CRISPR-Cas Part II

From Proteopedia

Jump to: navigation, search

E. coli CRISPR-Cas9 complex with RNA and DNA (PDB code 4qyz)

References

  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science. 2016 Aug 5;353(6299):aad5147. doi: 10.1126/science.aad5147. PMID:27493190 doi:http://dx.doi.org/10.1126/science.aad5147
  2. Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 2010 Aug;26(8):335-40. doi: 10.1016/j.tig.2010.05.008. Epub 2010, Jul 1. PMID:20598393 doi:http://dx.doi.org/10.1016/j.tig.2010.05.008
  3. 3.0 3.1 3.2 3.3 3.4 Yosef I, Goren MG, Qimron U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 2012 Jul;40(12):5569-76. doi: 10.1093/nar/gks216. Epub 2012, Mar 8. PMID:22402487 doi:http://dx.doi.org/10.1093/nar/gks216
  4. 4.0 4.1 Wei Y, Terns RM, Terns MP. Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation. Genes Dev. 2015 Feb 15;29(4):356-61. doi: 10.1101/gad.257550.114. PMID:25691466 doi:http://dx.doi.org/10.1101/gad.257550.114
  5. 5.0 5.1 5.2 Levy A, Goren MG, Yosef I, Auster O, Manor M, Amitai G, Edgar R, Qimron U, Sorek R. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature. 2015 Apr 23;520(7548):505-10. doi: 10.1038/nature14302. Epub 2015 Apr 13. PMID:25874675 doi:http://dx.doi.org/10.1038/nature14302
  6. Erdmann S, Le Moine Bauer S, Garrett RA. Inter-viral conflicts that exploit host CRISPR immune systems of Sulfolobus. Mol Microbiol. 2014 Mar;91(5):900-17. doi: 10.1111/mmi.12503. Epub 2014 Jan 17. PMID:24433295 doi:http://dx.doi.org/10.1111/mmi.12503
  7. Wigley DB. RecBCD: the supercar of DNA repair. Cell. 2007 Nov 16;131(4):651-3. PMID:18022359 doi:http://dx.doi.org/10.1016/j.cell.2007.11.004
  8. 8.0 8.1 Dupuis ME, Villion M, Magadan AH, Moineau S. CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance. Nat Commun. 2013;4:2087. doi: 10.1038/ncomms3087. PMID:23820428 doi:http://dx.doi.org/10.1038/ncomms3087
  9. 9.0 9.1 Swarts DC, Mosterd C, van Passel MW, Brouns SJ. CRISPR interference directs strand specific spacer acquisition. PLoS One. 2012;7(4):e35888. doi: 10.1371/journal.pone.0035888. Epub 2012 Apr 27. PMID:22558257 doi:http://dx.doi.org/10.1371/journal.pone.0035888
  10. Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569. Epub 2015, Sep 28. PMID:26411297 doi:http://dx.doi.org/10.1038/nrmicro3569
  11. 11.0 11.1 Nunez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol. 2014 May 4. doi: 10.1038/nsmb.2820. PMID:24793649 doi:http://dx.doi.org/10.1038/nsmb.2820
  12. Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y. Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems. Cell. 2015 Nov 5;163(4):840-53. doi: 10.1016/j.cell.2015.10.008. Epub 2015 Oct, 17. PMID:26478180 doi:http://dx.doi.org/10.1016/j.cell.2015.10.008
  13. 13.0 13.1 Nunez JK, Lee AS, Engelman A, Doudna JA. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature. 2015 Mar 12;519(7542):193-8. doi: 10.1038/nature14237. Epub 2015 Feb 18. PMID:25707795 doi:http://dx.doi.org/10.1038/nature14237
  14. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci. 2009 Aug;34(8):401-7. doi: 10.1016/j.tibs.2009.05.002. Epub, 2009 Jul 29. PMID:19646880 doi:http://dx.doi.org/10.1016/j.tibs.2009.05.002
  15. Silas S, Mohr G, Sidote DJ, Markham LM, Sanchez-Amat A, Bhaya D, Lambowitz AM, Fire AZ. Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science. 2016 Feb 26;351(6276):aad4234. doi: 10.1126/science.aad4234. PMID:26917774 doi:http://dx.doi.org/10.1126/science.aad4234
  16. Fineran PC, Charpentier E. Memory of viral infections by CRISPR-Cas adaptive immune systems: acquisition of new information. Virology. 2012 Dec 20;434(2):202-9. doi: 10.1016/j.virol.2012.10.003. Epub 2012, Nov 2. PMID:23123013 doi:http://dx.doi.org/10.1016/j.virol.2012.10.003
