Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System

Cell

Volumn 163, Issue 4, 2015, Pages 854-865

  Redding, Sy ^a   Sternberg, Samuel H ^b   Marshall, Myles ^a   Gibb, Bryan ^a   Bhat, Prashant ^b   Guegler, Chantal K ^b   Wiedenheft, Blake ^c   Doudna, Jennifer A ^b,d   Greene, Eric C ^a  

^a Howard Hughes Medical Institute   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MONTANA STATE UNIVERSITY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; BINDING PROTEIN; CAS1 PROTEIN; CAS2 PROTEIN; CAS3 PROTEIN; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; CRISPR ASSOCIATED PROTEIN; DNA; NUCLEAR PROTEIN; NUCLEASE; PAM PROTEIN; UNCLASSIFIED DRUG; CAS2 PROTEIN, E COLI; DEOXYRIBONUCLEASE; DNA HELICASE; ENDONUCLEASE; ESCHERICHIA COLI PROTEIN; VIRUS DNA; YGBT PROTEIN, E COLI; YGCB PROTEIN, E COLI;

ANIMAL CELL; ARTICLE; CRISPR CAS SYSTEM; DNA DEGRADATION; DNA METABOLISM; DNA SEQUENCE; ENTEROBACTERIA PHAGE LAMBDA; ENZYME INACTIVATION; ESCHERICHIA COLI; FUNGAL STRAIN; MOLECULAR IMAGING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; SIGNAL TRANSDUCTION; BIOLOGICAL MODEL; GENETICS; IMMUNOLOGY; METABOLISM; NUCLEOTIDE REPEAT; VIROLOGY;

BACTERIOPHAGE LAMBDA; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; DNA HELICASES; DNA, VIRAL; ENDODEOXYRIBONUCLEASES; ENDONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84946562795     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.10.003     Document Type: Article

References (38)

