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Mechanism for Cas4-assisted directional spacer acquisition in CRISPR–Cas

Abstract

Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers derived from foreign DNA in the CRISPR array1. Spacer insertion is carried out by the Cas1–Cas2 integrase complex2,3,4. A substantial fraction of CRISPR–Cas systems use a Fe–S cluster containing Cas4 nuclease to ensure that spacers are acquired from DNA flanked by a protospacer adjacent motif (PAM)5,6 and inserted into the CRISPR array unidirectionally, so that the transcribed CRISPR RNA can guide target searching in a PAM-dependent manner. Here we provide a high-resolution mechanistic explanation for the Cas4-assisted PAM selection, spacer biogenesis and directional integration by type I-G CRISPR in Geobacter sulfurreducens, in which Cas4 is naturally fused with Cas1, forming Cas4/Cas1. During biogenesis, only DNA duplexes possessing a PAM-embedded 3′-overhang trigger Cas4/Cas1–Cas2 assembly. During this process, the PAM overhang is specifically recognized and sequestered, but is not cleaved by Cas4. This ‘molecular constipation’ prevents the PAM-side prespacer from participating in integration. Lacking such sequestration, the non-PAM overhang is trimmed by host nucleases and integrated to the leader-side CRISPR repeat. Half-integration subsequently triggers PAM cleavage and Cas4 dissociation, allowing spacer-side integration. Overall, the intricate molecular interaction between Cas4 and Cas1–Cas2 selects PAM-containing prespacers for integration and couples the timing of PAM processing with the stepwise integration to establish directionality.

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Fig. 1: PAM-spacer acquisition and the dual-PAM prespacer-bound GsCas4/Cas1–Cas2 structure.
Fig. 2: Cas4-mediated PAM recognition delays overhang cleavage.
Fig. 3: Mechanistic insights from the single-PAM prespacer-bound GsCas4/Cas1–Cas2 structure.
Fig. 4: Structural basis for integration-coupled PAM cleavage by Cas4.

Data availability

The cryo-EM density maps that support the findings of this study have been deposited in the Electron Microscopy Data Bank (EMDB) under accession numbers EMD-23839 (PAM/PAM prespacer bound), EMD-23840 (PAM/non-PAM prespacer bound), EMD-23843 (full-integration complex), EMD-23845 (half-integration complex, Cas4 still blocking the PAM side), EMD-23849 (half-integration complex, Cas4 dissociated) and EMD-23847 (sub-complex). The coordinates have been deposited in the Protein Data Bank (PDB) under accession numbers 7MI4 (PAM/PAM prespacer-bound), 7MI5 (PAM/non-PAM prespacer-bound), 7MI9 (full integration), 7MIB (half integration, Cas4 still blocking the PAM side), 7MID (sub-complex). MiSeq sequencing data that support analysis of in vivo prespacer integration have been deposited in the European Nucleotide Archive (ENA) under accession number PRJEB41616. Plasmids used in this study are available upon request.

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Acknowledgements

This work is supported by the Netherlands Organization for Scientific Research (NWO) VICI grant (VI.C.182.027) to S.J.J.B. and the National Institutes of Health (NIH) grant (GM118174) to A.K. This work made use of the Cornell Center for Materials Research Shared Facilities which are supported through the NSF MRSEC program (DMR-1719875). We thank S. N. Kieper, R. Miojevic, M. Ramos, G. Schuler and K. Spoth for helpful discussions, advice and technical assistance.

Author information

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Authors

Contributions

A.K., S.J.J.B., C.H. and C.A. designed the research. C.H. is responsible for biochemistry and cryo-EM reconstructions; C.A., J.N.A.V., A.R.C. and A.C.H. are responsible for in vivo and bioinformatics analyses; K.H.N. and C.H. are responsible for structure building and refinement; and S.R.B. assisted with cryo-EM work. A.K. and C.H. wrote the manuscript with input from S.J.J.B., J.N.A.V. and A.R.C.

Corresponding authors

Correspondence to Stan J. J. Brouns or Ailong Ke.

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The authors declare no competing interests.

