Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

RNA

Volumn 18, Issue 11, 2012, Pages 2020-2028

  Garside, Erin L ^a   Schellenberg, Matthew J ^a,d   Gesner, Emily M ^a   Bonanno, Jeffrey B ^b   Sauder, J Michael ^c   Burley, Stephen K ^c   Almo, Steven C ^b,c   Mehta, Garima ^a   Macmillan, Andrew M ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^c ELI LILLY AND COMPANY   (United States)

^d NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

CRISPR; RNA endonuclease; RNA processing

Indexed keywords

CAS5D PROTEIN; ENDONUCLEASE; PROTEIN; RNA ENDONUCLEASE; RNA PRECURSOR; UNCLASSIFIED DRUG;

ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; CRYSTAL STRUCTURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA CLEAVAGE; RNA PROCESSING; RNA SEQUENCE; RNA STRUCTURE; SITE DIRECTED MUTAGENESIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENDORIBONUCLEASES; MANNHEIMIA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA CLEAVAGE; RNA PRECURSORS; STRUCTURAL HOMOLOGY, PROTEIN; SUBSTRATE SPECIFICITY;

EID: 84867678349     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.033100.112     Document Type: Article

References (37)

1. Beloglazova N, Petit P, Flick R, Brown G, Savchenko A, Yakunin AF. 2011. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J 30: 4616-4627.
2. Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960-964.
3. Carte J, Wang R, Li H, Terns RM, Terns MP. 2008. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev 22: 3489-3496.
4. Carte J, Pfister NT, Compton MM, Terns RM, Terns MP. 2010. Binding and cleavage of CRISPR RNA by Cas6. RNA 16: 2181-2188.
5. Deveau H, Garneau JE, Moineau S. 2010. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 64: 475-493.
6. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. 2011. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471: 602-607.
7. Emsley P, Cowtan K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132. (Pubitemid 41742764)
8. Gesner EM, Schellenberg MJ, Garside EL, George MM, MacMillan AM. 2011. Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat Struct Mol Biol 18: 688-692.
9. Grissa I, Vergnaud G, Pourcel C. 2007a. CRISPRFinder: A web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: W52-W57.
10. Grissa I, Vergnaud G, Pourcel C. 2007b. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BCM Bioinformatics 8: 172. doi: 10.1186/1471-2105-8-172.
11. Haft DH, Selengut J, Mongodin EF, Nelson KE. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1: e60. doi: 10.1371/journal.pcbi. 0010060.
12. Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139: 945-956.
13. Hatoum-Aslan A, Maniv I, Marraffini LA. 2011. Mature clustered regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc Natl Acad Sci 108: 21218-21222.
14. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. 2010. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329: 1355-1358.
15. Henne A, Brüggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, et al. 2004. The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22: 547-553. (Pubitemid 38585906)
16. Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ. 2004. The genomic sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 22: 1275-1281. (Pubitemid 39336781)
17. Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167-170.
18. Igloi GL, Kossel H. 1985. Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Applications of polyacrylamide containing a covalently bound boronic acid. Nucleic Acids Res 13: 6881-6898.
19. Jinek M, Chylinski K, Fonfara I, Hauer M, Dounda JA, Charpentier E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816-821.
20. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, et al. 2011. Structural basis for CRISPR RNA-guided DNA recognition by cascade. Nat Struct Mol Biol 18: 529-536.
21. Kelley LA, Sternberg MJE. 2009. Protein structure prediction on the web: A case study using the Phyre server. Nat Protoc 4: 363-371.
22. Kondo J, Westhof E. 2011. Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes. Nucleic Acids Res 39: 8628-8637.
23. Kunin V, Sorek R, Hugenholtz P. 2007. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 8: R61. doi: 10.1186/gb-2007-8-4-r61.
24. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin A, et al. 2011a. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9: 467-477.
25. Makarova KS, Aravind L, Wolf YI, Koonin EV. 2011b. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct 6: 38. doi: 10.1186/1745-6150-6-38.
26. Marraffini LA, Sontheimer EJ. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843-1845.
27. Marraffini LA, Sontheimer EJ. 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11: 181-190.
28. Mulepati S, Bailey S. 2011. Structural and biochemical analysis of the nuclease domain of the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3). J Biol Chem 286: 31896-31903.
29. Murshudov GN, Vagin AA, Dodson EJ. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240-255. (Pubitemid 27235885)
30. Neron B, Menager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C. 2009. Mobyle: A new full web bioinformatics framework. Bioinformatics 25: 3005-3011.
31. Pape T, Schneider TR. 2004. HKL2MAP: A graphical user interface for phasing with SHELX programs. J Appl Crystallogr 37: 843-844.
32. Perrakis A, Morris R, Lamzin VS. 1999. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6: 458-463. (Pubitemid 29218016)
33. Sashital DG, Jinek M, Doudna JA. 2011. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol 18: 680-687.
34. Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. 2011. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J 30: 1335-1342.
35. Sternberg SH, Haurwitz RE, Doudna JA. 2012. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 18: 661-672.
36. Wang R, Preamplume G, Terns MP, Terns RM, Li H. 2011. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: Recognition and cleavage. Structure 19: 257-264.
37. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna JA, Nogales E. 2011. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477: 486-489.