doi: 10.1016/j.str.2010.11.014.
Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage
Affiliations
- PMID:21300293
- PMCID: PMC3154685
- DOI: 10.1016/j.str.2010.11.014
Item in Clipboard
Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage
Ruiying Wang et al. Structure..
Display options
Format
Display options
Format
Abstract
The CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) found in prokaryotic genomes confer small RNA-mediated protection against viruses and other invaders. CRISPR loci contain iterations of a short repeat sequence alternating with small segments of varying invader-derived sequences. Distinct families of CRISPR-associated Cas proteins function to cleave within the repeat sequence of CRISPR transcripts and produce the individual invader-targeting crRNAs. Here, we report the crystal structure of Pyrococcus furiosus Cas6 bound with a repeat RNA at 3.2 Å resolution. In contrast to other Cas families of endonucleases, Cas6 clasps nucleotides 2-9 of the repeat RNA using its two ferredoxin-like domains, and the enzyme-anchored 5' end tethers the distal cleavage site of the RNA between nucleotides 22 and 23 to the predicted enzyme active site on the opposite side of the ferrodoxin-like domains. Our findings suggest a wrap-around mechanism for CRISPR RNA recognition and cleavage by Cas6 and related processing endonucleases.
Copyright © 2011 Elsevier Ltd. All rights reserved.
Figures
A, crRNA biogenesis. The primary CRISPR transcript contains repeats (R, red blocks) interspaced by guide sequences (G, grey blocks). The sequence of the repeat (RNA used in this study) is shown. Cas6 cleaves within each repeat (white dotted lines), releasing individual crRNA units (1X intermediates) that are further trimmed at the 3’ end by an unknown exonuclease(s).B, Overview of the Cas6-RNA complex structure shown in two orientations. The protein is shown in teal and RNA is in red. The α-helix α2 that contains the putative catalytic residue, His46, is indicated. Nucleotides of the repeat RNA are numbered from the 5’ end. See also Figures S1 and S2.
A, Superimposed structures of Cas6 bound to RNA (teal) and free Cas6 (grey). The putative catalytic residue (His46) is indicated in magenta.B, Electrostatic potentials of Cas6 in the RNA-bound complex are shown. The left view is the same as that in A. Cas6 binds nucleotides 2–10 of the repeat RNA (red) and is predicted to tether the 3’ end of the repeat RNA (dashed line) to its cleavage site (indicated by His46). Note that the potential path overlaps with the conserved Cas6-specific G-rich loop (G-loop).C, Impact on RNA cleavage (left) and binding (right) of Cas6 by alanine substation of Gly223, Gly225, Gly231, and Gly233 (G-loopm). The three concentrations of the G-loopm protein used in the cleavage and binding experiments were 0.5 µM, 1 µM and 10 µM, respectively.
The protein is represented by surface (upper panels) or stick models (lower panels) and the RNA is represented by red stick models. Contacts shorter than 3.4 Å between RNA and protein atoms are indicated by dashed lines.A, Interactions between Cas6 residues and nucleotides 2–6.B. Interactions between Cas6 residues and nucleotides 7–10.
RNA nucleotides are represented by red sticks and protein residues are by grey-blue-red sticks. Nucleotides 4 and 9 involve simple interactions and are thus not included.
A, Sequences of the wild-type (A) and mutant repeat RNAs (B–R) used in Cas6 cleavage and binding studies. Mutant B (2’-deoxy modification on positions 22 and 23) is used as a non-cleavable substrate control as previously established by Carte et al. (Carte et al., 2008). Substituted, inserted, or modified nucleotides are shown in red. Deletions are indicated by spaces. “d” denotes 2’-deoxy modification. Results are summarized on the right. For mutations near the cleavage site, the experimentally observed cleavage position is denoted.B, Cleavage (upper panels) and binding (lower panels) of wild-type (A) and mutant RNAs (B–K) by Cas6.C, Cleavage and mass spectrometry analysis of the wild-type and mutant RNAs (L–O).D, Cleavage of repeat RNAs containing mutation A23U. Sizes of cleavage products are indicated. Analysis of the 21 and 22 nt cleavage products by MALDI-TOF mass spectrometric methods (Bruker, autoflex III) is shown in the right panel. The red trace is the product of cleavage of the wild-type RNA and the black trace is that from cleavage of the A23U mutant RNA. The predicted molecular weights of the 21 and 22 nt products, both with 2’,3’ cyclic phosphate termini, are indicated.E, Depiction of a beads-on-a-string model of CRISPR RNA processing by Cas6. CRISPR repeats are shown in red and invader-derived guide sequences are shown in grey. Individual Cas6 proteins bind the 5’ regions of the CRISPR repeats and the 3’ regions of the repeats wrap around Cas6 to the cleavage site (scissors). See also Figure S3.
Comment in
- Recognition of archaeal CRISPR RNA: No P in the alindromic repeat?Lawrence CM, White MF.Lawrence CM, et al.Structure. 2011 Feb 9;19(2):142-4. doi: 10.1016/j.str.2011.01.003.Structure. 2011.PMID:21300282
References
- Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr. 2002;58:1948–1954. - PubMed
- Andersson AF, Banfield JF. Virus population dynamics and acquired virus resistance in natural microbial communities. Science. 2008;320:1047–1050. - PubMed
- Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315:1709–1712. - PubMed
- Bolotin A, Quinquis B, Sorokin A, Ehrlich SD. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005;151:2551–2561. - PubMed
Publication types
MeSH terms
Substances
Associated data
- Actions
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources