The RNA-and DNA-targeting CRISPR-Cas immune systems of Pyrococcus furiosus

Biochemical Society Transactions

Volumn 41, Issue 6, 2013, Pages 1416-1421

  Terns, Rebecca M ^a   Terns, Michael P ^a,b  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Clustered regularly interspaced short palindromic repeats (CRISPR); CRISPR associated (Cas); Non coding RNA; Prokaryotic immunity; Pyrococcus furiosus; Virus

Indexed keywords

CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; COMPLEMENTARY RNA; PLASMID DNA; RNA; RNA BINDING PROTEIN;

BINDING SITE; BIOGENESIS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONFERENCE PAPER; CRYSTAL STRUCTURE; DNA STRUCTURE; GENE CLUSTER; GENE LOCUS; GENE TARGETING; GENE TRANSFER; GENOME; HORIZONTAL GENE TRANSFER; IMMUNE SYSTEM; MUTATIONAL ANALYSIS; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEIN SUBUNIT; PYROCOCCUS FURIOSUS; RNA CLEAVAGE; RNA SEQUENCE; RNA TARGETING; TRANSCRIPTION INITIATION SITE; ZINC FINGER MOTIF;

CRISPR-CAS SYSTEMS; DNA; MODELS, MOLECULAR; PYROCOCCUS FURIOSUS; RNA;

EID: 84887908584     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20130056     Document Type: Conference Paper

References (43)

