201
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Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6. Mol Cell 2019; 76:922-937.e7. [PMID: 31604602 DOI: 10.1016/j.molcel.2019.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/02/2019] [Accepted: 09/06/2019] [Indexed: 12/26/2022]
Abstract
In the arms race against bacteria, bacteriophages have evolved diverse anti-CRISPR proteins (Acrs) that block CRISPR-Cas immunity. Acrs play key roles in the molecular coevolution of bacteria with their predators, use a variety of mechanisms of action, and provide tools to regulate Cas-based genome manipulation. Here, we present structural and functional analyses of AcrIIA6, an Acr from virulent phages, exploring its unique anti-CRISPR action. Our cryo-EM structures and functional data of AcrIIA6 binding to Streptococcus thermophilus Cas9 (St1Cas9) show that AcrIIA6 acts as an allosteric inhibitor and induces St1Cas9 dimerization. AcrIIA6 reduces St1Cas9 binding affinity for DNA and prevents DNA binding within cells. The PAM and AcrIIA6 recognition sites are structurally close and allosterically linked. Mechanistically, AcrIIA6 affects the St1Cas9 conformational dynamics associated with PAM binding. Finally, we identify a natural St1Cas9 variant resistant to AcrIIA6 illustrating Acr-driven mutational escape and molecular diversification of Cas9 proteins.
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202
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Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q. Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. PLoS Biol 2019; 17:e3000496. [PMID: 31603896 PMCID: PMC6808508 DOI: 10.1371/journal.pbio.3000496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/23/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been harnessed as powerful genome editing tools in diverse organisms. However, the off-target effects and the protospacer adjacent motif (PAM) compatibility restrict the therapeutic applications of these systems. Recently, a Streptococcus pyogenes Cas9 (SpCas9) variant, xCas9, was evolved to possess both broad PAM compatibility and high DNA fidelity. Through determination of multiple xCas9 structures, which are all in complex with single-guide RNA (sgRNA) and double-stranded DNA containing different PAM sequences (TGG, CGG, TGA, and TGC), we decipher the molecular mechanisms of the PAM expansion and fidelity enhancement of xCas9. xCas9 follows a unique two-mode PAM recognition mechanism. For non-NGG PAM recognition, xCas9 triggers a notable structural rearrangement in the DNA recognition domains and a rotation in the key PAM-interacting residue R1335; such mechanism has not been observed in the wild-type (WT) SpCas9. For NGG PAM recognition, xCas9 applies a strategy similar to WT SpCas9. Moreover, biochemical and cell-based genome editing experiments pinpointed the critical roles of the E1219V mutation for PAM expansion and the R324L, S409I, and M694I mutations for fidelity enhancement. The molecular-level characterizations of the xCas9 nuclease provide critical insights into the mechanisms of the PAM expansion and fidelity enhancement of xCas9 and could further facilitate the engineering of SpCas9 and other Cas9 orthologs.
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MESH Headings
- Amino Acid Substitution
- CRISPR-Associated Protein 9/chemistry
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Cloning, Molecular
- Clustered Regularly Interspaced Short Palindromic Repeats
- Crystallography, X-Ray
- DNA/chemistry
- DNA/genetics
- DNA/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Editing
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Isoenzymes/chemistry
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Klebsiella pneumoniae/genetics
- Klebsiella pneumoniae/metabolism
- Models, Molecular
- Mutagenesis, Site-Directed/methods
- Mutation
- Nucleotide Motifs
- Protein Binding
- Protein Engineering/methods
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Streptococcus pyogenes/genetics
- Streptococcus pyogenes/metabolism
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Affiliation(s)
- Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hongyuan Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yifei Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yu Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, Shanghai, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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203
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Dasgupta B, Miyashita O, Tama F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj 2019; 1864:129420. [PMID: 31472175 DOI: 10.1016/j.bbagen.2019.129420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial. METHOD We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image. RESULTS The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations. CONCLUSIONS The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail. GENERAL SIGNIFICANCE High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.
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Affiliation(s)
- Bhaskar Dasgupta
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Osamu Miyashita
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Florence Tama
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan; Department of Physics, Graduate School of Science, Nagoya University, Aichi, 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, 464-8601, Japan.
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204
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Abstract
The development of the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system has become a revolutionary step for genome engineering because it enables modification of target genomes. However, many biological applications with the CRISPR/Cas9 system are impeded by off-target effects and loci-dependent nuclease activity with various sgRNAs. Commonly used label-strategy-based CRISPR/Cas9 assays often suffer from possible disturbances to Cas9 activity and a time-consuming labeling procedure. Herein, we for the first time propose a DNA-templated CuNPs-based label-free CRISPR/Cas9 assay, with a low LOD of 0.13 nM and rapid detection in 35 min after CRISPR/Cas9 cleavage. Additionally, the site specificity of the DNA substrate was demonstrated. Through the proposed label-free strategy, a single-base change at a specific loci could lead to a significant reduction of the Cas9 cleavage effect, while the other common genetic modifications might be accepted by the CRIPR/Cas9 system. Therefore, the proposed label-free Cas9 assay may provide a new paradigm for the a priori in vitro CRISPR/Cas9 assay and exploration for in vivo biological applications.
