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Type III CRISPR–Cas systems produce cyclic oligoadenylate second messengers
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Csm6 is activated by cyclic oligoadenylates and has an auxiliary action by degrading foreign transcripts in a non-specific fashion.
“Csm6 is activated by these oligoadenylates, and even though it is not a part of the Cascade effector complex, it has an auxiliary action by degrading foreign transcripts in a non-specific fashion [51,52].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [52]
The Discussion (page unavailable) says cyclic oligoadenylates activate Csm6 and describes its additional role in targeting invader transcripts. The in vivo activity section reports degradation of phage transcripts by Csm6 and Csm3. The copy does not establish that Csm6 degrades those transcripts non-specifically, and it calls the relevant complex the type III interference complex, not Cascade. (LLM, conf=0.84)
Experimental — accuracy not yet measuredCas10 has a further role in activating non-specific RNase Csm6 by producing cyclic oligoadenylates from ATP molecules.
“Recent studies also suggest that Cas10 has a further role in activating non-specific RNase Csm6, by producing cyclic oligoadenylates from ATP molecules.”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [52]
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Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015) · Nature Protocols · doi:10.1038/nprot.2015.053 · Cited by 9,652
Diversity, classification and evolution of CRISPR-Cas systems
Koonin, E. V., Makarova, K. S., & Zhang, F. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.05.008 · Cited by 1,423
CRISPR-mediated adaptive immune systems in bacteria and archaea
Sorek, R., Lawrence, C. M., & Wiedenheft, B. (2013) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072911-172315 · Cited by 668
Flagged first, then by citations
Research works printed but not linked: 38
- Mohanraju, P. et al. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 353, aad5147 (2016) · DOI
- Marraffini, L. A. CRISPR–Cas immunity in prokaryotes. Nature 526, 55–61 (2015) · DOI
- Makarova, K. S. et al. An updated evolutionary classification of CRISPR–Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015) · DOI · Paper page
- Samai, P. et al. Co-transcriptional DNA and RNA cleavage during Type III CRISPR-Cas immunity. Cell 161, 1164–1174 (2015) · DOI · Paper page
- Goldberg, G. W., Jiang, W., Bikard, D. & Marraffini, L. A. Conditional tolerance of temperate phages via transcription-dependent CRISPR–Cas targeting. Nature 514, 633–637 (2014) · DOI
- Deng, L., Garrett, R. A., Shah, S. A., Peng, X. & She, Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088–1099 (2013) · DOI
- Elmore, J. R. et al. Bipartite recognition of target RNAs activates DNA cleavage by the type III-B CRISPR-Cas system. Genes Dev. 30, 447–459 (2016) · DOI
- Estrella, M. A., Kuo, F.-T. & Bailey, S. RNA-activated DNA cleavage by the type III-B CRISPR-Cas effector complex. Genes Dev. 30, 460–470 (2016) · DOI
- Kazlauskiene, M., Tamulaitis, G., Kostiuk, G., Venclovas, Č. & Siksnys, V. Spatiotemporal control of type III-A CRISPR-Cas immunity: coupling DNA degradation with the target RNA recognition. Mol. Cell 62, 295–306 (2016) · DOI · Paper page
- Tamulaitis, G., Venclovas, Č. & Siksnys, V. Type III CRISPR-Cas immunity: major differences brushed aside. Trends Microbiol. 25, 49–61 (2017) · DOI · Paper page
- Makarova, K. S., Anantharaman, V., Grishin, N. V., Koonin, E. V. & Aravind, L. CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. Front. Genet. 5, 102 (2014) · DOI
- Anantharaman, V., Makarova, K. S., Burroughs, A. M., Koonin, E. V. & Aravind, L. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol. Direct 8, 15 (2013) · DOI
- Hatoum-Aslan, A., Maniv, I., Samai, P. & Marraffini, L. A. Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system. J. Bacteriol. 196, 310–317 (2014) · DOI
- Jiang, W., Samai, P. & Marraffini, L. A. Degradation of phage transcripts by CRISPR-associated RNases enables type III CRISPR-Cas immunity. Cell 164, 710–721 (2016) · DOI
- Niewoehner, O. & Jinek, M. Structural basis for the endoribonuclease activity of the type III-A CRISPR-associated protein Csm6. RNA 22, 318–329 (2016) · DOI
- Sheppard, N. F., Glover, C. V. C., III, Terns, R. M. & Terns, M. P. The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease. RNA 22, 216–224 (2016) · DOI
- Staals, R. H. J. et al. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Mol. Cell 56, 518–530 (2014) · DOI