1. Sorek, R., Lawrence, C.M. and Wiedenheft, B. (2013) CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu. Rev. Biochem. 82, 237-266
2. Wiedenheft, B., Sternberg, S.H. and Doudna, J.A. (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331-338
3. Westra, E.R., Swarts, D.C., Staals, R.H., Jore, M.M., Brouns, S.J. and van der Oost, J. (2012) The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu. Rev. Genet. 46, 311-339
4. Terns, M.P. and Terns, R.M. (2011) CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. 14, 321-327
5. Bhaya, D., Davison, M. and Barrangou, R. (2011) CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu. Rev. Genet. 45, 273-297
6. Bolotin, A., Quinquis, B., Sorokin, A. and Ehrlich, S.D. (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551-2561
7. Lillestøl, R.K., Redder, P., Garrett, R.A. and Brügger, K. (2006) A putative viral defence mechanism in archaeal cells. Archaea 2, 59-72
8. Mojica, F.J., Diéez-Villasenor, C., Garciéa- Martiénez, J. and Soria, E. (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174-182
9. Pourcel, C., Salvignol, G. and Vergnaud, G. (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151, 653-663
10. Brouns, S.J., Jore, M.M., Lundgren, M., Westra, E.R., Slijkhuis, R.J., Snijders, A.P., Dickman, M.J., Makarova, K.S., Koonin, E.V. and van der Oost, J. (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960-964
11. Carte, J., Wang, R., Li, H., Terns, R.M. and Terns, M.P. (2008) Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22, 3489-3496
12. Deltcheva, E., Chylinski, K., Sharma, C.M., Gonzales, K., Chao, Y., Pirzada, Z.A., Eckert, M.R., Vogel, J. and Charpentier, E. (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602-607
13. Hale, C.R., Zhao, P., Olson, S., Duff, M.O., Graveley, B.R., Wells, L., Terns, R.M. and Terns, M.P. (2009) RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945-956
14. Haft, D.H., Selengut, J., Mongodin, E.F. and Nelson, K.E. (2005) A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1, e60
15. Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F.J., Wolf, Y.I., Yakunin, A.F. et al. (2011) Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467-477
16. Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I. and Koonin, E.V. (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1, 7
17. Makarova, K.S., Aravind, L., Wolf, Y.I. and Koonin, E.V. (2011) Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol. Direct 6, 38
18. Godde, J.S. and Bickerton, A. (2006) The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 62, 718-729
19. Robb, F.T., Maeder, D.L., Brown, J.R., DiRuggiero, J., Stump, M.D., Yeh, R.K., Weiss, R.B. and Dunn, D.M. (2001) Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol. 330, 134-157
20. Norais, C., Moisan, A., Gaspin, C. and Clouet-d'Orval, B. (2013) Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biol. 10, 659-670
21. Farkas, J., Chung, D., DeBarry, M., Adams, M.W. and Westpheling, J. (2011) Defining components of the chromosomal origin of replication of the hyperthermophilic archaeon Pyrococcus furiosus needed for construction of a stable replicating shuttle vector. Appl. Environ. Microbiol. 77, 6343-6349
22. Farkas, J., Stirrett, K., Lipscomb, G.L., Nixon, W., Scott, R.A., Adams, M.W. and Westpheling, J. (2012) Recombinogenic properties of Pyrococcus furiosus strain COM1 enable rapid selection of targeted mutants. Appl. Environ. Microbiol. 78, 4669-4676
23. Lipscomb, G.L., Stirrett, K., Schut, G.J., Yang, F., Jenney, Jr, F.E., Scott, R.A., Adams, M.W. and Westpheling, J. (2011) Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. Appl. Environ. Microbiol. 77, 2232-2238
24. Grissa, I., Vergnaud, G. and Pourcel, C. (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinf. 8, 172
25. Rousseau, C., Gonnet, M., Le Romancer, M. and Nicolas, J. (2009) CRISPI: a CRISPR interactive database. Bioinformatics 25, 3317-3318
26. Geslin, C., Le Romancer, M., Erauso, G., Gaillard, M., Perrot, G. and Prieur, D. (2003) PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, "Pyrococcus abyssi". J. Bacteriol. 185, 3888-3894
27. Soler, N., Marguet, E., Cortez, D., Desnoues, N., Keller, J., van Tilbeurgh, H., Sezonov, G. and Forterre, P. (2010) Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res. 38, 5088-5104
28. Carte, J., Pfister, N.T., Compton, M.M., Terns, R.M. and Terns, M.P. (2010) Binding and cleavage of CRISPR RNA by Cas6. RNA 16, 2181-2188
29. Kunin, V., Sorek, R. and Hugenholtz, P. (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, R61
30. Hale, C.R., Majumdar, S., Elmore, J., Pfister, N., Compton, M., Olson, S., Resch, A.M., Glover, 3rd, C.V., Graveley, B.R., Terns, R.M. and Terns, M.P. (2012) Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell 45, 292-302
31. Hale, C., Kleppe, K., Terns, R.M. and Terns, M.P. (2008) Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA 14, 2572-2479
32. Wang, R., Preamplume, G., Terns, M.P., Terns, R.M. and Li, H. (2011) Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 19, 257-264
33. Gesner, E.M., Schellenberg, M.J., Garside, E.L., George, M.M. and Macmillan, A.M. (2011) Recognition and maturation of effector RNAs in a CRISPR interference pathway. Nat. Struct. Mol. Biol. 18, 688-692
34. Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K. and Doudna, J. A. (2010) Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358
35. Marraffini, L.A. and Sontheimer, E.J. (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843-1845
36. Calvin, K. and Li, H. (2008) RNA-splicing endonuclease structure and function. Cell. Mol. Life Sci. 65, 1176-1185
37. Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P. and Li, H. (2012) Structure of the Cmr2 subunit of the CRISPR-Cas RNA silencing complex. Structure 20, 545-553
38. Zhu, X. and Ye, K. (2012) Crystal structure of Cmr2 suggests a nucleotide cyclase-related enzyme in type III CRISPR-Cas systems. FEBS Lett. 586, 939-945
39. Shao, Y., Cocozaki, A.I., Ramia, N.F., Terns, R.M., Terns, M.P. and Li, H. (2013) Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA silencing complex. Structure 21, 376-384
40. Osawa, T., Inanaga, H. and Numata, T. (2013) Crystal structure of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA silencing effector complex. J. Mol. Biol. 425, 3811-3823
41. Park, J.H., Sun, J., Park, S.Y., Hwang, H.J., Park, M.Y., Shin, M. and Kim, J.S. (2013) Crystal structure of Cmr5 from Pyrococcus furiosus and its functional implications. FEBS Lett. 587, 562-568
42. Shah, S.A. and Garrett, R.A. (2011) CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res. Microbiol. 162, 27-38
43. Elmore, J.R., Yokooji, Y., Sato, T., Olson, S., Glover, 3rd, C.V., Graveley, B.R., Atomi, H., Terns, R.M. and Terns, M.P. (2013) Programmable plasmid interference by the CRISPR-Cas system in Thermococcus kodakarensis. RNA Biol. 10, 828-840