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Affiliation(s)
- Jianyu Hu
- College of Architecture and Environment , Sichuan University , Chengdu 610064 , China
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Min Jiang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Rui Liu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Yi Lv
- Analytical and Testing Center , Sichuan University , Chengdu 610064 , China
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205
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O'Reilly D, Kartje ZJ, Ageely EA, Malek-Adamian E, Habibian M, Schofield A, Barkau CL, Rohilla KJ, DeRossett LB, Weigle AT, Damha MJ, Gagnon KT. Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity. Nucleic Acids Res 2019; 47:546-558. [PMID: 30517736 PMCID: PMC6344873 DOI: 10.1093/nar/gky1214] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeat) endonucleases are at the forefront of biotechnology, synthetic biology and gene editing. Methods for controlling enzyme properties promise to improve existing applications and enable new technologies. CRISPR enzymes rely on RNA cofactors to guide catalysis. Therefore, chemical modification of the guide RNA can be used to characterize structure-activity relationships within CRISPR ribonucleoprotein (RNP) enzymes and identify compatible chemistries for controlling activity. Here, we introduce chemical modifications to the sugar–phosphate backbone of Streptococcus pyogenes Cas9 CRISPR RNA (crRNA) to probe chemical and structural requirements. Ribose sugars that promoted or accommodated A-form helical architecture in and around the crRNA ‘seed’ region were tolerated best. A wider range of modifications were acceptable outside of the seed, especially D-2′-deoxyribose, and we exploited this property to facilitate exploration of greater chemical diversity within the seed. 2′-fluoro was the most compatible modification whereas bulkier O-methyl sugar modifications were less tolerated. Activity trends could be rationalized for selected crRNAs using RNP stability and DNA target binding experiments. Cas9 activity in vitro tolerated most chemical modifications at predicted 2′-hydroxyl contact positions, whereas editing activity in cells was much less tolerant. The biochemical principles of chemical modification identified here will guide CRISPR-Cas9 engineering and enable new or improved applications.
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Affiliation(s)
- Daniel O'Reilly
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Zachary J Kartje
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Eman A Ageely
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Elise Malek-Adamian
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Maryam Habibian
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Annabelle Schofield
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Christopher L Barkau
- Department of Biochemistry & Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Kushal J Rohilla
- Department of Biochemistry & Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Lauren B DeRossett
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Austin T Weigle
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Chemistry & Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, USA.,Department of Biochemistry & Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois 62901, USA
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206
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Kim Y, Lee SJ, Yoon H, Kim N, Lee B, Suh J. Anti‐CRISPR AcrIIC3 discriminates between Cas9 orthologs via targeting the variable surface of the HNH nuclease domain. FEBS J 2019; 286:4661-4674. [DOI: 10.1111/febs.15037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/26/2019] [Accepted: 08/05/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Youngim Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Korea
| | - Sang Jae Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy Seoul National University Gwanak‐gu Korea
- PAL‐XFEL, Pohang Accelerator Laboratory Pohang University of Science and Technology Korea
| | - Hye‐Jin Yoon
- Department of Chemistry, College of Natural Sciences Seoul National University Gwanak‐gu Korea
| | - Nak‐Kyoon Kim
- Advanced Analysis Center Korea Institute of Science and Technology Seoul Korea
| | - Bong‐Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy Seoul National University Gwanak‐gu Korea
| | - Jeong‐Yong Suh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Korea
- Institute for Biomedical Sciences Shinshu University Nagano Japan
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207
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Zhu X, Clarke R, Puppala AK, Chittori S, Merk A, Merrill BJ, Simonović M, Subramaniam S. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Nat Struct Mol Biol 2019; 26:679-685. [PMID: 31285607 PMCID: PMC6842131 DOI: 10.1038/s41594-019-0258-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/24/2019] [Indexed: 12/27/2022]
Abstract
The RNA-guided Cas9 endonuclease from Streptococcus pyogenes is a single-turnover enzyme that displays a stable product state after double-stranded-DNA cleavage. Here, we present cryo-EM structures of precatalytic, postcatalytic and product states of the active Cas9-sgRNA-DNA complex in the presence of Mg2+. In the precatalytic state, Cas9 adopts the 'checkpoint' conformation with the HNH nuclease domain positioned far away from the DNA. Transition to the postcatalytic state involves a dramatic ~34-Å swing of the HNH domain and disorder of the REC2 recognition domain. The postcatalytic state captures the cleaved substrate bound to the catalytically competent HNH active site. In the product state, the HNH domain is disordered, REC2 returns to the precatalytic conformation, and additional interactions of REC3 and RuvC with nucleic acids are formed. The coupled domain motions and interactions between the enzyme and the RNA-DNA hybrid provide new insights into the mechanism of genome editing by Cas9.
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Affiliation(s)
- Xing Zhu
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Clarke
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Anupama K Puppala
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
- Genome Editing Core, University of Illinois at Chicago, Chicago, IL, USA.
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia, Canada.
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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208
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Zuo Z, Zolekar A, Babu K, Lin VJT, Hayatshahi HS, Rajan R, Wang YC, Liu J. Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. eLife 2019; 8:e46500. [PMID: 31361218 PMCID: PMC6706240 DOI: 10.7554/elife.46500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/21/2019] [Indexed: 12/21/2022] Open
Abstract
The CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (SpyCas9), along with a programmable single-guide RNA (sgRNA), has been exploited as a significant genome-editing tool. Despite the recent advances in determining the SpyCas9 structures and DNA cleavage mechanism, the cleavage-competent conformation of the catalytic HNH nuclease domain of SpyCas9 remains largely elusive and debatable. By integrating computational and experimental approaches, we unveiled and validated the activated Cas9-sgRNA-DNA ternary complex in which the HNH domain is neatly poised for cleaving the target DNA strand. In this catalysis model, the HNH employs the catalytic triad of D839-H840-N863 for cleavage catalysis, rather than previously implicated D839-H840-D861, D837-D839-H840, or D839-H840-D861-N863. Our study contributes critical information to defining the catalytic conformation of the HNH domain and advances the knowledge about the conformational activation underlying Cas9-mediated DNA cleavage.
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Affiliation(s)
- Zhicheng Zuo
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
- College of Chemistry and Chemical EngineeringShanghai University of Engineering ScienceShanghaiChina
| | - Ashwini Zolekar
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research CenterUniversity of OklahomaNormanUnited States
| | - Victor JT Lin
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Hamed S Hayatshahi
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research CenterUniversity of OklahomaNormanUnited States
| | - Yu-Chieh Wang
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Jin Liu
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
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209
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Yang M, Peng S, Sun R, Lin J, Wang N, Chen C. The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed by Single-Molecule FRET. Cell Rep 2019; 22:372-382. [PMID: 29320734 DOI: 10.1016/j.celrep.2017.12.048] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 10/28/2017] [Accepted: 12/14/2017] [Indexed: 12/27/2022] Open
Abstract
Off-target binding and cleavage by Cas9 pose major challenges in its application. How the conformational dynamics of Cas9 govern its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single-molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms spontaneously transits among three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We also uncovered surprising long-range allosteric communication between the HNH domain and the RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated that a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the PAM-distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox.
