Cryo-EM structure of the transposon-associated TnpB enzyme.

Bacterial Proteins / chemistry CRISPR-Associated Proteins / chemistry CRISPR-Cas Systems Cryoelectron Microscopy DNA / chemistry DNA Transposable Elements / genetics RNA, Guide, CRISPR-Cas Systems / chemistry Endodeoxyribonucleases / chemistry Deinococcus / enzymology Substrate Specificity

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
04 2023
Historique:
received: 04 10 2022
accepted: 08 03 2023
medline: 14 4 2023
pubmed: 6 4 2023
entrez: 5 4 2023
Statut: ppublish

Résumé

The class 2 type V CRISPR effector Cas12 is thought to have evolved from the IS200/IS605 superfamily of transposon-associated TnpB proteins

Identifiants

DOI: 10.1038/s41586-023-05933-9 PMID: 37020030 PMC: PMC10097598
pubmed: 37020030
doi: 10.1038/s41586-023-05933-9
pii: 10.1038/s41586-023-05933-9
pmc: PMC10097598
doi:

Substances chimiques

Bacterial Proteins 0
CRISPR-Associated Proteins 0
DNA 9007-49-2
DNA Transposable Elements 0
RNA, Guide, CRISPR-Cas Systems 0
Endodeoxyribonucleases EC 3.1.-

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

390-397

Subventions

Organisme : NIGMS NIH HHS
ID : T32 GM007753
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM144273
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009761
Pays : United States

Informations de copyright

© 2023. The Author(s).

Références

Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).
doi: 10.1038/s41579-019-0299-x pubmed: 31857715
Altae-Tran, H. et al. The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374, 57–65 (2021).
doi: 10.1126/science.abj6856 pubmed: 34591643 pmcid: 8929163
Karvelis, T. et al. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature 599, 692–696 (2021).
doi: 10.1038/s41586-021-04058-1 pubmed: 34619744 pmcid: 8612924
Hille, F. et al. The biology of CRISPR–Cas: backward and forward. Cell 172, 1239–1259 (2018).
doi: 10.1016/j.cell.2017.11.032 pubmed: 29522745
Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, 2579–2586 (2012).
doi: 10.1073/pnas.1208507109
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
doi: 10.1126/science.1225829 pubmed: 22745249 pmcid: 6286148
Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR–Cas system. Cell 163, 759–771 (2015).
doi: 10.1016/j.cell.2015.09.038 pubmed: 26422227 pmcid: 4638220
Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR–Cas systems. Mol. Cell 60, 385–397 (2015).
doi: 10.1016/j.molcel.2015.10.008 pubmed: 26593719 pmcid: 4660269
Yan, W. X. et al. Functionally diverse type V CRISPR–Cas systems. Science 363, 88–91 (2019).
doi: 10.1126/science.aav7271 pubmed: 30523077
Burstein, D. et al. New CRISPR–Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).
doi: 10.1038/nature21059 pubmed: 28005056
Harrington, L. B. et al. Programmed DNA destruction by miniature CRISPR–Cas14 enzymes. Science 362, 839 (2018).
doi: 10.1126/science.aav4294 pubmed: 30337455 pmcid: 6659742
Pausch, P. et al. Crispr–CasФ from huge phages is a hypercompact genome editor. Science 69, 333–337 (2020).
doi: 10.1126/science.abb1400
Strecker, J. et al. RNA-guided DNA insertion with CRISPR-associated transposases. Science 365, 48–53 (2019).
doi: 10.1126/science.aax9181 pubmed: 31171706 pmcid: 6659118
Urbaitis, T. et al. A new family of CRISPR‐type V nucleases with C‐rich PAM recognition. EMBO Rep. 23, e55481 (2022).
doi: 10.15252/embr.202255481 pubmed: 36268581 pmcid: 9724661
Wu, W. Y. et al. The miniature CRISPR–Cas12m effector binds DNA to block transcription. Mol. Cell 82, 4487–4502.e7 (2022).
doi: 10.1016/j.molcel.2022.11.003 pubmed: 36427491
Schuler, G., Hu, C. & Ke, A. Structural basis for RNA-guided DNA cleavage by IscB–ωRNA and mechanistic comparison with Cas9. Science 376, 1476–1481 (2022).
doi: 10.1126/science.abq7220 pubmed: 35617371 pmcid: 10041819
Kato, K. et al. Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR–Cas9. Nat. Commun. 13, 6719 (2022).
doi: 10.1038/s41467-022-34378-3 pubmed: 36344504 pmcid: 9640706
Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569–573 (2014).
doi: 10.1038/nature13579 pubmed: 25079318 pmcid: 4176945
Takeda, S. N. et al. Structure of the miniature type V-F CRISPR–Cas effector enzyme. Mol. Cell 81, 558–570.e3 (2021).
doi: 10.1016/j.molcel.2020.11.035 pubmed: 33333018
Swarts, D. C. & Jinek, M. Mechanistic insights into the cis- and trans-acting DNase activities of Cas12a. Mol. Cell 73, 589–600.e4 (2019).
doi: 10.1016/j.molcel.2018.11.021 pubmed: 30639240 pmcid: 6858279
Liu, J. J. et al. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566, 218–223 (2019).
doi: 10.1038/s41586-019-0908-x pubmed: 30718774 pmcid: 6662743
Gomes-Filho, J. V. et al. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA Biol. 12, 490–500 (2015).
doi: 10.1080/15476286.2015.1019998 pubmed: 25806405 pmcid: 4615843
Kim, D. Y. et al. Efficient CRISPR editing with a hypercompact Cas12f1 and engineered guide RNAs delivered by adeno-associated virus. Nat. Biotechnol. 40, 94–102 (2022).
doi: 10.1038/s41587-021-01009-z pubmed: 34475560
Wang, Y. et al. Guide RNA engineering enables efficient CRISPR editing with a miniature Syntrophomonas palmitatica Cas12f1 nuclease. Cell Rep. 40, 111481 (2022).
doi: 10.1016/j.celrep.2022.111418
Schmid-Burgk, J. L. et al. Highly parallel profiling of Cas9 variant specificity. Mol. Cell 78, 794–800.e8 (2020).
doi: 10.1016/j.molcel.2020.02.023 pubmed: 32187529 pmcid: 7370240
Yang, H., Gao, P., Rajashankar, K. R. & Patel, D. J. PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR–Cas endonuclease. Cell 167, 1814–1828.e12 (2016).
doi: 10.1016/j.cell.2016.11.053 pubmed: 27984729 pmcid: 5278635
Hirano, S. et al. Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Nature 610, 575–581 (2022).
doi: 10.1038/s41586-022-05324-6 pubmed: 36224386 pmcid: 9581776
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
doi: 10.1038/nmeth.4169 pubmed: 28165473
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).
doi: 10.1038/s41592-020-00990-8 pubmed: 33257830
Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003).
doi: 10.1016/j.jmb.2003.07.013 pubmed: 14568533
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
doi: 10.1038/s41586-021-03819-2 pubmed: 34265844 pmcid: 8371605
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D D60, 2126–2132 (2004).
doi: 10.1107/S0907444904019158
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).
doi: 10.1107/S2059798318006551
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
doi: 10.1107/S0907444909042073 pubmed: 20057044
Barad, B. A. et al. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015).
doi: 10.1038/nmeth.3541 pubmed: 26280328 pmcid: 4589481
Zi Tan, Y. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
doi: 10.1038/nmeth.4347
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
doi: 10.1002/pro.3943 pubmed: 32881101
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
doi: 10.1038/s41587-019-0032-3 pubmed: 30809026 pmcid: 6533916
Söding, J. Protein homology detection by HMM–HMM comparison. Bioinformatics 21, 951–960 (2005).
doi: 10.1093/bioinformatics/bti125 pubmed: 15531603