  17. Arslan Z, Hermanns V, Wurm R, Wagner R, Pul U. Detection and characterization of spacer integration intermediates in type I-E CRISPR-Cas system. Nucleic Acids Res. 2014 Jul;42(12):7884-93. doi: 10.1093/nar/gku510. Epub 2014, Jun 11. PMID:24920831 doi:http://dx.doi.org/10.1093/nar/gku510
  18. Amitai G, Sorek R. CRISPR-Cas adaptation: insights into the mechanism of action. Nat Rev Microbiol. 2016 Feb;14(2):67-76. doi: 10.1038/nrmicro.2015.14. Epub 2016 , Jan 11. PMID:26751509 doi:http://dx.doi.org/10.1038/nrmicro.2015.14
  19. Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun. 2012 Jul 10;3:945. doi: 10.1038/ncomms1937. PMID:22781758 doi:http://dx.doi.org/10.1038/ncomms1937
  20. 20.0 20.1 20.2 Li M, Wang R, Zhao D, Xiang H. Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process. Nucleic Acids Res. 2014 Feb;42(4):2483-92. doi: 10.1093/nar/gkt1154. Epub 2013, Nov 21. PMID:24265226 doi:http://dx.doi.org/10.1093/nar/gkt1154
  21. Richter C, Dy RL, McKenzie RE, Watson BN, Taylor C, Chang JT, McNeil MB, Staals RH, Fineran PC. Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res. 2014 Jul;42(13):8516-26. doi: 10.1093/nar/gku527. Epub 2014, Jul 2. PMID:24990370 doi:http://dx.doi.org/10.1093/nar/gku527
  22. 22.0 22.1 Fineran PC, Gerritzen MJ, Suarez-Diez M, Kunne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38. doi:, 10.1073/pnas.1400071111. Epub 2014 Apr 7. PMID:24711427 doi:http://dx.doi.org/10.1073/pnas.1400071111
  23. Xue C, Seetharam AS, Musharova O, Severinov K, Brouns SJ, Severin AJ, Sashital DG. CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Res. 2015 Dec 15;43(22):10831-47. doi: 10.1093/nar/gkv1259. Epub, 2015 Nov 19. PMID:26586800 doi:http://dx.doi.org/10.1093/nar/gkv1259
  24. 24.0 24.1 Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res. 2015 Dec 15;43(22):10848-60. doi: 10.1093/nar/gkv1261. Epub, 2015 Nov 19. PMID:26586803 doi:http://dx.doi.org/10.1093/nar/gkv1261
  25. 25.0 25.1 Ivancic-Bace I, Cass SD, Wearne SJ, Bolt EL. Different genome stability proteins underpin primed and naive adaptation in E. coli CRISPR-Cas immunity. Nucleic Acids Res. 2015 Dec 15;43(22):10821-30. doi: 10.1093/nar/gkv1213. Epub, 2015 Nov 17. PMID:26578567 doi:http://dx.doi.org/10.1093/nar/gkv1213
  26. 26.0 26.1 26.2 Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature. 2015 Mar 12;519(7542):199-202. doi: 10.1038/nature14245. Epub 2015 Feb, 18. PMID:25707807 doi:http://dx.doi.org/10.1038/nature14245
  27. Hooton SP, Connerton IF. Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein. Front Microbiol. 2015 Jan 5;5:744. doi: 10.3389/fmicb.2014.00744. eCollection, 2014. PMID:25601859 doi:http://dx.doi.org/10.3389/fmicb.2014.00744
  28. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 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. 2006 Mar 16;1:7. PMID:16545108 doi:http://dx.doi.org/10.1186/1745-6150-1-7
  29. van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci. 2009 Aug;34(8):401-7. doi: 10.1016/j.tibs.2009.05.002. Epub, 2009 Jul 29. PMID:19646880 doi:http://dx.doi.org/10.1016/j.tibs.2009.05.002
  30. 30.0 30.1 Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science. 2008 Dec 19;322(5909):1843-5. doi: 10.1126/science.1165771. PMID:19095942 doi:http://dx.doi.org/10.1126/science.1165771
  31. Charpentier E, Richter H, van der Oost J, White MF. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev. 2015 May;39(3):428-41. doi: 10.1093/femsre/fuv023. Epub 2015 , May 19. PMID:25994611 doi:http://dx.doi.org/10.1093/femsre/fuv023
  32. Hochstrasser ML, Doudna JA. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci. 2015 Jan;40(1):58-66. doi: 10.1016/j.tibs.2014.10.007. Epub, 2014 Nov 18. PMID:25468820 doi:http://dx.doi.org/10.1016/j.tibs.2014.10.007

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Michal Harel

Personal tools