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Affiliation(s)
- Mengyi Yang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Sijia Peng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Ruirui Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Jingdi Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Nan Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
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210
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Berckman EA, Chen W. Exploiting dCas9 fusion proteins for dynamic assembly of synthetic metabolons. Chem Commun (Camb) 2019; 55:8219-8222. [PMID: 31210215 PMCID: PMC7725109 DOI: 10.1039/c9cc04002a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here we reported a new strategy to construct synthetic metabolons using dCas9-guided assembly. Three orthogonal dCas9 proteins were exploited to guide the independent and site-specific assembly of their fusion partners onto a single DNA scaffold. This new platform was applied towards the construction of a two-component cellulosome. Because of the superior binding affinity, the resulting structures exhibited both improved assembly and reducing sugar production. Conditional enzyme assembly was made possible by utilizing toehold-gated sgRNA (thgRNA), which blocks cellulosome formation until the spacer region is unblocked by a RNA trigger. This platform is highly modular owing to the ease of target synthesis, combinations of possible Cas9-fusion arrangements, and expansion to other metabolic pathways.
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Affiliation(s)
- Emily A Berckman
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA. and Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
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211
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Ka D, Jang DM, Han BW, Bae E. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Nucleic Acids Res 2019; 46:9805-9815. [PMID: 30102386 PMCID: PMC6182153 DOI: 10.1093/nar/gky702] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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212
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Thavalingam A, Cheng Z, Garcia B, Huang X, Shah M, Sun W, Wang M, Harrington L, Hwang S, Hidalgo-Reyes Y, Sontheimer EJ, Doudna J, Davidson AR, Moraes TF, Wang Y, Maxwell KL. Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2. Nat Commun 2019; 10:2806. [PMID: 31243272 PMCID: PMC6594998 DOI: 10.1038/s41467-019-10577-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/15/2019] [Indexed: 01/25/2023] Open
Abstract
CRISPR-Cas adaptive immune systems function to protect bacteria from invasion by foreign genetic elements. The CRISPR-Cas9 system has been widely adopted as a powerful genome-editing tool, and phage-encoded inhibitors, known as anti-CRISPRs, offer a means of regulating its activity. Here, we report the crystal structures of anti-CRISPR protein AcrIIC2Nme alone and in complex with Nme1Cas9. We demonstrate that AcrIIC2Nme inhibits Cas9 through interactions with the positively charged bridge helix, thereby preventing sgRNA loading. In vivo phage plaque assays and in vitro DNA cleavage assays show that AcrIIC2Nme mediates its activity through a large electronegative surface. This work shows that anti-CRISPR activity can be mediated through the inhibition of Cas9 complex assembly.
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Affiliation(s)
- Annoj Thavalingam
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Zhi Cheng
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bianca Garcia
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Xue Huang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Megha Shah
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Wei Sun
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Min Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lucas Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sungwon Hwang
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Yurima Hidalgo-Reyes
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jennifer Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada.,Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada.
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213
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Zhang B, Ye Y, Ye W, Perčulija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S. Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Nat Commun 2019; 10:2544. [PMID: 31186424 PMCID: PMC6559982 DOI: 10.1038/s41467-019-10507-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/16/2019] [Indexed: 12/18/2022] Open
Abstract
Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.
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Affiliation(s)
- Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China
| | - Yangmiao Ye
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Weiwei Ye
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Han Jiang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yiyang Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yu Li
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Jing Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Siqi Wang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Qi Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., 10617, Taipei, Taiwan
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
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214
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Palermo G, Casalino L, Magistrato A, Andrew McCammon J. Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations. J Struct Biol 2019; 206:267-279. [PMID: 30880083 PMCID: PMC6637970 DOI: 10.1016/j.jsb.2019.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
Noncoding RNA (ncRNA) has a key role in regulating gene expression, mediating fundamental processes and diseases via a variety of yet unknown mechanisms. Here, we review recent applications of conventional and enhanced Molecular Dynamics (MD) simulations methods to address the mechanistic function of large biomolecular systems that are tightly involved in the ncRNA function and that are of key importance in life sciences. This compendium focuses of three biomolecular systems, namely the CRISPR-Cas9 genome editing machinery, group II intron ribozyme and the ribonucleoprotein complex of the spliceosome, which edit and process ncRNA. We show how the application of a novel accelerated MD simulations method has been key in disclosing the conformational transitions underlying RNA binding in the CRISPR-Cas9 complex, suggesting a mechanism for RNA recruitment and clarifying the conformational changes required for attaining genome editing. As well, we discuss the use of mixed quantum-classical MD simulations in deciphering the catalytic mechanism of RNA splicing as operated by group II intron ribozyme, one of the largest ncRNA structures crystallized so far. Finally, we debate the future challenges and opportunities in the field, discussing the recent application of MD simulations for unraveling the functional biophysics of the spliceosome, a multi-mega Dalton complex of proteins and small nuclear RNAs that performs RNA splicing in humans. This showcase of applications highlights the current talent of MD simulations to dissect atomic-level details of complex biomolecular systems instrumental for the design of finely engineered genome editing machines. As well, this review aims at inspiring future investigations of several other ncRNA regulatory systems, such as micro and small interfering RNAs, which achieve their function and specificity using RNA-based recognition and targeting strategies.
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Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, Bourns College of Engineering, University of California Riverside, 900 University Avenue, Riverside, CA 92521, United States.