Auteurs

Ryoya Nakagawa (R)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Hisato Hirano (H)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Satoshi N Omura (SN)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Suchita Nety (S)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.
ORCID: 0000-0002-4201-1061

Soumya Kannan (S)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.
ORCID: 0000-0002-7332-9662

Han Altae-Tran (H)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.

Xiao Yao (X)

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.

Yuriko Sakaguchi (Y)

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.

Takayuki Ohira (T)

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
ORCID: 0000-0002-1487-1312

Wen Y Wu (WY)

Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.

Hiroshi Nakayama (H)

Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan.

Yutaro Shuto (Y)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Tatsuki Tanaka (T)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Fumiya K Sano (FK)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Tsukasa Kusakizako (T)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
ORCID: 0000-0002-6186-6647

Yoshiaki Kise (Y)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Curreio, The University of Tokyo, Tokyo, Japan.

Yuzuru Itoh (Y)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

Naoshi Dohmae (N)

Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan.
ORCID: 0000-0002-5242-9410

John van der Oost (J)

Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
ORCID: 0000-0001-5024-1871

Tsutomu Suzuki (T)

Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.

Feng Zhang (F)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, Cambridge, MA, USA.
ORCID: 0000-0003-0178-7995

Osamu Nureki (O)

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. nureki@bs.s.u-tokyo.ac.jp.
Curreio, The University of Tokyo, Tokyo, Japan. nureki@bs.s.u-tokyo.ac.jp.
ORCID: 0000-0003-1813-7008

Articles similaires

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells.

Daipayan Sarkar, Christopher Maffeo, Markus Sutter et al.
1.00
Photosynthesis Ribulose-Bisphosphate Carboxylase Carbon Dioxide Molecular Dynamics Simulation Cyanobacteria

Generation of isogenic models of Angelman syndrome and Prader-Willi syndrome in CRISPR/Cas9-engineered human embryonic stem cells.

Rachel B Gilmore, Dea Gorka, Christopher E Stoddard et al.
1.00
Prader-Willi Syndrome Humans Angelman Syndrome CRISPR-Cas Systems Human Embryonic Stem Cells

Two codependent routes lead to high-level MRSA.

Abimbola Feyisara Adedeji-Olulana, Katarzyna Wacnik, Lucia Lafage et al.
1.00
Methicillin-Resistant Staphylococcus aureus Penicillin-Binding Proteins Peptidoglycan Bacterial Proteins Anti-Bacterial Agents

REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers.

Christopher J F Cameron, Sebastian J H Seager, Fred J Sigworth et al.
1.00
Cryoelectron Microscopy Algorithms Image Processing, Computer-Assisted Consensus Software

Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines associées aux CRISPR › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Techniques d'investigation › Microscopie électronique › Cryomicroscopie électronique › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées dispersées › Éléments transposables d'ADN › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › Systèmes CRISPR-Cas, ARN, guide › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Hydrolases › Esterases › Endonucleases › Endodeoxyribonucleases › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Cocci à Gram positif › Deinococcus › Cryo-EM structure of the transposon-associated...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Spécificité du substrat › Cryo-EM structure of the transposon-associated...