Abstract
CRISPR drives prokaryotic adaptation to invasive nucleic acids such as phages and plasmids, using an RNA-mediated interference mechanism. Interference in type I CRISPR-Cas systems requires a targeting Cascade complex and a degradation machine, Cas3, which contains both nuclease and helicase activities. Here we report the crystal structures of Thermobifida fusca Cas3 bound to single-stranded (ss) DNA substrate and show that it is an obligate 3′-to-5′ ssDNase that preferentially accepts substrate directly from the helicase moiety. Conserved residues in the HD-type nuclease coordinate two irons for ssDNA cleavage. We demonstrate ATP coordination and conformational flexibility of the SF2-type helicase domain. Cas3 is specifically guided toward Cascade-bound target DNA by a PAM sequence, through physical interactions with both the nontarget substrate strand and the CasA protein. The sequence of recognition events ensures well-controlled DNA targeting and degradation of foreign DNA by Cascade and Cas3.
Similar content being viewed by others
References
Terns, M.P. & Terns, R.M. CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. 14, 321–327 (2011).
Wiedenheft, B., Sternberg, S.H. & Doudna, J.A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 482, 331–338 (2012).
Jore, M.M., Brouns, S.J. & van der Oost, J. RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements. Cold Spring Harb. Perspect. Biol. 4, a003657 (2012).
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).
Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I. & Koonin, E.V. 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 (2006).
Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).
Marraffini, L.A. & Sontheimer, E.J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322, 1843–1845 (2008).
Hale, C.R. et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945–956 (2009).
Makarova, K.S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011).
Brouns, S.J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008).
Jackson, R.N., Lavin, M., Carter, J. & Wiedenheft, B. Fitting CRISPR-associated Cas3 into the helicase family tree. Curr. Opin. Struct. Biol. 24, 106–114 (2014).
Jore, M.M. et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat. Struct. Mol. Biol. 18, 529–536 (2011).
Wiedenheft, B. et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486–489 (2011).
Westra, E.R. et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol. Cell 46, 595–605 (2012).
Sinkunas, T. et al. In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. EMBO J. 32, 385–394 (2013).
Mulepati, S. & Bailey, S. In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target. J. Biol. Chem. 288, 22184–22192 (2013).
Singleton, M.R., Dillingham, M.S. & Wigley, D.B. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76, 23–50 (2007).
Singleton, M.R., Dillingham, M.S., Gaudier, M., Kowalczykowski, S.C. & Wigley, D.B. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432, 187–193 (2004).
Taylor, D.W. et al. Substrate-specific structural rearrangements of human Dicer. Nat. Struct. Mol. Biol. 20, 662–670 (2013).
Perry, J.J. et al. WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat. Struct. Mol. Biol. 13, 414–422 (2006).
Mulepati, S. & Bailey, S. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3). J. Biol. Chem. 286, 31896–31903 (2011).
Beloglazova, N. et al. Structure and activity of the Cas3 HD nuclease MJ0384, an effector enzyme of the CRISPR interference. EMBO J. 30, 4616–4627 (2011).
Sinkunas, T. et al. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system. EMBO J. 30, 1335–1342 (2011).
Hochstrasser, M.L. et al. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc. Natl. Acad. Sci. USA 111, 6618–6623 (2014).
Yang, W. Lessons learned from UvrD helicase: mechanism for directional movement. Annu. Rev. Biophys. 39, 367–385 (2010).
Yang, W. Nucleases: diversity of structure, function and mechanism. Q. Rev. Biophys. 44, 1–93 (2011).
Büttner, K., Nehring, S. & Hopfner, K.P. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat. Struct. Mol. Biol. 14, 647–652 (2007).
Lee, J.Y. & Yang, W. UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Cell 127, 1349–1360 (2006).
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
Sheldrick, G.M. Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D Biol. Crystallogr. 66, 479–485 (2010).
Terwilliger, T.C. et al. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr. D Biol. Crystallogr. 65, 582–601 (2009).