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali, Democritos National Simulation Center c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States; Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, United States; National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093, United States
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215
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Klein M, Eslami-Mossallam B, Arroyo DG, Depken M. Hybridization Kinetics Explains CRISPR-Cas Off-Targeting Rules. Cell Rep 2019; 22:1413-1423. [PMID: 29425498 DOI: 10.1016/j.celrep.2018.01.045] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/07/2017] [Accepted: 01/17/2018] [Indexed: 12/26/2022] Open
Abstract
Due to their specificity, efficiency, and ease of programming, CRISPR-associated nucleases are popular tools for genome editing. On the genomic scale, these nucleases still show considerable off-target activity though, posing a serious obstacle to the development of therapies. Off targeting is often minimized by choosing especially high-specificity guide sequences, based on algorithms that codify empirically determined off-targeting rules. A lack of mechanistic understanding of these rules has so far necessitated their ad hoc implementation, likely contributing to the limited precision of present algorithms. To understand the targeting rules, we kinetically model the physics of guide-target hybrid formation. Using only four parameters, our model elucidates the kinetic origin of the experimentally observed off-targeting rules, thereby rationalizing the results from both binding and cleavage assays. We favorably compare our model to published data from CRISPR-Cas9, CRISPR-Cpf1, CRISPR-Cascade, as well as the human Argonaute 2 system.
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Affiliation(s)
- Misha Klein
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, the Netherlands
| | - Behrouz Eslami-Mossallam
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, the Netherlands
| | - Dylan Gonzalez Arroyo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, the Netherlands
| | - Martin Depken
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, the Netherlands.
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216
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Zhang D, Hurst T, Duan D, Chen SJ. Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Proc Natl Acad Sci U S A 2019; 116:8693-8698. [PMID: 30988204 PMCID: PMC6500161 DOI: 10.1073/pnas.1820523116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
While CRISPR/Cas9 is a powerful tool in genome engineering, the on-target activity and off-target effects of the system widely vary because of the differences in guide RNA (gRNA) sequences and genomic environments. Traditional approaches rely on separate models and parameters to treat on- and off-target cleavage activities. Here, we demonstrate that a free-energy scheme dominates the Cas9 editing efficacy and delineate a method that simultaneously considers on-target activities and off-target effects. While data-driven machine-learning approaches learn rules to model particular datasets, they may not be as transferrable to new systems or capable of producing new mechanistic insights as principled physical approaches. By integrating the energetics of R-loop formation under Cas9 binding, the effect of the protospacer adjacent motif sequence, and the folding stability of the whole single guide RNA, we devised a unified, physical model that can apply to any cleavage-activity dataset. This unified framework improves predictions for both on-target activities and off-target efficiencies of spCas9 and may be readily transferred to other systems with different guide RNAs or Cas9 ortholog proteins.
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Affiliation(s)
- Dong Zhang
- Department of Physics, University of Missouri, Columbia, MO 65211
- Department of Biochemistry, University of Missouri, Columbia, MO 65211
- University of Missouri Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Travis Hurst
- Department of Physics, University of Missouri, Columbia, MO 65211
- Department of Biochemistry, University of Missouri, Columbia, MO 65211
- University of Missouri Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211
- Department of Neurology, School of Medicine, University of Missouri, Columbia, MO 65211
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211
- Department of Bioengineering, University of Missouri, Columbia, MO 65211
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO 65211;
- Department of Biochemistry, University of Missouri, Columbia, MO 65211
- University of Missouri Informatics Institute, University of Missouri, Columbia, MO 65211
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217
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Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9. Nat Commun 2019; 10:1968. [PMID: 31036811 PMCID: PMC6488586 DOI: 10.1038/s41467-019-09741-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/29/2019] [Indexed: 12/26/2022] Open
Abstract
The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets bearing a protospacer adjacent motif (PAM) and complementarity to an RNA guide. Unlike other Cas9 orthologs, Corynebacterium diphtheriae Cas9 (CdCas9) recognizes the promiscuous NNRHHHY PAM. However, the CdCas9-mediated PAM recognition mechanism remains unknown. Here, we report the crystal structure of CdCas9 in complex with the guide RNA and its target DNA at 2.9 Å resolution. The structure reveals that CdCas9 recognizes the NNRHHHY PAM via a combination of van der Waals interactions and base-specific hydrogen bonds. Moreover, we find that CdCas9 exhibits robust DNA cleavage activity with the optimal 22-nucleotide length guide RNAs. Our findings highlight the mechanistic diversity of the PAM recognition by Cas9 orthologs, and provide a basis for the further engineering of the CRISPR-Cas9 genome-editor nucleases.
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218
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Zhu Y, Gao A, Zhan Q, Wang Y, Feng H, Liu S, Gao G, Serganov A, Gao P. Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins. Mol Cell 2019; 74:296-309.e7. [PMID: 30850331 PMCID: PMC6750902 DOI: 10.1016/j.molcel.2019.01.038] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/19/2018] [Accepted: 01/27/2019] [Indexed: 12/13/2022]
Abstract
Anti-CRISPR proteins (Acrs) targeting CRISPR-Cas9 systems represent natural "off switches" for Cas9-based applications. Recently, AcrIIC1, AcrIIC2, and AcrIIC3 proteins were found to inhibit Neisseria meningitidis Cas9 (NmeCas9) activity in bacterial and human cells. Here we report biochemical and structural data that suggest molecular mechanisms of AcrIIC2- and AcrIIC3-mediated Cas9 inhibition. AcrIIC2 dimer interacts with the bridge helix of Cas9, interferes with RNA binding, and prevents DNA loading into Cas9. AcrIIC3 blocks the DNA loading step through binding to a non-conserved surface of the HNH domain of Cas9. AcrIIC3 also forms additional interactions with the REC lobe of Cas9 and induces the dimerization of the AcrIIC3-Cas9 complex. While AcrIIC2 targets Cas9 orthologs from different subtypes, albeit with different efficiency, AcrIIC3 specifically inhibits NmeCas9. Structure-guided changes in NmeCas9 orthologs convert them into anti-CRISPR-sensitive proteins. Our studies provide insights into anti-CRISPR-mediated suppression mechanisms and guidelines for designing regulatory tools in Cas9-based applications.
