Cited by 228

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In vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus

Sinkunas, Tomas, Gasiunas, Giedrius, Waghmare, Sakharam P, Dickman, Mark J, Barrangou, Rodolphe, Horvath, Philippe, Siksnys, Virginijus·2013·The EMBO Journal

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Crossref · 10.1038/emboj.2012.352

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  • Although degradation by Cas3 handicaps the invader, it might not lead to full destruction of the target; complete degradation might be induced by other cellular nucleases or by Cascade-independent Cas3 nuclease activity.

    “Although this degradation handicaps the invader, it might not lead to the full destruction of the target. Complete degradation might be induced by other cellular nucleases or by Cascade-independent Cas3 nuclease activity, which has been previously documented [44,45,46].”

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Citations

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Research works printed but not linked: 35

  1. Al‐Attar S, Westra ER, van der Oost J, Brouns SJJ (2011) Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem 392: 277–289 · DOI
  2. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709–1712 · DOI · Paper page
  3. Bhaya D, Davison M, Barrangou R (2011) CRISPR‐Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45: 273–297 · DOI · Paper page
  4. 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 · DOI · Paper page
  5. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188–1190 · DOI
  6. Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E (2012) Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun 3: 945 · DOI · Paper page
  7. Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, Romero DA, Horvath P, Moineau S (2008) Phage response to CRISPR‐encoded resistance in Streptococcus thermophilus. J Bacteriol 190: 1390–1400 · DOI
  8. Dickman MJ, Hornby DP (2006) Enrichment and analysis of RNA centered on ion pair reverse phase methodology. RNA 12: 691–696 · DOI
  9. Garneau JE, Dupuis M‐È, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468: 67–71 · DOI
  10. Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9‐crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA 109: E2579–E2586 · DOI · Paper page
  11. Goren MG, Yosef I, Auster O, Qimron U (2012) Experimental Definition of a Clustered Regularly Interspaced Short Palindromic Duplicon in Escherichia coli. J Mol Biol 423: 14–16 · DOI
  12. Hale CR, Majumdar S, Elmore J, Pfister N, Compton M, Olson S, Resch AM, Glover CV 3rd, Graveley BR, Terns RM, Terns MP (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 · DOI
  13. Horvath P, Barrangou R (2010) CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167–170 · DOI
  14. Horvath P, Romero DA, Coûté‐Monvoisin A‐C, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190: 1401–1412 · DOI
  15. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169: 5429–5433 · DOI · Paper page
  16. Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43: 1565–1575 · DOI · Paper page
  17. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders APL, Dickman MJ, Doudna JA, Boekema EJ, Heck AJR, van der Oost J, Brouns SJJ (2011) Structural basis for CRISPR RNA‐guided DNA recognition by Cascade. Nat Struct Mol Biol 18: 529–536 · DOI
  18. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8: 317–327 · DOI
  19. Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E, Horvath P, Moineau S, Mojica FJM, Wolf YI, Yakunin AF, van der Oost J, Koonin EV (2011) Evolution and classification of the CRISPR‐Cas systems. Nat Rev Microbiol 9: 467–477 · DOI · Paper page
  20. Marraffini LA, Sontheimer EJ (2010) Self versus non‐self discrimination during CRISPR RNA‐directed immunity. Nature 463: 568–571 · DOI
  21. Mojica FJM, Díez‐Villaseñor C, García‐Martínez J, Almendros C (2009) Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155: 733–740 · DOI · Paper page
  22. 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 3: 1–18
  23. Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39: 9275–9282 · DOI
  24. Sashital DG, Wiedenheft B, Doudna JA (2012) Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell 46: 606–615 · DOI
  25. Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJJ, Severinov K (2011) Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci USA 108: 10098–10103 · DOI · Paper page
  26. 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 · DOI
  27. Sturino JM, Klaenhammer TR (2006) Engineered bacteriophage‐defence systems in bioprocessing. Nat Rev Microbiol 4: 395–404 · DOI
  28. Swarts DC, Mosterd C, van Passel MW, Brouns SJ (2012) CRISPR Interference Directs Strand Specific Spacer Acquisition. PLoS ONE 7: e35888 · DOI
  29. Tamulaitis G, Mucke M, Siksnys V (2006) Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes. FEBS Lett 580: 1665–1671 · DOI
  30. Terns MP, Terns RM (2011) CRISPR‐based adaptive immune systems. Curr Opin Microbiol 14: 321–327 · DOI
  31. Waghmare SP, Pousinis P, Hornby DP, Dickman MJ (2009) Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions. J Chromatogr A 1216: 1377–1382 · DOI
  32. Westra ER, van Erp PB, Kunne T, Wong SP, Staals RH, Seegers CL, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJ, van der Oost J (2012) CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell 46: 595–605 · DOI
  33. Wiedenheft B, van Duijn E, Bultema JB, Waghmare SP, Zhou K, Barendregt A, Westphal W, Heck AJ, Boekema EJ, Dickman MJ, Doudna JA (2011) RNA‐guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci USA 108: 10092–10097 · DOI
  34. Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, Verberkmoes NC (2012) Phage‐induced expression of CRISPR‐associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One 7: e38077 · DOI
  35. Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, Naismith JH, Spagnolo L, White MF (2012) Structure and mechanism of the CMR complex for CRISPR‐mediated antiviral immunity. Mol Cell 45: 303–313 · DOI

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Metadata

Authors
Sinkunas, T., Gasiunas, G., Waghmare, S. P., Dickman, M. J., Barrangou, R., Horvath, P., & Siksnys, V.
Venue
The EMBO Journal
Published
2013-01-18
Volume
32
Issue
3
Pages
385-394
ISSN
  • 0261-4189
  • 1460-2075
Cited by
228
References
3
Language
en

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