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Peer review information Nature thanks Martin Jinek, Lennart Randau and Malcolm White for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Fig. 1 Reconstitution and characterization of the GsuCas4/Cas1-Cas2 complex.

a. Active site substitution in Cas4 nuclease center (H48G, D100A) reduced in vivo spacer acquisition efficiency dramatically. Left three panels display the WebLogo of PAM code from spacers integrated by each Cas4/1-2 variant. Rightmost panel displays the number of deep-sequencing reads that confirm spacer integration. b–d. GsuCas4/1 purification analyzed by SDS-PAGE, coloring from the Fe-S cluster, and SEC profile, respectively. e,f. Affinity purification of GsuCas2, SDS-PAGE, and SEC analysis, respectively. g. GST pull-down experiments revealing the physical interaction between GsuCas4/1 and GsuCas2, with or without prespacer present. h. Metal ion dependency in PAM cleavage reaction. i. Biochemistry showing Cas4/1-2 specifically cleaves the PAM-embedded 3′-overhang in prespacer. j. PAM-cleavage specificity is lost over time, presumably due to Fe-S oxidation in Cas4. k. SEC profile of GsuCas4/Cas1-Cas2, alone or programmed with different prespacer substrates. PAM-containing prespacers drive high-order complex formation. l. Cryo-electron micrographs of three different complexes, with corresponding preliminary 2D averages to investigate sample quality.

Extended Data Fig. 2 In-depth analysis of the dual-PAM prespacer bound GsuCas4/Cas1-Cas2 structure.

a. Comparison between the current 3.2 Å cryo-EM reconstruction with the previous negative staining reconstruction of the B. hal Cas4/1-2 complex (EMDB 20131)22. b–d. Pairwise alignment between GsuCas4/Cas1-Cas2/prespacer and EcoCas1-Cas2/prespacer8,31 (PDB 5DS4), EfaCas1-Cas2/prespacer12 (PDB 5XVN), and EfaCas1-Cas2/full-integration12 (PDB 5XVO), respectively. Alignments details are noted on the figure panel. Inset: the C-terminal tail of Cas2 plays similar roles in G. sul and E. fae structures in mediating edge-stacking with both Cas2 and Cas1. e. PAM was processed similarly in 22-bp or 26-bp mid-duplex containing prespacer by GsuCas4/Cas1-Cas2. f. SEC profile was similar when the two different prespacers were used to assemble the complex. g. Validation that prespacers containing a 22-bp mid-duplex are actively acquired in vivo. N=3 biologically independent assays were evaluated by PCR detection as shown, as well as relative percentages of expanded and non-expanded bands. Data presented as mean ± s.e.m.

Extended Data Fig. 3 Flow-chart of the cryo-EM single particle reconstruction of the dual-PAM prespacer bound GsuCas4/Cas1-Cas2.

a. Cryo-EM reconstruction workflow for the dual-PAM prespacer bound Cas4/1-2 complex. b. Cryo-EM density of the dual-PAM prespacer bound Cas4/1-2 complex, colored according to local resolution (top). The viewing direction distribution plot (middle) and FSC curves (bottom) for data processing. c. Representative EM densities for Cas2, Cas4, and Cas1, superimposed with their corresponding structural model.

Extended Data Fig. 4 In-depth GsuCas4/Cas1-Cas2 interface analysis and structure-guided mutagenesis attempt to switch PAM specificity.

a. Overall dual-PAM structure. Insets: zoom-ins of interface between Cas4 and the two neighboring Cas1s. Cas4 connects to the non-catalytic Cas1 through a 20-amino acid fusion linker (colored in yellow), which mediates the dynamic docking and dissociation of Cas4. b. Surface electrostatic potential. Left inset: Cas2 contacts to the mid-duplex; Right inset: Cas1 end-stacking to the mid-duplex. Residues responsible for guiding the 3’-overhang are also shown. Cas1-Cas2 was found to specify a 22-bp mid-duplex rather than a 26-bp mid-duplex as defined by the integration assay; an additional two base-pairs are unwound from each end, and the mid-duplex is end-stacked by the N-terminal domain of the catalytic Cas1s on opposite ends. The 22-bp specification and the limited end-unwinding activity was previously observed in EfaCas1-Cas211,12. c. Cas1-Cas2 and Cas4-Cas2 interfaces. Top inset: the highly conserved C-terminus of Cas2 inserting into a hydrophobic pocket in Cas1, stabilizing complex formation. Bottom inset: the ceiling helix of Cas4 (aa 39–50) makes extensive polar contacts with a helix in Cas2 (aa 42–53). d. SEC, SDS-PAGE, and urea-PAGE analyses of the prespacer-bound complex used in cryo-EM analysis. They reveal the molecular weight, protein integrity, and prespacer integrity, respectively. For example, urea-PAGE reveals the PAM-overhang is not cleaved inside the Cas4/1-2 complex. e. Modeling the impact on PAM recognition by introducing the equivalent residues of E18 and S191 in P. fur Cas4 into G. sul Cas4 (E18Y and S191A substitutions). Specific atom changes in A-to-G switching (N6O substitution and N2 amine addition) are highlighted in colored balls. The steric clashes (lightening arrows) to PfuPAM (3’-GGN in the 3’-overhang) are expected to be partially relieved when substitutions are in place. f. Impact of E18Y and S191A substitutions on PAM cleavage activity. g. In vivo spacer acquisition assay results for the wild type and PAM-specificity Cas4 mutants. While E18Y/S191A Cas4 showed compromised Gsu-PAM (TTN) prespacer integration, it was able to support integration of Pfu-PAM (CCN) containing prespacers in vivo. N = 3 biological independent assays were analyzed by PCR and the band quantification revealed integration efficiency. Data presented as mean ± s.e.m.