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Affiliation(s)
- Yalan Zhu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ang Gao
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Qi Zhan
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Wang
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Feng
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Songqing Liu
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guangxia Gao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
| | - Pu Gao
- CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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219
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Das J, Bhatia P, Singh A. CRISP Points on Establishing CRISPR- Cas9 In Vitro Culture Experiments in a Resource Constraint Haematology Oncology Research Lab. Indian J Hematol Blood Transfus 2019; 35:208-214. [PMID: 30988554 DOI: 10.1007/s12288-018-1008-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022] Open
Abstract
Gene editing research has seen rapid growth over the past decade or so, however with the discovery of CRISPR-Cas9 gene editing tool in recent years, the same has witnessed a global interest with many scientists and research groups worldwide carrying out cutting edge experiments to target various diseases and cancers and develop a cure. This has been made possible partially due to the ease of use and flexibility of the CRISPR-Cas9 system as compared to other conventional gene editing tools. Hence, CRISPR-Cas9 has found its way into most basic molecular laboratories and within reach of most low-middle income research groups. Despite these favourable advantages, there exists a cost barrier and lack of proper knowledge and awareness on the correct work flow desired, especially in molecular laboratories looking forward to develop and experiment with high end research. This mini review attempts to iron out these factors and project an algorithmic approach to tide over and establish a workable in vitro gene editing experiment in a resource constraint haematology oncology laboratory setting. However, the basic principle and steps outlined in this review can also be translated for research in any other medical specialty laboratory setting.
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Affiliation(s)
- Jhumki Das
- 1Pediatric Allergy Immunology Unit, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Prateek Bhatia
- 2Pediatric Hematology-Oncology Unit, Advanced Paediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Aditya Singh
- 3Pediatric Hematology-Oncology Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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220
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Babu K, Amrani N, Jiang W, Yogesha S, Nguyen R, Qin PZ, Rajan R. Bridge Helix of Cas9 Modulates Target DNA Cleavage and Mismatch Tolerance. Biochemistry 2019; 58:1905-1917. [PMID: 30916546 PMCID: PMC6496953 DOI: 10.1021/acs.biochem.8b01241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection for bacteria and archaea against intruding genomic materials. The programmable nature of CRISPR-targeting mechanisms has enabled their adaptation as powerful genome engineering tools. Cas9, a type II CRISPR effector protein, has been widely used for gene-editing applications owing to the fact that a single-guide RNA can direct Cas9 to cleave desired genomic targets. An understanding of the role of different domains of the protein and guide RNA-induced conformational changes of Cas9 in selecting target DNA has been and continues to enable development of Cas9 variants with reduced off-targeting effects. It has been previously established that an arginine-rich bridge helix (BH) present in Cas9 is critical for its activity. In the present study, we show that two proline substitutions within a loop region of the BH of Streptococcus pyogenes Cas9 impair the DNA cleavage activity by accumulating nicked products and reducing target DNA linearization. This in turn imparts a higher selectivity in DNA targeting. We discuss the probable mechanisms by which the BH-loop contributes to target DNA recognition.
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Affiliation(s)
- Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Sherman Center, AS5.2007, Worcester MA 01605, USA
| | - Wei Jiang
- Department of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, CA, 90089, USA
| | - S.D. Yogesha
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
- Current Address: Krystal Biotech, Inc. 2100 Wharton Street, Suite 701 Pittsburgh, PA, 15203, USA
| | - Richard Nguyen
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
- Current Address: College of Medicine, University of Oklahoma, Stanton L Young Blvd, Oklahoma City, OK 73117
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, CA, 90089, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
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221
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Gisler S, Gonçalves JP, Akhtar W, de Jong J, Pindyurin AV, Wessels LFA, van Lohuizen M. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency. Nat Commun 2019; 10:1598. [PMID: 30962441 PMCID: PMC6453899 DOI: 10.1038/s41467-019-09551-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5' overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.
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Affiliation(s)
- Santiago Gisler
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
- Data & Translational Sciences Group, UCB Biosciences GmbH, Alfred-Nobel-Straße 10, Monheim am Rhein, 40789, Germany
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
- Division of Gene Regulation, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands.
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
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222
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Li Y, Teng X, Zhang K, Deng R, Li J. RNA Strand Displacement Responsive CRISPR/Cas9 System for mRNA Sensing. Anal Chem 2019; 91:3989-3996. [PMID: 30810036 DOI: 10.1021/acs.analchem.8b05238] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 has already become a powerful tool for genomic manipulation, and further engineering of the system allows it to be precisely regulated in response to external signals, thus, broadening its application possibilities, such as biosensing or bioimaging. However, most stimuli-responsive CRISPR systems are built based on elaborately designed and engineered inducible Cas9 proteins, and external stimuli are still mostly limited as small molecules and light. To construct more precise and easy-to-build responsive CRISPR systems and broaden their responsive species, we seek to engineer conditional guide RNA, rather than Cas9 protein, to mediate conditional CRISPR corresponding to logic operation. Here, we construct mRNA-sensing CRISPR by gRNA reconfiguration and toehold mediated strand displacement, in which each target site could be independently controlled. We show that switches can be embedded into the gRNA and used as RNA sensors, capable of detecting multiple mRNA inputs orthogonally and providing CRISPR/Cas9 response outputs. NOR and NAND logical gates are also constructed, demonstrating its orthogonality and programmability. This strategy promises potential uses in constructing genetic circuits to detect endogenous mRNAs and initiate cellular responses.
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Affiliation(s)
- Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
- School of Pharmaceutical Sciences , Zhengzhou University , Zhengzhou 450001 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China
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223
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Xiao Y, Shi K, Qu Y, Chu B, Qian Z. Engineering Nanoparticles for Targeted Delivery of Nucleic Acid Therapeutics in Tumor. Mol Ther Methods Clin Dev 2019; 12:1-18. [PMID: 30364598 PMCID: PMC6197778 DOI: 10.1016/j.omtm.2018.09.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the past 10 years, with the increase of investment in clinical nano-gene therapy, there are many trials that have been discontinued due to poor efficacy and serious side effects. Therefore, it is particularly important to design a suitable gene delivery system. In this paper, we introduce the application of liposomes, polymers, and inorganics in gene delivery; also, different modifications with some stimuli-responsive systems can effectively improve the efficiency of gene delivery and reduce cytotoxicity and other side effects. Besides, the co-delivery of chemotherapy drugs with a drug tolerance-related gene or oncogene provides a better theoretical basis for clinical cancer gene therapy.
