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. 2017 Jul 6;67(1):117-127.e5.
doi: 10.1016/j.molcel.2017.05.024. Epub 2017 Jun 9.

Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9

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Free PMC article

Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9

Hui Yang et al. Mol Cell. .
Free PMC article

Abstract

Prokaryotic CRISPR-Cas adaptive immune systems utilize sequence-specific RNA-guided endonucleases to defend against infection by viruses, bacteriophages, and mobile elements, while these foreign genetic elements evolve diverse anti-CRISPR proteins to overcome the CRISPR-Cas-mediated defense of the host. Recently, AcrIIA2 and AcrIIA4, encoded by Listeria monocytogene prophages, were shown to block the endonuclease activity of type II-A Streptococcus pyogene Cas9 (SpyCas9). We now report the crystal structure of AcrIIA4 in complex with single-guide RNA-bound SpyCas9, thereby establishing that AcrIIA4 preferentially targets critical residues essential for PAM duplex recognition, as well as blocks target DNA access to key catalytic residues lining the RuvC pocket. These structural insights, validated by biochemical assays on key mutants, demonstrate that AcrIIA4 competitively occupies both PAM-interacting and non-target DNA strand cleavage catalytic pockets. Our studies provide insights into anti-CRISPR-mediated suppression mechanisms for inactivating SpyCas9, thereby broadening the applicability of CRISPR-Cas regulatory tools for genome editing.

Keywords: AcrIIA4; CRISPR RNA; CRISPR-Cas; Cas9; RuvC; anti-CRISPR protein; endonuclease; genome editing; target DNA cleavage; trans-activating crRNA.

Figures

Figure 1
Figure 1. AcrIIA4 directly interacts with sgRNA-bound SpyCas9 and inactivates SpyCas9
(A) In vitro enzymatic assay monitoring cleavage of linear dsDNA by SpyCas9 and sgRNA in the presence of AcrIIA4. The molar ratios of AcrIIA4:SpyCas9 are shown at the top of each lanes (left panel). The inhibition between MBP-tagged SpyCas9 and AcrIIA4 are also detected and compared with dSpyCas9 (right panel). (B) AcrIIA4 selectively forms a stable complex with sgRNA-bound SpyCas9 rather than apo or DNA-bound SpyCas9-sgRNA in solution. SEC was performed using SpyCas9 in the presence or absence of sgRNA and sgRNA-dsDNA. (C) AcrIIA4 physically interacts with sgRNA-bound SpyCas9. MBP pull-down assays were performed using MBP-tagged AcrIIA4 and SpyCas9 in presence or absence of sgRNA and sgRNA-dsDNA. (D) Oligomeric state of AcrIIA4 in solution detected by SEC-MALS. The horizontal red line represents the SEC-MALS calculated mass for AcrIIA4. The calculated and theoretical molecular masses are 10.4 kDa and 10.2 kDa, respectively, indicating that AcrIIA4 exists as a monomer in solution. See also Figure S1.
Figure 2
Figure 2. Overall structure of AcrIIA4-SpyCas9-sgRNA complex
(A) Domain organization of SpyCas9 and AcrIIA4. (B) Ribbon and surface representations of AcrIIA4-SpyCas9-sgRNA ternary complex, color-coded as defined in panel A. The AcrIIA4 molecule in each view is highlighted by a red circle. (C, D) Structural comparison of domain movement on proceeding from the SpyCas9-sgRNA binary complex to the SpyCas9-sgRNA-AcrIIA4 ternary complex (panel C) and to the SpyCas9-sgRNA-dsDNA ternary complex (panel D). Vector lengths correlate with the domain motion scales. TS and NTS represent target and non-target DNA strands, respectively. See also Figures S2 and S4.
Figure 3
Figure 3. Detailed Interactions of AcrIIA4 with sgRNA-bound SpyCas9
(A, C, E) Surface views of the interfaces between AcrIIA4 and Topo domain (panel A), CTD domain (panel C), and RuvC domain (panel E). The interface segments are highlighted by black boxes. (B, D, F) Detailed interactions at the interfaces between AcrIIA4 and Topo domain (panel B), CTD domain (panel D), and RuvC domain (panel F) are shown in stick representations. The color code is the same as Figure 2A. Hydrogen bonds and salt bridges are colored as black and red dashed lines, respectively. (G) Mutation analysis of AcrIIA4 residues involving in the binding to sgRNA-bound SpyCas9 by MBP pull-down assay of MBP-tagged AcrIIA4. (H) In vitro enzymatic assay of Ala mutations of AcrIIA4 residues that impaired or abolished binding of AcrIIA4 to sgRNA-bound SpyCas9. See also Figure S3.
Figure 4
Figure 4. Inhibition mechanism of SpyCas9 by AcrIIA4
(A, B) Recognition of AcrIIA4 (panel A) and the PAM duplex (panel B) by Topo, CTD, and RuvC domains of SpyCas9. The active site of RuvC domain for non-target DNA strand in each panel is highlighted by a yellow star. TS and NTS represent target and non-target DNA strands, respectively. (C) AcrIIA4 competitively binding to preformed SpyCas9-sgRNA binary complex (left panel) rather and SpyCas9-sgRNA-dsDNA ternary complex (right panel) in EMSA assays. The molar ratios of AcrIIA4:SpyCas9 are shown at the top of the gel. (D, E) Detailed interactions between AcrIIA4 (panel D) and PAM duplex (panel E) with the Topo and CTD domains of SpyCas9, respectively. (F, G) Recognition of key catalytic residues in the RuvC active site by AcrIIA4 (panel F) and non-target DNA strand (panel F). The modeled side chain of catalytic residue Asp10 is marked by asterisk. The position of cleavage site in non-target DNA strand is pointed by a black arrow. See also Figure S4.

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