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Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity

Nuñez, James K, Kranzusch, Philip J, Noeske, Jonas, Wright, Addison V, Davies, Christopher W, Doudna, Jennifer A·2014·Nature Structural & Molecular Biology
DOI 10.1038/nsmb.2820PMC PMC4075942
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  • The Cas1-Cas2 complex plays a dual role in the adaptation step: excision of protospacer DNA and its incorporation into the CRISPR sequence.

    “The Cas1-Cas2 complex plays a dual role on the adaptation step, both in the excision of protospacer DNA (segment present in the foreign DNA molecule that precedes the spacer sequence) and its incorporation into the CRISPR sequence [23].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [23]

    The Discussion (page not available) says Cas1–Cas2 complex formation is essential for incorporating foreign DNA spacers into the CRISPR locus. It identifies Cas1 as a nuclease involved in adaptation, but does not establish that the complex excises protospacer DNA from foreign DNA; the Introduction calls the adaptation process poorly understood. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Cas2 nuclease activity is not crucial for spacer acquisition.

    “although Cas2 nuclease activity is not crucial for spacer acquisition [23].”

    From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [23]

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Research works printed but not linked: 40

  1. Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J. & Soria, E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60, 174–182 (2005). · DOI · Paper page
  2. Bolotin, A., Quinquis, B., Sorokin, A. & Ehrlich, S.D. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151, 2551–2561 (2005). · DOI · Paper page
  3. Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007). · DOI · Paper page
  4. Yosef, I., Goren, M.G. & Qimron, U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40, 5569–5576 (2012). · DOI · Paper page
  5. Swarts, D.C., Mosterd, C., van Passel, M.W. & Brouns, S.J. CRISPR interference directs strand specific spacer acquisition. PLoS ONE 7, e35888 (2012). · DOI
  6. Datsenko, K.A. et al. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat. Commun. 3, 945 (2012). · DOI · Paper page
  7. Brouns, S.J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008). · DOI · Paper page
  8. Carte, J., Wang, R., Li, H., Terns, R.M. & Terns, M.P. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 22, 3489–3496 (2008). · DOI
  9. Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J.A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010). · DOI
  10. Sashital, D.G., Jinek, M. & Doudna, J.A. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat. Struct. Mol. Biol. 18, 680–687 (2011). · DOI
  11. Wiedenheft, B. et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486–489 (2011). · DOI
  12. Garneau, J.E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67–71 (2010). · DOI
  13. Jore, M.M. et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat. Struct. Mol. Biol. 18, 529–536 (2011). · DOI
  14. Makarova, K.S. et al. Evolution and classification of the CRISPR–Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011). · DOI · Paper page
  15. Savitskaya, E., Semenova, E., Dedkov, V., Metlitskaya, A. & Severinov, K. High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli. RNA Biol. 10, 716–725 (2013). · DOI
  16. Diez-Villaseñor, C., Guzman, N.M., Almendros, C., Garcia-Martinez, J. & Mojica, F.J. CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli. RNA Biol. 10, 792–802 (2013). · DOI
  17. Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J. & Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733–740 (2009). · DOI · Paper page
  18. Sashital, D.G., Wiedenheft, B. & Doudna, J.A. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol. Cell 46, 606–615 (2012). · DOI
  19. Beloglazova, N. et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J. Biol. Chem. 283, 20361–20371 (2008). · DOI
  20. Wiedenheft, B. et al. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure 17, 904–912 (2009). · DOI · Paper page
  21. Babu, M. et al. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 79, 484–502 (2011). · DOI · Paper page
  22. Nam, K.H. et al. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. J. Biol. Chem. 287, 35943–35952 (2012). · DOI
  23. Kim, T.Y., Shin, M., Huynh Thi Yen, L. & Kim, J.S. Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity. Biochem. Biophys. Res. Commun. 441, 720–725 (2013). · DOI
  24. Diez-Villaseñor, C., Almendros, C., Garcia-Martinez, J. & Mojica, F.J. Diversity of CRISPR loci in Escherichia coli. Microbiology 156, 1351–1361 (2010). · DOI
  25. Goren, M.G., Yosef, I., Auster, O. & Qimron, U. Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J. Mol. Biol. 423, 14–16 (2012). · DOI
  26. Samai, P., Smith, P. & Shuman, S. Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66, 1552–1556 (2010). · DOI
  27. Han, D., Lehmann, K. & Krauss, G. SSO1450–a CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA. FEBS Lett. 583, 1928–1932 (2009). · DOI
  28. Makarova, K.S., Anantharaman, V., Aravind, L. & Koonin, E.V. Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. Biol. Direct 7, 40 (2012). · DOI
  29. Plagens, A., Tjaden, B., Hagemann, A., Randau, L. & Hensel, R. Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax. J. Bacteriol. 194, 2491–2500 (2012). · DOI
  30. Richter, C., Gristwood, T., Clulow, J.S. & Fineran, P.C. In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas System. PLoS ONE 7, e49549 (2012). · DOI
  31. Kranzusch, P.J., Lee, A.S., Berger, J.M. & Doudna, J.A. Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Reports 3, 1362–1368 (2013). · DOI
  32. Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L. & Clardy, J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105–124 (1993). · DOI
  33. Kabsch, W. Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010). · DOI · Paper page
  34. Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 62, 72–82 (2006). · DOI
  35. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). · DOI · Paper page
  36. Brown, P.H. & Schuck, P. Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys. J. 90, 4651–4661 (2006). · DOI
  37. Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78, 1606–1619 (2000). · DOI
  38. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990). · DOI · Paper page
  39. Pei, J., Kim, B.H. & Grishin, N.V. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res. 36, 2295–2300 (2008). · DOI
  40. Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. & Barton, G.J. Jalview Version 2: a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009). · DOI

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Metadata

Authors
Nuñez, J. K., Kranzusch, P. J., Noeske, J., Wright, A. V., Davies, C. W., & Doudna, J. A.
Venue
Nature Structural & Molecular Biology
Publisher
Springer Science and Business Media LLC
Published
2014-05-04
Volume
21
Issue
6
Pages
528-534
ISSN
  • 1545-9993
  • 1545-9985
DOI
10.1038/nsmb.2820
PMC
PMC4075942
Cited by
458
References
4
Language
en
Licence
www.springer.com/tdm (tdm)

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