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Affiliation(s)
- Yao Xiao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Kun Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ying Qu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Bingyang Chu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Zhiyong Qian
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, China
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224
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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225
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Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
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Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
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226
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RNA-Independent DNA Cleavage Activities of Cas9 and Cas12a. Cell Rep 2019; 21:3728-3739. [PMID: 29281823 PMCID: PMC5760271 DOI: 10.1016/j.celrep.2017.11.100] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/13/2017] [Accepted: 11/29/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with sequence-specific protection against invading mobile genetic elements. In the presence of divalent metal ions, Cas9 and Cas12a (formerly Cpf1) proteins target and cleave DNA that is complementary to a cognate guide RNA. The recognition of a protospacer adjacent motif (PAM) sequence in the target DNA by Cas9 and Cas12a is essential for cleavage. This RNA-guided DNA targeting is widely used for gene-editing methods. Here, we show that Francisella tularensis novicida (Fno) Cas12a, FnoCas9, and Streptococcus pyogenes Cas9 (SpyCas9) cleave DNA without a guide RNA in the presence of Mn2+ ions. Substrate requirements for the RNA-independent activity vary. FnoCas9 preferentially nicks double-stranded plasmid, SpyCas9 degrades single-stranded plasmid, and FnoCas12a cleaves both substrates. These observations suggest that the identities and levels of intracellular metals, along with the Cas9/Cas12a ortholog employed, could have significant impacts in genome editing applications.
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227
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Guo M, Ren K, Zhu Y, Tang Z, Wang Y, Zhang B, Huang Z. Structural insights into a high fidelity variant of SpCas9. Cell Res 2019; 29:183-192. [PMID: 30664728 PMCID: PMC6460432 DOI: 10.1038/s41422-018-0131-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/11/2018] [Indexed: 01/24/2023] Open
Abstract
The RNA-guided endonucleases of the CRISPR-Cas9 system, including the most widely used Cas9 from Streptococcus pyogenes (SpCas9), are becoming a robust genome editing tool in model organisms and hold immense promise for therapeutic applications. Many strategies have been employed to overcome the limitations caused by SpCas9's off-target effects and its stringent requirement for the protospacer adjacent motif (PAM) sequence. However, the structural mechanisms underlying these strategies remain undefined. Here, we present crystal structure of a SpCas9 variant, xCas9 3.7 that has broad PAM compatibility and high DNA targeting specificity, in complex with a single-guide RNA and its double-stranded DNA targets. Structural comparison revealed that salt bridge-stabilized R1335 is critical for the stringent selection of PAM sequence by SpCas9. Unrestricted rotamerization of this residue by the E1219V mutation in xCas9 3.7 lessens the stringency for PAM recognition and allows SpCas9 to recognize multiple PAM sequences as further supported by biochemical data. Compared to those in wild-type (WT) SpCas9, REC2 and REC3 domains in xCas9 3.7 undergo striking conformational changes, leading to reduced contact with DNA substrate. SpCas9 mutants engineered to display less interaction with DNA and have conformationally more flexible REC2 and REC3 domains display enhanced specificity for DNA substrates in both biochemical and cellular assays. Taken together, our findings reveal the structural mechanisms underlying the broadened PAM compatibility and high DNA fidelity of xCas9 3.7, which can assist rational engineering of more efficient SpCas9 variants and probably other Cas9 orthologs.
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Affiliation(s)
- Minghui Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China
| | - Kuan Ren
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China
| | - Ziyun Tang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China
| | - Yuhang Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China
| | - Bailing Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150080, China.
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228
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Abstract
CRISPR-Cas9 is a bacterial immune system with exciting applications for genome editing. In spite of extensive experimental characterization, the active site chemistry of the RuvC domain-which performs DNA cleavages-has remained elusive. Its knowledge is key for structure-based engineering aimed at improving DNA cleavages. Here, we deliver an in-depth characterization by using quantum-classical (QM/MM) molecular dynamics (MD) simulations and a Gaussian accelerated MD method, coupled with bioinformatics analysis. We disclose a two-metal aided architecture in the RuvC active site, which is poised to operate DNA cleavages, in analogy with other DNA/RNA processing enzymes. The conformational dynamics of the RuvC domain further reveals that an "arginine finger" stably contacts the scissile phosphate, with the function of stabilizing the active complex. Remarkably, the formation of a catalytically competent state of the RuvC domain is only observed upon the conformational activation of the other nuclease domain of CRISPR-Cas9-i.e., the HNH domain-such allowing concerted cleavages of double stranded DNA. This structure is in agreement with the available experimental data and remarkably differs from previous models based on classical mechanics, demonstrating also that only quantum mechanical simulations can accurately describe the metal-aided active site in CRISPR-Cas9. This fully catalytic structure-in which both the HNH and RuvC domains are prone to perform DNA cleavages-constitutes a stepping-stone for understanding DNA cleavage and specificity. It calls for novel experimental verifications and offers the structural foundations for engineering efforts aimed at improving the genome editing capability of CRISPR-Cas9.
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Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, Bourns College of Engineering , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States
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229
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Liu L, Yin M, Wang M, Wang Y. Phage AcrIIA2 DNA Mimicry: Structural Basis of the CRISPR and Anti-CRISPR Arms Race. Mol Cell 2019; 73:611-620.e3. [PMID: 30606466 DOI: 10.1016/j.molcel.2018.11.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/04/2018] [Accepted: 11/09/2018] [Indexed: 12/27/2022]
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems provide prokaryotic cells with adaptive immunity against invading bacteriophages. Bacteriophages counteract bacterial responses by encoding anti-CRISPR inhibitor proteins (Acr). However, the structural basis for their inhibitory actions remains largely unknown. Here, we report the crystal structure of the AcrIIA2-SpyCas9-sgRNA (single-guide RNA) complex at 3.3 Å resolution. We show that AcrIIA2 binds SpyCas9 at a position similar to the target DNA binding region. More specifically, AcrIIA2 interacts with the protospacer adjacent motif (PAM) recognition residues of Cas9, preventing target double-stranded DNA (dsDNA) detection. Thus, phage-encoded AcrIIA2 appears to act as a DNA mimic that blocks subsequent dsDNA binding by virtue of its highly acidic residues, disabling bacterial Cas9 by competing with target dsDNA binding with a binding motif distinct from AcrIIA4. Our study provides a more detailed mechanistic understanding of AcrIIA2-mediated inhibition of SpyCas9, the most widely used genome-editing tool, opening new avenues for improved regulatory precision during genome editing.