1. R. Barrangou, and L.A. Marraffini CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity Mol. Cell 54 2014 234 244
2. T.R. Blosser, L. Loeff, E.R. Westra, M. Vlot, T. Künne, M. Sobota, C. Dekker, S.J. Brouns, and C. Joo Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex Mol. Cell 58 2015 60 70
3. A. Bolotin, B. Quinquis, A. Sorokin, and S.D. Ehrlich Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin Microbiology 151 2005 2551 2561
4. K.A. Datsenko, K. Pougach, A. Tikhonov, B.L. Wanner, K. Severinov, and E. Semenova Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system Nat. Commun. 3 2012 945
5. P.C. Fineran, M.J. Gerritzen, M. Suárez-Diez, T. Künne, J. Boekhorst, S.A. van Hijum, R.H. Staals, and S.J. Brouns Degenerate target sites mediate rapid primed CRISPR adaptation Proc. Natl. Acad. Sci. USA 111 2014 E1629 E1638
6. J. Gorman, A.J. Plys, M.L. Visnapuu, E. Alani, and E.C. Greene Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice Nat. Struct. Mol. Biol. 17 2010 932 938
7. J. Gorman, F. Wang, S. Redding, A.J. Plys, T. Fazio, S. Wind, E.E. Alani, and E.C. Greene Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair Proc. Natl. Acad. Sci. USA 109 2012 E3074 E3083
8. E.C. Greene, S. Wind, T. Fazio, J. Gorman, and M.L. Visnapuu DNA curtains for high-throughput single-molecule optical imaging Methods Enzymol. 472 2010 293 315
9. S.E. Halford An end to 40 years of mistakes in DNA-protein association kinetics? Biochem. Soc. Trans. 37 2009 343 348
10. R. Heler, L.A. Marraffini, and D. Bikard Adapting to new threats: the generation of memory by CRISPR-Cas immune systems Mol. Microbiol. 93 2014 1 9
11. M.L. Hochstrasser, D.W. Taylor, P. Bhat, C.K. Guegler, S.H. Sternberg, E. Nogales, and J.A. Doudna CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference Proc. Natl. Acad. Sci. USA 111 2014 6618 6623
12. Y. Ishino, H. Shinagawa, K. Makino, M. Amemura, and A. Nakata Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product J. Bacteriol. 169 1987 5429 5433
13. M. Jinek, K. Chylinski, I. Fonfara, M. Hauer, J.A. Doudna, and E. Charpentier A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity Science 337 2012 816 821
14. K.S. Makarova, N.V. Grishin, S.A. Shabalina, Y.I. Wolf, and E.V. Koonin 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 2006 7
15. F.J. Mojica, C. Díez-Villaseñor, J. García-Martínez, and E. Soria Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements J. Mol. Evol. 60 2005 174 182
16. S. Mulepati, and S. Bailey Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3) J. Biol. Chem. 286 2011 31896 31903
17. S. Mulepati, and S. Bailey In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target J. Biol. Chem. 288 2013 22184 22192
18. S. Myong, I. Rasnik, C. Joo, T.M. Lohman, and T. Ha Repetitive shuttling of a motor protein on DNA Nature 437 2005 1321 1325
19. J.K. Nuñez, P.J. Kranzusch, J. Noeske, A.V. Wright, C.W. Davies, and J.A. Doudna Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity Nat. Struct. Mol. Biol. 21 2014 528 534
20. J.K. Nuñez, A.S. Lee, A. Engelman, and J.A. Doudna Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity Nature 519 2015 193 198
21. J. Park, S. Myong, A. Niedziela-Majka, K.S. Lee, J. Yu, T.M. Lohman, and T. Ha PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps Cell 142 2010 544 555
22. Y. Qiu, E. Antony, S. Doganay, H.R. Koh, T.M. Lohman, and S. Myong Srs2 prevents Rad51 filament formation by repetitive motion on DNA Nat. Commun. 4 2013 2281
23. C. Richter, T. Gristwood, J.S. Clulow, and P.C. Fineran In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas System PLoS ONE 7 2012 e49549
24. C. Richter, R.L. Dy, R.E. McKenzie, B.N. Watson, C. Taylor, J.T. Chang, M.B. McNeil, R.H. Staals, and P.C. Fineran Priming in the type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer Nucleic Acids Res. 42 2014 8516 8526
25. M.F. Rollins, J.T. Schuman, K. Paulus, H.S. Bukhari, and B. Wiedenheft Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa Nucleic Acids Res. 43 2015 2216 2222
26. M. Rutkauskas, T. Sinkunas, I. Songailiene, M.S. Tikhomirova, V. Siksnys, and R. Seidel Directional R-loop formation by the CRISPR-Cas surveillance complex cascade provides efficient off-target site rejection Cell Rep. 2015 S2211-1247(15)00135-7
27. D.G. Sashital, B. Wiedenheft, and J.A. Doudna Mechanism of foreign DNA selection in a bacterial adaptive immune system Mol. Cell 46 2012 606 615
28. E. Savitskaya, E. Semenova, V. Dedkov, A. Metlitskaya, and K. Severinov High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli RNA Biol. 10 2013 716 725
29. E. Semenova, M.M. Jore, K.A. Datsenko, A. Semenova, E.R. Westra, B. Wanner, J. van der Oost, S.J. Brouns, and K. Severinov Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence Proc. Natl. Acad. Sci. USA 108 2011 10098 10103
30. T. Sinkunas, G. Gasiunas, C. Fremaux, R. Barrangou, P. Horvath, and V. Siksnys Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system EMBO J. 30 2011 1335 1342
31. T. Sinkunas, G. Gasiunas, S.P. Waghmare, M.J. Dickman, R. Barrangou, P. Horvath, and V. Siksnys In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus EMBO J. 32 2013 385 394
32. S.H. Sternberg, S. Redding, M. Jinek, E.C. Greene, and J.A. Doudna DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 Nature 507 2014 62 67
33. M.D. Szczelkun, M.S. Tikhomirova, T. Sinkunas, G. Gasiunas, T. Karvelis, P. Pschera, V. Siksnys, and R. Seidel Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes Proc. Natl. Acad. Sci. USA 111 2014 9798 9803
34. J. van der Oost, E.R. Westra, R.N. Jackson, and B. Wiedenheft Unravelling the structural and mechanistic basis of CRISPR-Cas systems Nat. Rev. Microbiol. 12 2014 479 492
35. P.H. von Hippel, and O.G. Berg Facilitated target location in biological systems J. Biol. Chem. 264 1989 675 678
36. E.R. Westra, D.C. Swarts, R.H. Staals, M.M. Jore, S.J. Brouns, and J. van der Oost The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity Annu. Rev. Genet. 46 2012 311 339
37. E.R. Westra, P.B. van Erp, T. Künne, S.P. Wong, R.H. Staals, C.L. Seegers, S. Bollen, M.M. Jore, E. Semenova, K. Severinov, and et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3 Mol. Cell 46 2012 595 605
38. R. Zhou, J. Zhang, M.L. Bochman, V.A. Zakian, and T. Ha Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA eLife 3 2014 e02190