AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex

Nature Communications - Tập 11 Số 1
Marscha Hirschi1, Wangting Lu2, Andrew Santiago‐Frangos3, Royce A. Wilkinson3, Sarah Golden3, Alan R. Davidson2, Gabriel C. Lander1, Blake Wiedenheft3
1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92121, USA
2Department of Molecular Genetics, and Department of Biochemistry, University of Toronto, 661 University Avenue, Room 1634, Toronto, ON, M5G 1M1, Canada
3Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA

Tóm tắt

AbstractBacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.

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Tài liệu tham khảo

McGinn, J. & Marraffini, L. A. Molecular mechanisms of CRISPR-Cas spacer acquisition. Nat. Rev. Microbiol. 17, 7–12 (2019).

Jackson, S. A. et al. CRISPR-Cas: adapting to change . Science 356, eaal5056 (2017).

Barrangou, R. et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709–1712 (2007).

Jackson, R. N., van Erp, P. B., Sternberg, S. H. & Wiedenheft, B. Conformational regulation of CRISPR-associated nucleases. Curr. Opin. Microbiol. 37, 110–119 (2017).

Klompe, S. E. & Sternberg, S. H. Harnessing “A Billion Years of Experimentation”: the ongoing exploration and exploitation of CRISPR–Cas immune systems. CRISPR J. 1, 141–158 (2018).

Koonin, E. V. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol. Direct 12, 5 (2017).

Makarova, K. S. et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).

Pawluk, A., Davidson, A. R. & Maxwell, K. L. Anti-CRISPR: discovery, mechanism and function. Nat. Rev. Microbiol. 16, 12–17 (2018).

Pawluk, A. et al. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat. Microbiol. 1, 16085 (2016).

Chowdhury, S. et al. Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex. Cell 169, 47–57 (2017).

Peng, R. et al. Alternate binding modes of anti-CRISPR viral suppressors AcrF1/2 to Csy surveillance complex revealed by cryo-EM structures. Cell Res. 27, 853–864 (2017).

Guo, T. W. et al. Cryo-EM structures reveal mechanism and inhibition of DNA targeting by a CRISPR-Cas surveillance complex. Cell 171, 414–426 (2017).

Rollins, M. F., Schuman, J. T., Paulus, K., Bukhari, H. S. & Wiedenheft, B. Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa. Nucleic Acids Res. 43, 2216–2222 (2015).

Rollins, M. F. et al. Structure reveals a mechanism of CRISPR-RNA-guided nuclease recruitment and anti-CRISPR viral mimicry. Mol. Cell 74, 132–142 (2019).

Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform 20, 1160–1166 (2019).

Zhang, K. et al. Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM. Proc. Natl Acad. Sci. USA 117, 7176–7182 (2020).

Forsberg, K. J. et al. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. eLife 8, e46540 (2019).

Rollins, M. F. et al. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity. Proc Natl Acad Sci USA 114, E5113–E5121 (2017).

Wiedenheft, B. et al. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci USA 108, 10092–10097 (2011).

Rio, D. C. 5'-end labeling of RNA with [gamma-32P]ATP and T4 polynucleotide kinase. Cold Spring Harb Protoc 2014, 441–443 (2014).

Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J Struct Biol 151, 41–60 (2005).

Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods 14, 793–796 (2017).

Lander, G. C. et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol 166, 95–102 (2009).

Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14, 331–332 (2017).

Zhang, K. Gctf: Real-time CTF determination and correction. J Struct Biol 193, 1–12 (2016).

Voss, N. R., Yoshioka, C. K., Radermacher, M., Potter, C. S. & Carragher, B. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. J Struct Biol 166, 205–213 (2009).

Scheres, S. H. A Bayesian view on cryo-EM structure determination. J Mol Biol 415, 406–418 (2012).

Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14, 290–296 (2017).

Goddard, T. D., Huang, C. C. & Ferrin, T. E. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure 13, 473–482 (2005).

Heymann, J. B. & Belnap, D. M. Bsoft: image processing and molecular modeling for electron microscopy. J Struct Biol 157, 3–18 (2007).

Nicholls, R. A., Long, F. & Murshudov, G. N. Low-resolution refinement tools in REFMAC5. Acta Crystallogr D Biol Crystallogr 68, 404–417 (2012).

Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 74, 531–544 (2018).

Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallographica Section D-Biological Crystallography 60, 2126–2132 (2004).

Williams, C. J. et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci 27, 293–315 (2018).

Goddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci 27, 14–25 (2018).