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Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.

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Niewoehner O, Jinek M, Doudna JA
OpenAccess logo Nucleic Acids Res 42 1341-53 (2014)
Related entries: 4c8y, 4c8z, 4c97, 4c9d

Cited: 49 times
EuropePMC logo PMID: 24150936

Abstract

In many bacteria and archaea, small RNAs derived from clustered regularly interspaced short palindromic repeats (CRISPRs) associate with CRISPR-associated (Cas) proteins to target foreign DNA for destruction. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. CRISPR repeats differ widely in both sequence and structure, with varying propensity to form hairpin folds immediately preceding the cleavage site. To investigate the evolution of distinct mechanisms for the recognition of diverse CRISPR repeats by Cas6 enzymes, we determined crystal structures of two Thermus thermophilus Cas6 enzymes both alone and bound to substrate and product RNAs. These structures show how the scaffold common to all Cas6 endonucleases has evolved two binding sites with distinct modes of RNA recognition: one specific for a hairpin fold and the other for a single-stranded 5'-terminal segment preceding the hairpin. These findings explain how divergent Cas6 enzymes have emerged to mediate highly selective pre-CRISPR-derived RNA processing across diverse CRISPR systems.

Articles - 4c98 mentioned but not cited (2)

  1. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Niewoehner O, Jinek M, Doudna JA. Nucleic Acids Res 42 1341-1353 (2014)
  2. Structural Principles of CRISPR RNA Processing. Li H. Structure 23 13-20 (2015)


Reviews citing this publication (16)

  1. Unravelling the structural and mechanistic basis of CRISPR-Cas systems. van der Oost J, Westra ER, Jackson RN, Wiedenheft B. Nat Rev Microbiol 12 479-492 (2014)
  2. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Science 353 aad5147 (2016)
  3. Annotation and Classification of CRISPR-Cas Systems. Makarova KS, Koonin EV. Methods Mol Biol 1311 47-75 (2015)
  4. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. Charpentier E, Richter H, van der Oost J, White MF. FEMS Microbiol Rev 39 428-441 (2015)
  5. Cutting it close: CRISPR-associated endoribonuclease structure and function. Hochstrasser ML, Doudna JA. Trends Biochem Sci 40 58-66 (2015)
  6. DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. Plagens A, Richter H, Charpentier E, Randau L. FEMS Microbiol Rev 39 442-463 (2015)
  7. Current and future prospects for CRISPR-based tools in bacteria. Luo ML, Leenay RT, Beisel CL. Biotechnol Bioeng 113 930-943 (2016)
  8. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. J Genet Eng Biotechnol 19 128 (2021)
  9. Resilience of biochemical activity in protein domains in the face of structural divergence. Zhang D, Iyer LM, Burroughs AM, Aravind L. Curr Opin Struct Biol 26 92-103 (2014)
  10. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. FEMS Microbiol Rev 42 579-613 (2018)
  11. CRISPR-Cas Technologies and Applications in Food Bacteria. Stout E, Klaenhammer T, Barrangou R. Annu Rev Food Sci Technol 8 413-437 (2017)
  12. CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool. Loureiro A, da Silva GJ. Antibiotics (Basel) 8 E18 (2019)
  13. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. J Biol Eng 12 13 (2018)
  14. Precise gene replacement in plants through CRISPR/Cas genome editing technology: current status and future perspectives. Li S, Xia L. aBIOTECH 1 58-73 (2020)
  15. Cas6 processes tight and relaxed repeat RNA via multiple mechanisms: A hypothesis. Sefcikova J, Roth M, Yu G, Li H. Bioessays 39 (2017)
  16. Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. J Struct Biol X 6 100066 (2022)

Articles citing this publication (31)



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