- Tamulaitis, G. et al. Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus. Mol. Cell 56, 506–517 (2014) · DOI
- Hatoum-Aslan, A., Samai, P., Maniv, I., Jiang, W. & Marraffini, L. A. A ruler protein in a complex for antiviral defense determines the length of small interfering CRISPR RNAs. J. Biol. Chem. 288, 27888–27897 (2013) · DOI
- Burroughs, A. M., Zhang, D., Schäffer, D. E., Iyer, L. M. & Aravind, L. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Nucleic Acids Res. 43, 10633–10654 (2015) · DOI
- Yan, X., Guo, W. & Yuan, Y. A. Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease. RNA Biol. 12, 749–760 (2015) · DOI
- Topuzlu, E. & Lawrence, C. M. Recognition of a pseudo-symmetric RNA tetranucleotide by Csx3, a new member of the CRISPR associated Rossmann fold superfamily. RNA Biol. 13, 254–257 (2016) · DOI
- Carroll, S. S. et al. Activation of RNase L by 2′,5′-oligoadenylates. Kinetic characterization. J. Biol. Chem. 272, 19193–19198 (1997) · DOI
- Prischi, F., Nowak, P. R., Carrara, M. & Ali, M. M. U. Phosphoregulation of Ire1 RNase splicing activity. Nat. Commun. 5, 3554 (2014) · DOI
- Staals, R. H. J. et al. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol. Cell 52, 135–145 (2013) · DOI
- Hale, C. R., Cocozaki, A., Li, H., Terns, R. M. & Terns, M. P. Target RNA capture and cleavage by the Cmr type III-B CRISPR-Cas effector complex. Genes Dev. 28, 2432–2443 (2014) · DOI
- Makarova, K. S. et al. Evolution and classification of the CRISPR–Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011) · DOI · Paper page
- Osawa, T., Inanaga, H. & Numata, T. Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. J. Mol. Biol. 425, 3811–3823 (2013) · DOI
- Kalia, D. et al. Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis. Chem. Soc. Rev. 42, 305–341 (2013) · DOI
- Hornung, V., Hartmann, R., Ablasser, A. & Hopfner, K.-P. OAS proteins and cGAS: unifying concepts in sensing and responding to cytosolic nucleic acids. Nat. Rev. Immunol. 14, 521–528 (2014) · DOI
- East-Seletsky, A. et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270–273 (2016) · DOI · Paper page
- He, F., Vestergaard, G., Peng, W., She, Q. & Peng, X. CRISPR-Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b. Nucleic Acids Res. 45, 1902–1913 (2017)
- Lintner, N. G. et al. The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. J. Mol. Biol. 405, 939–955 (2011) · DOI
- Geertsma, E. R. FX cloning: a simple and robust high-throughput cloning method for protein expression. Methods Mol. Biol. 1116, 153–164 (2014) · DOI
- Kreiswirth, B. N. et al. The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage. Nature 305, 709–712 (1983) · DOI
- Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256–2268 (2004) · DOI
- Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011) · DOI
- Gouet, P., Courcelle, E., Stuart, D. I. & Métoz, F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305–308 (1999) · DOI
Cited by
Sorted by citations
Origins and evolution of CRISPR-Cas systems
Koonin, E. V., & Makarova, K. S. (2019) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2018.0087 · Cited by 494
Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d
Zhang, C., Konermann, S., Brideau, N. J., Lotfy, P., Wu, X., Novick, S. J., Strutzenberg, T., Griffin, P. R., Hsu, P. D., & Lyumkis, D. (2018) · Cell · doi:10.1016/j.cell.2018.09.001 · Cited by 276
CRISPR-Based Technologies: Impact of RNA-Targeting Systems
Terns, M. P. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.09.018 · Cited by 168
Loureiro, A., & da Silva, G. J. (2019) · Antibiotics · doi:10.3390/antibiotics8010018 · Cited by 129
RNA-Targeting CRISPR-Cas systems and their applications
Burmistrz, M., Krakowski, K., & Krawczyk-Balska, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21031122 · Cited by 125
Structural basis of CRISPR-Cas Type III prokaryotic defence systems
Molina, R., Sofos, N., & Montoya, G. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.06.010 · Cited by 48
Guo, T., Zheng, F., Zeng, Z., Yang, Y., Li, Q., She, Q., & Han, W. (2019) · RNA Biology · doi:10.1080/15476286.2019.1642725 · Cited by 11
Metadata
- Authors
- Niewoehner, O., Garcia-Doval, C., Rostøl, J. T., Berk, C., Schwede, F., Bigler, L., Hall, J., Marraffini, L. A., & Jinek, M.
- Venue
- Nature
- Published
- 2017-07-19
- Volume
- 548
- Issue
- 7669
- Pages
- 543-548
- ISSN
- 0028-0836
- 1476-4687
- Cited by
- 509
- References
- 3
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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