Terwilliger, T.C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D Biol. Crystallogr. 64, 61–69 (2008).
Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (2010).
Cowtan, K.D. & Main, P. Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta Crystallogr. D Biol. Crystallogr. 49, 148–157 (1993).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
Winn, M.D., Murshudov, G.N. & Papiz, M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300–321 (2003).
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
Evans, G. & Pettifer, R.F. CHOOCH: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra. J. Appl. Crystallogr. 34, 82–86 (2001).
Acknowledgements
This work was supported by US National Institutes of Health (NIH) grants GM-086766 and GM-102543 to A.K. and Korean Postdoctoral Fellowship NRF-2010-357-C00106 to K.H.N. NE-CAT and MACCHESS beamlines were supported by NIH grants GM103403 and GM103485, respectively. We thank Y. Chen and K. Perry for technical help and J. van der Oost, J. Grigg, R. Hayes and I. Price for helpful discussions.
Author information
Authors and Affiliations
Contributions
Y.H., K.H.N., A.K., K.R. and I.K. collected diffraction data. K.H.N., L.W., R.Z. and A.K. determined the structure. F.D., H.L., A.K., Y.X., M.D.F., Y.H. and S.Z. performed the biochemical analyses. A.K. designed the research and wrote the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 Sequence-conservation analysis.
Sequence alignment among the Cas3 family of proteins from Thermobifida fusca (accession code: Q47PJ0), Saccharomonospora viridis (C7MTA6), Thermomonospora curvata (D1A6Q2), Streptomyces avermitilis (Q825B5), Streptomyces bottropensis (M3DI13), Thermus thermophilus strain HD8 (Q53VY2) and Escherichia coli (P38036). The absolutely conserved residues are boxed in red, and highly conserved ones are colored in red and in unfilled boxes. Residues involved in the binding of Fe2+, ATP, and ss-DNA are marked with orange, blue and red asterisks, respectively.
Supplementary Figure 2 Chemical property of the cleavage product, metal dependency and mutagenesis of the HD nuclease domain in T. fusca Cas3 protein.
(a) Identity of the co-purifying nucleic acids in Cas3. Phenol extraction of the purified Cas3 sample followed by DNase I or RNase A treatment and PAGE separation revealed that the Cas3-bound nucleic acids are DNA, not RNA. The average DNA size may be further trimmed during the crystallization process. (b) Cas3 cleaves ss-DNA to produce a 5’ phosphate and a 3’-OH. Left: a 3’-HEX-lebeled fluorescent ss-DNA oligo was cleaved by Tfu_Cas3 (lane 1) and the reaction product was further incubated with alkaline phosphatase (AP, lane 2). AP removes the 5’-phosphate from the cleavage products, causing these bands to migrate slower due to reduced negative charges. Right: a 5’-HEX-labeled fluorescent ss-DNA oligo was cleaved by Cas3 and the product was further incubated with Terminal deoxynucleotidyl Transferase (TdT) in the presence of dTTP. The disappearance of product bands and the presence of the slow-migrating TdT polymerized band suggest that Cas3 product contains a 3’-OH. (c) Survey of the Cas3 activity in the presence of various metal ions. Mg2+, Mn2+, and Co2+ significantly stimulated the ss-DNase activity in Cas3. (d) D84A inactivates the HD nuclease activity in Cas3. The activities of 0.1 mg/ml (1 μM) of D84A, D451A, and D84A/D451A(DM) Cas3 proteins were compared with that of the wild type enzyme ranging from 0.025-0.1 mg/ml in concentration.
Supplementary Figure 3 Surface conservation and electrostatic properties in the Cas3 family of proteins.
(a) Top-down and side views of Cas3 revealing the surface conservation along the ss-DNA recruitment pathway (left) and in the ATP-binding cleft between the two RecA domains (right). Conserved residues are colored in dark red, variable ones in light blue. The CTD is flipped 180˚ to reveal the surface conservation inside the ss-DNA binding channel. (b) The same two views reviewing the electrostatic properties on the Cas3 surface. Positive and negative charges are colored in blue and red, respectively.
