Structural basis for the activity of the type VII CRISPR-Cas system.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
14 Aug 2024
14 Aug 2024
Historique:
received:
19
03
2024
accepted:
11
07
2024
medline:
15
8
2024
pubmed:
15
8
2024
entrez:
14
8
2024
Statut:
aheadofprint
Résumé
The newly identified type VII CRISPR-Cas candidate system uses a CRISPR RNA-guided ribonucleoprotein complex formed by Cas5 and Cas7 proteins to target RNA
Identifiants
pubmed: 39143216
doi: 10.1038/s41586-024-07815-0
pii: 10.1038/s41586-024-07815-0
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Altae-Tran, H. et al. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. Science 382, eadi1910 (2023).
doi: 10.1126/science.adi1910
pubmed: 37995242
pmcid: 10910872
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
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
Liu, T. Y. & Doudna, J. A. Chemistry of class 1 CRISPR-Cas effectors: binding, editing, and regulation. J. Biol. Chem. 295, 14473–14487 (2020).
doi: 10.1074/jbc.REV120.007034
pubmed: 32817336
pmcid: 7573268
You, L. et al. Structure studies of the CRISPR-Csm complex reveal mechanism of co-transcriptional interference. Cell 176, 239–253.e16 (2019).
doi: 10.1016/j.cell.2018.10.052
pubmed: 30503210
Jia, N. et al. Type III-A CRISPR-Cas Csm complexes: assembly, periodic RNA cleavage, DNase activity regulation, and autoimmunity. Mol. Cell 73, 264–277.e65 (2019).
doi: 10.1016/j.molcel.2018.11.007
pubmed: 30503773
Yu, G. et al. Structure and function of a bacterial type III–E CRISPR-Cas7–11 complex. Nat. Microbiol. 7, 2078–2088 (2022).
doi: 10.1038/s41564-022-01256-z
pubmed: 36302881
Wang, S., Guo, M., Zhu, Y., Lin, Z. & Huang, Z. Cryo-EM structure of the type III-E CRISPR-Cas effector gRAMP in complex with TPR-CHAT. Cell Res. 32, 1128–1131 (2022).
doi: 10.1038/s41422-022-00738-3
pubmed: 36280712
pmcid: 9715532
Strecker, J. et al. RNA-activated protein cleavage with a CRISPR-associated endopeptidase. Science 378, 874–881 (2022).
doi: 10.1126/science.add7450
pubmed: 36423276
pmcid: 10028731
Liu, X. et al. Target RNA activates the protease activity of Craspase to confer antiviral defense. Mol. Cell 82, 4503–4518.e8 (2022).
doi: 10.1016/j.molcel.2022.10.007
pubmed: 36306795
Kato, K. et al. RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Science 378, 882–889 (2022).
doi: 10.1126/science.add7347
pubmed: 36423304
pmcid: 11126364
Hu, C. et al. Craspase is a CRISPR RNA-guided, RNA-activated protease. Science 377, 1278–1285 (2022).
doi: 10.1126/science.add5064
pubmed: 36007061
pmcid: 10041820
Wang, X. et al. Target RNA-guided protease activity in type III-E CRISPR-Cas system. Nucleic Acids Res. 50, 12913–12923 (2022).
doi: 10.1093/nar/gkac1151
pubmed: 36484100
pmcid: 9825189
Sofos, N. et al. Structures of the Cmr-β complex reveal the regulation of the immunity mechanism of type III-B CRISPR-Cas. Mol Cell. 79, 741–757.e7 (2020).
doi: 10.1016/j.molcel.2020.07.008
pubmed: 32730741
Callebaut, I., Moshous, D., Mornon, J. P. & de Villartay, J. P. Metallo-β-lactamase fold within nucleic acids processing enzymes: the β-CASP family. Nucleic Acids Res. 30, 3592–3601 (2002).
doi: 10.1093/nar/gkf470
pubmed: 12177301
pmcid: 134238
Moshous, D. et al. Artemis, a novel DNA double-strand break repair/V(D)J recombination protein, is mutated in human severe combined immune deficiency. Cell 105, 177–186 (2001).
doi: 10.1016/S0092-8674(01)00309-9
pubmed: 11336668
Phung, D. K. et al. RNA processing machineries in Archaea: the 5′–3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′–5′ exoribonucleolytic RNA exosome machinery. Nucleic Acids Res. 48, 3832–3847 (2020).
doi: 10.1093/nar/gkaa052
pubmed: 32030412
pmcid: 7144898
Zhao, Y. et al. Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase J. Nucleic Acids Res. 43, 5550–5559 (2015).
doi: 10.1093/nar/gkv444
pubmed: 25940620
pmcid: 4477667
Sun, Y. et al. Structure of an active human histone pre-mRNA 3′-end processing machinery. Science 367, 700–703 (2020).
doi: 10.1126/science.aaz7758
pubmed: 32029631
pmcid: 7008720
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
Wang, Z., Fast, W., Valentine, A. M. & Benkovic, S. J. Metallo-β-lactamase: structure and mechanism. Curr. Opin. Chem. Biol. 3, 614–622 (1999).
doi: 10.1016/S1367-5931(99)00017-4
pubmed: 10508665
Yang, X. C., Sullivan, K. D., Marzluff, W. F. & Dominski, Z. Studies of the 5′ exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing. Mol. Cell. Biol. 29, 31–42 (2009).
doi: 10.1128/MCB.00776-08
pubmed: 18955505
Xiao, Y. et al. Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPR-Cas system. Cell 170, 48–60.e11 (2017).
doi: 10.1016/j.cell.2017.06.012
pubmed: 28666122
pmcid: 5841471
O’Brien, R. E. et al. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. Nat. Commun. 11, 5931 (2020).
doi: 10.1038/s41467-020-19785-8
pubmed: 33230133
pmcid: 7684278
Hu, C. et al. Allosteric control of type I–A CRISPR–Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Mol. Cell 82, 2754–2768.e5 (2022).
doi: 10.1016/j.molcel.2022.06.007
pubmed: 35835111
pmcid: 9357151
Schwartz, E. A. et al. Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. Nat. Commun. 13, 2829 (2022).
doi: 10.1038/s41467-022-30402-8
pubmed: 35595728
pmcid: 9123187
O’Brien, R. E. et al. Structural snapshots of R-loop formation by a type I-C CRISPR Cascade. Mol. Cell 83, 746–758.e5 (2023).
doi: 10.1016/j.molcel.2023.01.024
pubmed: 36805026
pmcid: 10026943
Goswami, H. N., Rai, J., Das, A. & Li, H. Molecular mechanism of active Cas7-11 in processing CRISPR RNA and interfering target RNA. eLife 11, e81678 (2022).
doi: 10.7554/eLife.81678
pubmed: 36190192
pmcid: 9629832
Mathy, N. et al. Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol. Microbiol. 75, 489–498 (2010).
doi: 10.1111/j.1365-2958.2009.07004.x
pubmed: 20025672
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
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
doi: 10.1038/s41592-022-01488-1
pubmed: 35637307
pmcid: 9184281
Meng, E. C. et al. UCSF ChimeraX: tools for structure building and analysis. Protein Sci. 32, e4792 (2023).
doi: 10.1002/pro.4792
pubmed: 37774136
pmcid: 10588335
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
pubmed: 20383002
pmcid: 2852313
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
Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018).
doi: 10.1002/pro.3330
pubmed: 29067766
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
doi: 10.1107/S2059798319011471