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Recognition and maturation of effector RNAs in a CRISPR interference pathway
Abstract
In bacteria and archaea, small RNAs derived from clustered, regularly interspaced, short palindromic repeat (CRISPR) loci are involved in an adaptable and heritable gene-silencing pathway. Resistance to phage infection is conferred by the incorporation of short invading DNA sequences into the genome as CRISPR spacer elements separated by short repeat sequences. Processing of long primary transcripts (pre-crRNAs) containing these repeats by an RNA endonuclease generates the mature effector RNAs that interfere with phage gene expression. Here we describe structural and functional analyses of the Thermus thermophilus CRISPR Cse3 endonuclease. High-resolution X-ray structures of Cse3 bound to repeat RNAs model both the pre- and post-cleavage complexes associated with processing the pre-crRNA. These structures establish the molecular basis of a specific CRISPR RNA recognition and suggest the mechanism for generation of effector RNAs responsible for gene silencing.
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In type I-E, spacers form a stem-loop shape after transcription that is recognised and cleaved by Cas6e.
“As an example, spacers in type I-E form a stem-loop shape after transcription that is recognised and cleaved by Cas6e.”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [33]
The type I-E specific protein Cas6e remains attached to the 3′ end of the crRNA after cleavage.
“This type I-E specific protein remains attached to the 3′ end of the crRNA after cleavage [33].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [33]
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Research works printed but not linked: 31
- Ishino, Y., Shinagawa, H., Makino, K., Amemura, M. & Nakata, A. 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 (1987). · DOI · Paper page
- Nakata, A., Amemura, M. & Makino, K. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J. Bacteriol. 171, 3553–3556 (1989). · DOI
- Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007). · DOI · Paper page
- Brouns, S.J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008). · DOI · Paper page
- 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
- Jansen, R., Embden, J.D., Gaastra, W. & Schouls, L.M. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43, 1565–1575 (2002). · DOI · Paper page
- Marraffini, L.A. & Sontheimer, E.J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008). · DOI · Paper page
- Haft, D.H., Selengut, J., Mongodin, E.F. & Nelson, K.E. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1, e60 (2005). · DOI
- Kunin, V., Sorek, R. & Hugenholtz, P. Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8, R61 (2007). · DOI
- Makarova, K.S., Grishin, N., Shabalina, S., Wolf, Y. & Koonin, E. 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, 7–33 (2006). · DOI · Paper page
- Grissa, I., Vergnaud, G. & Pourcel, C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8, 172–182 (2007). · DOI · Paper page
- Agari, Y. et al. Transcription profile of Thermus thermophilus CRISPR systems after phage infection. J. Mol. Biol. 395, 270–281 (2010). · DOI
- 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
- Han, D. & Krauss, G. Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2. FEBS Lett. 583, 771–776 (2009). · DOI
- Pougach, K. et al. Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol. Microbiol. 77, 1367–1379 (2010). · DOI
- Xue, S., Calvin, K. & Li, H. RNA recognition and cleavage by a splicing endonuclease. Science 312, 906–910 (2006). · DOI
- Calvin, K., Xue, S., Ellis, C., Mitchell, M. & Li, H. Probing the catalytic triad of an archaeal RNA splicing endonuclease. Biochemistry 47, 13659–13665 (2008). · DOI
- Ebihara, A. et al. Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif-like domain. Protein Sci. 15, 1494–1499 (2006). · DOI
- Haurwitz, R.E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010). · DOI
- Deo, R.C., Bonanno, J.B., Sonenberg, N. & Burley, S.K. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98, 835–845 (1999). · DOI
- Handa, N. et al. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398, 579–585 (1999). · DOI
- Wang, R., Preamplume, G., Terns, M.P., Terns, R.M. & Li, H. Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage. Structure 19, 257–264 (2011). · DOI
- Schmidt, B.H., Burgin, A.B., Deweese, J.W., Osheroff, N. & Berger, J.M. A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature 465, 641–644 (2010). · DOI
- Guillén Schlippe, Y.V. & Hedstrom, L. A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Arch. Biochem. Biophys. 433, 266–278 (2005). · DOI
- Steitz, T.A. & Steitz, J.A. A general two-metal ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498–6502 (1993). · DOI · Paper page
- Igloi, G.L. & Kossel, H. Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid. Nucleic Acids Res. 13, 6881–6898 (1985). · DOI
- Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997). · DOI · Paper page
- Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). · DOI · Paper page
- Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997). · DOI
- Read, R.J. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D Biol. Crystallogr. 57, 1373–1382 (2001). · DOI
- Lovell, S.C. et al. Structure validation by Cα geometry: ϕ,ψ and Cβ deviation. Proteins 50, 437–450 (2003). · DOI · Paper page
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RNA-guided genetic silencing systems in bacteria and archaea
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CRISPR-mediated adaptive immune systems in bacteria and archaea
Sorek, R., Lawrence, C. M., & Wiedenheft, B. (2013) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072911-172315 · Cited by 668
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Metadata
- Authors
- Gesner, E. M., Schellenberg, M. J., Garside, E. L., George, M. M., & MacMillan, A. M.
- Venue
- Nature Structural & Molecular Biology
- Published
- 2011-05-15
- Volume
- 18
- Issue
- 6
- Pages
- 688-692
- ISSN
- 1545-9993
- 1545-9985
- Cited by
- 149
- References
- 0
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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