Supplementary Figure 4 Comparison of the active site configuration among HD-nuclease-domain structures.
Views of the HD nuclease active site in the crystal structures of T. fusca Cas3 (this study; panel a), M. jannaschii Cas3 (PDB code: 3S4L; panel b), T. thermophilus Cas3 (3SKD; panel c) and predicted HD domain from an uncultured thermotogales bacterium (2PQ7; panel d). Note the absence of one metal ion in panels b and c. Metal coordination is similar in panels a and d, although Fe2 coordination in panel d involves one less histidine residue.
Supplementary Figure 5 X-ray–absorption fine-structure (XAFS) analysis and anomalous difference map confirming the presence of iron in the Cas3 crystal.
(a) Energy-dispersive X-ray spectroscopy (EDS) spectrum taken through a SeMet-Cas3 crystal. Significant fluorescent emission lines are labeled 1 to 5. The following are the peak identities. Peak 1: 6.42keV, Fe Kα1; peak 2: 7.08keV, Fe Kβ1; peak 3: 11.21keV, Se Kα1; peak 4: 12.11keV - Compton scattered X-rays; peak 5: 12.66 keV - incident X-rays. The peak corresponding to selenium is observed due to SeMet labeling. The inset zooms into the region where Fe fluorescent emission lines are observed. (b) Same experiment as (b) except the X-ray beam was centered at the cryo-protectant region, away from the crystal. Fe and Se peaks are absent in this spectrum. (c, d) Near edge XAFS scanning of the Iron absorption edge taken through the crystal and through the solvent region, respectively. The through-crystal spectrum clearly reveals the presence of Fe anomalous absorption edge, whereas the through-solvent spectrum does not. (e) Anomalous difference map from data collected at the Fe absorption edge, contoured at 5 sigma level. Strong anomalous densities are coincident with the two Fe2+ ions, further confirming the identity and location of the Fe2+ ions in the HD nuclease active site.
Supplementary Figure 6 ATP binding and domain movement inside Cas3 molecules.
(a) Sequence alignment of the conserved SF2 helicase motifs in Cas3. Red triangles mark the residues involved in ATP binding and hydrolysis, blue diamonds for DNA-translocation residues. (b-d) Comparison of the binding of ATP (b), AMPPNP (c), and ADP (d) to the SF2 helicase of Cas3. 2Fo-Fc electron density map corresponding to the ligand is shown in light grey. Side chains of the contacting residues are shown in sticks, the rest of the protein in cartoon. (e) The arrangement of the four Cas3 proteins in the asymmetric unit of the crystal lattice. Their conformation varies due to rigid-body hinge motions between domains. (f) Significant conformational differences between Molecules A and D. Molecules A (colored in pale brown) and D (the five domains colored in grey, cyan, green, pink, and magenta) are superimposed along the RecA2 domain in the helicase. A hinge motion in the ATP-binding cleft resulted in a closing-in motion in molecule D, such that its HD domain shifts as much as 3 Å, causing the active site metal ions and ss-DNA substrate to move ~1.7 Å.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–6 and Supplementary Table 1 (PDF 4977 kb)
Rights and permissions
About this article
Cite this article
Huo, Y., Nam, K., Ding, F. et al. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nat Struct Mol Biol 21, 771–777 (2014). https://doi.org/10.1038/nsmb.2875
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nsmb.2875
- Springer Nature America, Inc.
This article is cited by
-
Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays
Nature Structural & Molecular Biology (2023)
-
Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system
Nature Communications (2023)
-
Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3
Nature Communications (2022)
-
Structural basis for inhibition of an archaeal CRISPR–Cas type I-D large subunit by an anti-CRISPR protein
Nature Communications (2020)
-
Genome editing in plants using CRISPR type I-D nuclease
Communications Biology (2020)