Extended Data Fig. 5 In-depth analysis of the structure and sequence conservation in Cas4.

a. Superposition of GsuCas4 with a standalone Cas419,20, and the nuclease domains in helicase-nuclease fusion proteins AddAB32, AdnAB26, RecBCD33, and eukaryotic Dna234. The caging of the ssDNA substrate and the arrangement of the Fe-S cluster and the catalytic triad are conserved themes. Interestingly, the Cas4 structure aligns poorly with the RecB nuclease in RecBCD; it agrees better with the RecB-like fold in RecC instead. b, c. Sequence alignment of GsuCas4, GsuCas1, and PfuCas4 with their close homologs. Based on the structural analysis, we marked the residues important for subunit interaction, substrate binding, catalysis and Fe-S cluster formation. d. Quality of the purified GsuCas4 mutants that carry the PAM-recognition residues from PfuCas4. These mutants were used in the structure-guided PAM-switching experiments in Extended Data Fig. 4.

Extended Data Fig. 6 Cryo-EM single particle reconstruction of the single-PAM prespacer bound GsuCas4/Cas1-Cas2.

a. Flow-chart of the cryo-EM single particle reconstruction process that led to the reconstruction of two major snapshots. Left: Asymmetrical PAM/Non-PAM prespacer bound Cas4/1-2 complex. Right: That of the sub complex lacking (Cas4/1)2 on the non-PAM side. b. Cryo-EM density of the two reconstructions colored according to local resolution (top); viewing direction distribution plot (middle); and FSC curves (bottom). c. Superposition of the PAM side and non-PAM side densities showing that Cas4 density is largely missing at the non-PAM side, and the non-PAM 3’-overhang is largely disordered. Only the first four nucleotides of the non-PAM 3′-overhang can be traced in the density, along a similar path as in the PAM-side.

Extended Data Fig. 7 In vitro assays to distinguish integration directionality.

a, b. Biochemistry showing that GsuCas4/1-2 is unable to integrate prespacer into the linear form of leader-repeat DNA. c. Successful prespacer integration into a leader-repeat containing plasmid by Cas4/1-2. d. The leader-repeat sequence cloned into the plasmid. We cleaved the leader-repeat sequence via the EcoRI and XhoI sites after the integration assay to further resolve the integration directionality on urea-PAGE. e. Schematic diagram explaining how the integration directionality can be resolved based on the fluorescent ssDNA sizes. f. Integration profile in urea-PAGE when both overhangs are integration-ready (7-nt long). Results showed that from the leader-repeat point of view, integration preferentially initiates from the leader-side, as the spacer-side integration trails after the leader-side integration in the time-course experiment. From the prespacer point of view, the integration directionality is scrambled. Each integration band contains two overlapping fluorescent signals. g. Native PAGE showing that in the concentration-gradient experiment, complex formation between Cas4/1-2 and prespacer takes place in a stepwise and PAM-dependent fashion.

