The University of Tokyo
Yuriko Sakaguchi: The University of Tokyo
Takayuki Ohira: The University of Tokyo
Wen Y. Wu: Wageningen University and Research
Hiroshi Nakayama: Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
Yutaro Shuto: The University of Tokyo
Tatsuki Tanaka: The University of Tokyo
Fumiya K. Sano: The University of Tokyo
Tsukasa Kusakizako: The University of Tokyo
Yoshiaki Kise: The University of Tokyo
Yuzuru Itoh: The University of Tokyo
Naoshi Dohmae: Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
John Oost: Wageningen University and Research
Tsutomu Suzuki: The University of Tokyo
Feng Zhang: Broad Institute of MIT and Harvard
Osamu Nureki: The University of Tokyo

Nature, 2023, vol. 616, issue 7956, 390-397

Abstract: Abstract The class 2 type V CRISPR effector Cas12 is thought to have evolved from the IS200/IS605 superfamily of transposon-associated TnpB proteins1. Recent studies have identified TnpB proteins as miniature RNA-guided DNA endonucleases2,3. TnpB associates with a single, long RNA (ωRNA) and cleaves double-stranded DNA targets complementary to the ωRNA guide. However, the RNA-guided DNA cleavage mechanism of TnpB and its evolutionary relationship with Cas12 enzymes remain unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of Deinococcus radiodurans ISDra2 TnpB in complex with its cognate ωRNA and target DNA. In the structure, the ωRNA adopts an unexpected architecture and forms a pseudoknot, which is conserved among all guide RNAs of Cas12 enzymes. Furthermore, the structure, along with our functional analysis, reveals how the compact TnpB recognizes the ωRNA and cleaves target DNA complementary to the guide. A structural comparison of TnpB with Cas12 enzymes suggests that CRISPR–Cas12 effectors acquired an ability to recognize the protospacer-adjacent motif-distal end of the guide RNA–target DNA heteroduplex, by either asymmetric dimer formation or diverse REC2 insertions, enabling engagement in CRISPR–Cas adaptive immunity. Collectively, our findings provide mechanistic insights into TnpB function and advance our understanding of the evolution from transposon-encoded TnpB proteins to CRISPR–Cas12 effectors.

Date: 2023
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41586-023-05933-9 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:616:y:2023:i:7956:d:10.1038_s41586-023-05933-9

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-023-05933-9

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().