Academic Journal
Structural mechanism of bridge RNA-guided recombination.
| Τίτλος: | Structural mechanism of bridge RNA-guided recombination. |
|---|---|
| Συγγραφείς: | Hiraizumi M; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan., Perry NT; Arc Institute, Palo Alto, CA, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA., Durrant MG; Arc Institute, Palo Alto, CA, USA., Soma T; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan., Nagahata N; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan., Okazaki S; Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan., Athukoralage JS; Arc Institute, Palo Alto, CA, USA., Isayama Y; Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan., Pai JJ; Arc Institute, Palo Alto, CA, USA., Pawluk A; Arc Institute, Palo Alto, CA, USA., Konermann S; Arc Institute, Palo Alto, CA, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Yamashita K; Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan., Hsu PD; Arc Institute, Palo Alto, CA, USA. patrick@arcinstitute.org.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. patrick@arcinstitute.org.; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. patrick@arcinstitute.org., Nishimasu H; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.; Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. nisimasu@g.ecc.u-tokyo.ac.jp.; Inamori Research Institute for Science, Kyoto, Japan. nisimasu@g.ecc.u-tokyo.ac.jp. |
| Πηγή: | Nature [Nature] 2024 Jun; Vol. 630 (8018), pp. 994-1002. Date of Electronic Publication: 2024 Jun 26. |
| Τύπος έκδοσης: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE |
| Imprint Name(s): | Publication: Basingstoke : Nature Publishing Group Original Publication: London, Macmillan Journals ltd. |
| Ιατρικοί όροι (MeSH): | DNA*/chemistry , DNA*/metabolism , DNA*/ultrastructure , RNA, Untranslated*/chemistry , RNA, Untranslated*/genetics , RNA, Untranslated*/metabolism , RNA, Untranslated*/ultrastructure , Recombination, Genetic*, DNA Transposable Elements/genetics ; Recombinases/chemistry ; Recombinases/genetics ; Recombinases/metabolism ; Catalytic Domain ; Cryoelectron Microscopy ; Models, Molecular ; Nucleic Acid Conformation ; Protein Multimerization ; Substrate Specificity |
| Περίληψη: | Insertion sequence (IS) elements are the simplest autonomous transposable elements found in prokaryotic genomes1. We recently discovered that IS110 family elements encode a recombinase and a non-coding bridge RNA (bRNA) that confers modular specificity for target DNA and donor DNA through two programmable loops2. Here we report the cryo-electron microscopy structures of the IS110 recombinase in complex with its bRNA, target DNA and donor DNA in three different stages of the recombination reaction cycle. The IS110 synaptic complex comprises two recombinase dimers, one of which houses the target-binding loop of the bRNA and binds to target DNA, whereas the other coordinates the bRNA donor-binding loop and donor DNA. We uncovered the formation of a composite RuvC-Tnp active site that spans the two dimers, positioning the catalytic serine residues adjacent to the recombination sites in both target and donor DNA. A comparison of the three structures revealed that (1) the top strands of target and donor DNA are cleaved at the composite active sites to form covalent 5'-phosphoserine intermediates, (2) the cleaved DNA strands are exchanged and religated to create a Holliday junction intermediate, and (3) this intermediate is subsequently resolved by cleavage of the bottom strands. Overall, this study reveals the mechanism by which a bispecific RNA confers target and donor DNA specificity to IS110 recombinases for programmable DNA recombination. (© 2024. The Author(s).) |
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| Grant Information: | T32 GM139780 United States GM NIGMS NIH HHS |
| Substance Nomenclature: | 9007-49-2 (DNA) 0 (DNA Transposable Elements) 0 (Recombinases) 0 (RNA, Untranslated) |
| Entry Date(s): | Date Created: 20240626 Date Completed: 20240627 Latest Revision: 20260426 |
| Update Code: | 20260426 |
| PubMed Central ID: | PMC11208158 |
| DOI: | 10.1038/s41586-024-07570-2 |
| PMID: | 38926616 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 1476-4687 |
|---|---|
| DOI: | 10.1038/s41586-024-07570-2 |