Extended Data Fig. 8 In-depth analysis of the mechanistic coupling between half-integration and PAM cleavage by Cas4.

a. Time-course experiment showing ExoI trims PAM and non-PAM overhangs differently. The non-PAM 3′-overhang was trimmed to within one nucleotide of the preferred length, 7 nt. The PAM-side 3′-overhang was protected by the footprint of Cas4 in the same reaction. b. Time-course experiment resolving the order of events from prespacer processing to full integration. Using the Cas4/1-2 (left set) and Cas4/1-2 plus ExoI (middle set) lanes as controls, the right set of experiment shows ExoI trimming triggers the integration of the non-PAM overhang into the leader-proximal target DNA. This is followed by the stimulation of PAM cleavage, and then the full integration from PAM-overhang to spacer-side target. c. Temperature-dependency of PAM cleavage and spacer-side integration. d. Side-by-side comparison of PAM cleavage at 50 °C, prespacer alone or programmed to the half-integrated state. e. Quantification of the cleaved band in c. and d. revealing the elevated PAM cleavage and full integration when leader-side integration already took place. Data were collected from N = 3 biologically independent experiments and presented with mean ± s.e.m. Statistical significance was assessed by two-tailed t-test, with the exact P values displayed. f. Salt-dependency of PAM cleavage and full integration. gi. Optimization of full integration reaction by defining its time course, Cas2-dependency, and pH-dependency, respectively. j. Defining pH-dependency of PAM cleavage by Cas4. k. SEC analysis of the Cas4/1-2 complex programmed with the half-integration product mimic. Samples in the integrated complex peak was used for cryo-EM data collection and single particle reconstruction. l, Schematics of the half-integration product mimic annealed from oligonucleotides. m. Urea-PAGE analysis of the SEC peak in k. revealing that Cas4/1-2 further catalyzed the full-integration reaction after binding to the half-integration mimic.

Extended Data Fig. 9 Cryo-EM single particle reconstruction of GsuCas4/Cas1-Cas2 programmed with a half-integration mimic.

a. Workflow of cryo-EM data processing. b. Overall cryo-EM density showing resolution distribution, viewing direction distribution plot, and FSC curves of three different snapshots. Left: half-integration, Cas4 disappeared; Middle: full-integration; Right: half-integration, Cas4 still blocking PAM-side.

Extended Data Fig. 10 In-depth analysis of the three snapshots captured from GsuCas4/Cas1-Cas2 programmed with a half-integration mimic.

a. Superposition of cryo-EM reconstructions to reveal the structural differences among three functional states. b. Orientation view of the full integration snapshot for additional interface analysis. The entire leader- repeat DNA is contacted in a quasi-symmetric fashion at the following four regions. c. Contacts from the two Cas1 subunits to the spacer-repeat DNA. The spacer-side DNA density is degenerate and DNA bending is not significant. The leader-recognition α-helix in the catalytic Cas1 is not inserted into the minor groove of the spacer-side DNA. d. The backbone of the central dyad of CRISPR repeat is contacted by the positive charges and a proline-rich motif on the ridge of the Cas2 dimer. e. Immediately adjacent to the catalytic loop, the linker connecting Cas4 to Cas1 is involved in DNA contact. A conserved PRPI motif is exposed upon Cas4 dissociation and is involved in DNA minor groove contact. f. The 4-bp leader region immediately upstream of the CRISPR repeat is favorably recognized and significantly bent upwards by the DNA minor groove insertion of a glycine-rich α-helix in Cas1. As previously revealed, this recognition leads to strong leader-proximal preference at the first half-integration reaction10,11,12. A pair of inverted repeats is found at the border region of the CRISPR repeat. This inverted repeat is recognized at the major groove region by the catalytic Histidine-containing loop in Cas112. g. Overall structure of the “Half-integration, Cas4 still blocking PAM-side” snapshot. This represents an early state, when Cas4 is still engaged in PAM recognition and the spacer-side leader-repeat is not allowed to enter into the integration site. h. The low-resolution EM density defines that the leader-repeat DNA preferentially contact a positively charged patch in Cas1. It should be noted that we are not able to define which specific DNA contact activates Cas4. This will require even higher temporal and spatial resolutions to resolve.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

Supplementary information

Supplementary Figure 1

This file contains the uncropped gels shown in Figs 1, 3, 4 and Extended Data Figs 1, 2, 4, 7, 8.

Reporting Summary

Supplementary Tables

This file contains Supplementary Tables 1, 2, which contain lists of plasmids, primers and reagents used in the study.

Video 1

| Mechanism for Cas4-assisted prespacer biogenesis. This video illustrates the mechanism of Cas4-assisted prespacer biogenesis process. The animation made use of Pymol to interpolate structural transitions from one functional state to the next.

Video 2

| Mechanism for Cas4-assisted directional spacer integration.

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Hu, C., Almendros, C., Nam, K.H. et al. Mechanism for Cas4-assisted directional spacer acquisition in CRISPR–Cas. Nature 598, 515–520 (2021). https://doi.org/10.1038/s41586-021-03951-z

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