Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme

Nature Structural and Molecular Biology

Volumn 24, Issue 10, 2017, Pages 825-833

  Knott, Gavin J ^a   East Seletsky, Alexandra ^a   Cofsky, Joshua C ^a   Holton, James M ^b,c,d   Charles, Emeric ^a   O'Connell, Mitchell R ^a,e   Doudna, Jennifer A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; CRISPR CAS13A ENZYME; RIBONUCLEASE; SINGLE STRANDED RNA; UNCLASSIFIED DRUG; ENDONUCLEASE; GUIDE RNA;

ADAPTIVE IMMUNITY; ARTICLE; BACTERIAL IMMUNITY; CRISPR CAS SYSTEM; CRYSTAL STRUCTURE; ENZYME STRUCTURE; LACHNOSPIRACEAE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN TARGETING; RNA DEGRADATION; CHEMISTRY; CLOSTRIDIALES; ENZYMOLOGY; METABOLISM; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

CLOSTRIDIALES; CRISPR-CAS SYSTEMS; CRYSTALLOGRAPHY, X-RAY; ENDONUCLEASES; PROTEIN CONFORMATION; RNA, GUIDE;

EID: 85030750820     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.3466     Document Type: Article

References (41)

1. Dy, R.L., Richter, C., Salmond, G.P. & Fineran, P.C. Remarkable mechanisms in microbes to resist phage infections. Annu. Rev. Virol. 1, 307-331 (2014).
2. Barrangou, R. & Marraffini, L.A. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell 54, 234-244 (2014).
3. Marraffini, L.A. CRISPR-Cas immunity in prokaryotes. Nature 526, 55-61 (2015).
4. Hsu, P.D., Lander, E.S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278 (2014).
5. Wright, A.V., Nuñez, J.K. & Doudna, J.A. Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell 164, 29-44 (2016).
6. Barrangou, R. & Doudna, J.A. Applications of CRISPR technologies in research and beyond. Nat. Biotechnol. 34, 933-941 (2016).
7. O'Connell, M.R. et al. Programmable RNA recognition and cleavage by CRISPR/ Cas9. Nature 516, 263-266 (2014).
8. Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60, 385-397 (2015).
9. Nelles, D.A. et al. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165, 488-496 (2016).
10. East-Seletsky, A. et al. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270-273 (2016).
11. Shmakov, S. et al. Diversity and evolution of class 2 CRISPR-Cas systems. Nat. Rev. Microbiol. 15, 169-182 (2017).
12. Smargon, A.A. et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol. Cell 65, 618-630.e7 (2017).
13. Gootenberg, J.S. et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356, 438-442 (2017).
14. East-Seletsky, A., O?Connell, M.R., Burstein, D., Knott, G.J. & Doudna, J.A. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell 66, 373-383.e3 (2017).
15. Mojica, F.J., Díez-Villaseñor, C., García-Martínez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740 (2009).
16. Liu, L. et al. Two distant catalytic sites are responsible for C2c2 RNase activities. Cell 168, 121-134.e12 (2017).
17. Abudayyeh, O.O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016).
18. Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J.A. Sequence-and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358 (2010).
19. Sternberg, S.H., Haurwitz, R.E. & Doudna, J.A. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 18, 661-672 (2012).
20. Li, H. Structural principles of CRISPR RNA processing. Structure 23, 13-20 (2015).
21. Hochstrasser, M.L. & Doudna, J.A. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem. Sci. 40, 58-66 (2015).
22. Charpentier, E., Richter, H., van der Oost, J. & White, M.F. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol. Rev. 39, 428-441 (2015).
23. Schirle, N.T., Sheu-Gruttadauria, J. & MacRae, I.J. Structural basis for microRNA targeting. Science 346, 608-613 (2014).
24. Liu, L. et al. The molecular architecture for RNA-guided RNA cleavage by Cas13a. Cell 170, 714-726.e10 (2017).
25. Jiang, F. & Doudna, J.A. The structural biology of CRISPR-Cas systems. Curr. Opin. Struct. Biol. 30, 100-111 (2015).
26. Nakanishi, K. Anatomy of RISC: how do small RNAs and chaperones activate Argonaute proteins? Wiley Interdiscip. Rev. RNA 7, 637-660 (2016).
27. Osawa, T., Inanaga, H., Sato, C. & Numata, T. Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog. Mol. Cell 58, 418-430 (2015).
28. Parker, J.S., Parizotto, E.A., Wang, M., Roe, S.M. & Barford, D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol. Cell 33, 204-214 (2009).
29. Jiang, F., Zhou, K., Ma, L., Gressel, S. & Doudna, J.A. STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition. Science 348, 1477-1481 (2015).
30. Salomon, W.E., Jolly, S.M., Moore, M.J., Zamore, P.D. & Serebrov, V. Single-molecule imaging reveals that Argonaute reshapes the binding properties of its nucleic acid guides. Cell 162, 84-95 (2015).
31. Kabsch, W. Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125-132 (2010).
32. Winn, M.D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235-242 (2011).
33. Evans, P.R. & Murshudov, G.N. How good are my data and what is the resolution? Acta Crystallogr. D Biol. Crystallogr. 69, 1204-1214 (2013).
34. Powell, H.R. The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Crystallogr. D Biol. Crystallogr. 55, 1690-1695 (1999).
35. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
36. Terwilliger, T.C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D Biol. Crystallogr. 64, 61-69 (2008).
37. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
38. Keating, K.S. & Pyle, A.M. Semiautomated model building for RNA crystallography using a directed rotameric approach. Proc. Natl. Acad. Sci. USA 107, 8177-8182 (2010).
39. Afonine, P.V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352-367 (2012).
40. Terwilliger, T.C. et al. Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallogr. D Biol. Crystallogr. 64, 515-524 (2008).
41. Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21 (2010).