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Affiliation(s)
- Liang Liu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Maolu Yin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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230
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Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA. Temperature-Responsive Competitive Inhibition of CRISPR-Cas9. Mol Cell 2019; 73:601-610.e5. [PMID: 30595438 PMCID: PMC6480404 DOI: 10.1016/j.molcel.2018.11.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/23/2018] [Accepted: 11/14/2018] [Indexed: 01/17/2023]
Abstract
CRISPR-Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory "anti-CRISPR" (Acr) proteins, including six inhibitors (AcrIIA1-AcrIIA6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here that AcrIIA2 and its more potent homolog, AcrIIA2b, prevent Cas9 binding to DNA by occluding protein residues required for DNA binding. Cryo-EM-determined structures of AcrIIA2 or AcrIIA2b bound to S. pyogenes Cas9 reveal a mode of competitive inhibition of DNA binding that is distinct from other known Acrs. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arise from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. These findings expand the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially, and conditionally.
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Affiliation(s)
- Fuguo Jiang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jun-Jie Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Beatriz A Osuna
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joel D Berry
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin J Rauch
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Berkeley; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA; Howard Hughes Medical Institute, Berkeley; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA.
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231
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Swarts DC, Jinek M. Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. Mol Cell 2019; 73:589-600.e4. [PMID: 30639240 PMCID: PMC6858279 DOI: 10.1016/j.molcel.2018.11.021] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/14/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA in cis and non-target single-stranded DNAs (ssDNAs) in trans. To elucidate the molecular basis for both DNase cleavage modes, we performed structural and biochemical studies on Francisella novicida Cas12a. We show that guide RNA-target strand DNA hybridization conformationally activates Cas12a, triggering its trans-acting, non-specific, single-stranded DNase activity. In turn, cis cleavage of double-stranded DNA targets is a result of protospacer adjacent motif (PAM)-dependent DNA duplex unwinding, electrostatic stabilization of the displaced non-target DNA strand, and ordered sequential cleavage of the non-target and target DNA strands. Cas12a releases the PAM-distal DNA cleavage product and remains bound to the PAM-proximal DNA cleavage product in a catalytically competent, trans-active state. Together, these results provide a revised model for the molecular mechanisms of both the cis- and the trans-acting DNase activities of Cas12a enzymes, enabling their further exploitation as genome editing tools.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Enzyme Activation
- Francisella/enzymology
- Francisella/genetics
- Gene Editing/methods
- Models, Molecular
- Nucleic Acid Conformation
- Protein Conformation
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Daan C Swarts
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
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232
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Wu X, Mao S, Ying Y, Krueger CJ, Chen AK. Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:119-128. [PMID: 30710789 PMCID: PMC6620262 DOI: 10.1016/j.gpb.2018.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/11/2018] [Accepted: 10/31/2018] [Indexed: 12/26/2022]
Abstract
Chromatin conformation, localization, and dynamics are crucial regulators of cellular behaviors. Although fluorescence in situ hybridization-based techniques have been widely utilized for investigating chromatin architectures in healthy and diseased states, the requirement for cell fixation precludes the comprehensive dynamic analysis necessary to fully understand chromatin activities. This has spurred the development and application of a variety of imaging methodologies for visualizing single chromosomal loci in the native cellular context. In this review, we describe currently-available approaches for imaging single genomic loci in cells, with special focus on clustered regularly interspaced short palindromic repeats (CRISPR)-based imaging approaches. In addition, we discuss some of the challenges that limit the application of CRISPR-based genomic imaging approaches, and potential solutions to address these challenges. We anticipate that, with continued refinement of CRISPR-based imaging techniques, significant understanding can be gained to help decipher chromatin activities and their relevance to cellular physiology and pathogenesis.
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Affiliation(s)
- Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
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233
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Abstract
Bacterial adaptive immune systems employ clustered regularly interspaced short palindromic repeats (CRISPR) along with their CRISPR-associated genes (Cas) to form CRISPR RNA (crRNA)-guided surveillance complexes, which target foreign nucleic acids for destruction. Cas9 is unique in that it is composed of a single polypeptide that utilizes both a crRNA and a trans-activating crRNA (tracrRNA) or a single guide RNA to create double-stranded breaks in sequences complementary to the RNA via the HNH and RuvC nuclease domains. Cas9 has become a revolutionary tool for gene-editing applications. Here, we describe methods for studying the cleavage activities of Cas9. We describe protocols for rapid quench-flow and stopped-flow kinetics and interpretation of the results. The protocols detailed here will be paramount for understanding the mechanistic basis for specificity of this enzyme, especially in efforts to improve accuracy for clinical use.
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Affiliation(s)
- Mu-Sen Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States; Institute for Molecular and Cellular Biology, University of Texas at Austin, Austin, TX, United States
| | - Shanzhong Gong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States; Institute for Molecular and Cellular Biology, University of Texas at Austin, Austin, TX, United States
| | - Helen-Hong Yu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States; Institute for Molecular and Cellular Biology, University of Texas at Austin, Austin, TX, United States
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States; Institute for Molecular and Cellular Biology, University of Texas at Austin, Austin, TX, United States; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, United States; LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, United States.
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States; Institute for Molecular and Cellular Biology, University of Texas at Austin, Austin, TX, United States.
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234
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Liang Y, Eudes A, Yogiswara S, Jing B, Benites VT, Yamanaka R, Cheng-Yue C, Baidoo EE, Mortimer JC, Scheller HV, Loqué D. A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:130. [PMID: 31143243 PMCID: PMC6532251 DOI: 10.1186/s13068-019-1467-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/14/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Single guide RNA (sgRNA) selection is important for the efficiency of CRISPR/Cas9-mediated genome editing. However, in plants, the rules governing selection are not well established. RESULTS We developed a facile transient assay to screen sgRNA efficiency. We then used it to test top-performing bioinformatically predicted sgRNAs for two different Arabidopsis genes. In our assay, these sgRNAs had vastly different editing efficiencies, and these efficiencies were replicated in stably transformed Arabidopsis lines. One of the genes, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT), is an essential gene, required for lignin biosynthesis. Previously, HCT function has been studied using gene silencing. Here, to avoid the negative growth effects that are due to the loss of HCT activity in xylem vessels, we used a fiber-specific promoter to drive CAS9 expression. Two independent transgenic lines showed the expected lignin decrease. Successful editing was confirmed via the observation of mutations at the HCT target loci, as well as an approximately 90% decrease in HCT activity. Histochemical analysis and a normal growth phenotype support the fiber-specific knockout of HCT. For the targeting of the second gene, Golgi-localized nucleotide sugar transporter2 (GONST2), a highly efficient sgRNA drastically increased the rate of germline editing in T1 generation. CONCLUSIONS This screening method is widely applicable, and the selection and use of efficient sgRNAs will accelerate the process of expanding germplasm for both molecular breeding and research. In addition, this, to the best of our knowledge, is the first application of constrained genome editing to obtain chimeric plants of essential genes, thereby providing a dominant method to avoid lethal growth phenotypes.
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Affiliation(s)
- Yan Liang
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Beibei Jing
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Veronica T. Benites
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Reo Yamanaka
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- School of Public Health, University of California, Berkeley, CA 94720 USA
| | - Clarabelle Cheng-Yue
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Edward E. Baidoo
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jenny C. Mortimer
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
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235
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Yourik P, Fuchs RT, Mabuchi M, Curcuru JL, Robb GB. Staphylococcus aureus Cas9 is a multiple-turnover enzyme. RNA (NEW YORK, N.Y.) 2019; 25:35-44. [PMID: 30348755 PMCID: PMC6298560 DOI: 10.1261/rna.067355.118] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 10/18/2018] [Indexed: 05/21/2023]
Abstract
Cas9 nuclease is the key effector of type II CRISPR adaptive immune systems found in bacteria. The nuclease can be programmed by a single guide RNA (sgRNA) to cleave DNA in a sequence-specific manner. This property has led to its widespread adoption as a genome editing tool in research laboratories and holds great promise for biotechnological and therapeutic applications. The general mechanistic features of catalysis by Cas9 homologs are comparable; however, a high degree of diversity exists among the protein sequences, which may result in subtle mechanistic differences. S. aureus (SauCas9) and especially S. pyogenes (SpyCas9) are among the best-characterized Cas9 proteins and share ∼17% sequence identity. A notable feature of SpyCas9 is an extremely slow rate of reaction turnover, which is thought to limit the amount of substrate DNA cleavage. Using in vitro biochemistry and enzyme kinetics, we directly compare SpyCas9 and SauCas9 activities. Here, we report that in contrast to SpyCas9, SauCas9 is a multiple-turnover enzyme, which to our knowledge is the first report of such activity in a Cas9 homolog. We also show that DNA cleaved with SauCas9 does not undergo any detectable single-stranded degradation after the initial double-stranded break observed previously with SpyCas9, thus providing new insights and considerations for future design of CRISPR/Cas9-based applications.
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Affiliation(s)
- Paul Yourik
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, Massachusetts 01938, USA
| | - Ryan T Fuchs
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, Massachusetts 01938, USA
| | - Megumu Mabuchi
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, Massachusetts 01938, USA
| | - Jennifer L Curcuru
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, Massachusetts 01938, USA
| | - G Brett Robb
- RNA and Genome Editing, New England Biolabs Inc., Ipswich, Massachusetts 01938, USA
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236
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Wilkinson RA, Martin C, Nemudryi AA, Wiedenheft B. CRISPR RNA-guided autonomous delivery of Cas9. Nat Struct Mol Biol 2019; 26:14-24. [PMID: 30598555 PMCID: PMC7703833 DOI: 10.1038/s41594-018-0173-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/13/2018] [Indexed: 02/06/2023]
Abstract
Cas9 is an endonuclease that can be programed to autonomously deliver diverse effectors to specified genetic addresses. High-resolution structures of this protein and its associated CRISPR RNA guide explain the molecular mechanisms of CRISPR-RNA-guided DNA recognition and provide a molecular blueprint that has facilitated structure-guided functional remodeling. Here we retrace events that led from early efforts to understand the central role of Cas9 in CRISPR-mediated adaptive immunity to contemporary efforts aimed at developing and deploying this enzyme for programmable genetic editing.
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Affiliation(s)
- Royce A Wilkinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Coleman Martin
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Artem A Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA.
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237
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Abstract
Though making up nearly half of the known CRISPR-Cas9 family of enzymes, the Type II-C CRISPR-Cas9 has been underexplored for their molecular mechanisms and potential in safe gene editing applications. In comparison with the more popular Type II-A CRISPR-Cas9, the Type II-C enzymes are generally smaller in size and utilize longer base pairing in identification of their DNA substrates. These characteristics suggest easier portability and potentially less off-targets for Type II-C in gene editing applications. We describe identification and biochemical characterization of a thermophilic Type II-C CRISPR-Cas from Acidothermus cellulolyticus (AceCas9). We describe several library-based methods that enabled us to identify the PAM sequence and elements critical to protospacer mismatch surveillance of AceCas9.
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238
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Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, Settle AH, Lied AM, McGovern K, Fuller CK, Cameron P, Fazzio TG, Zhu LJ, Wolfe SA, Sontheimer EJ. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol 2018; 19:214. [PMID: 30518407 PMCID: PMC6282386 DOI: 10.1186/s13059-018-1591-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/17/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wildtype SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively large open reading frame, limiting its utility in applications that require size-restricted delivery strategies such as adeno-associated virus vectors. In contrast, some genome-editing-validated Cas9 orthologs are considerably smaller and therefore better suited for viral delivery. RESULTS Here we show that wildtype NmeCas9, when programmed with guide sequences of the natural length of 24 nucleotides, exhibits a nearly complete absence of unintended editing in human cells, even when targeting sites that are prone to off-target activity with wildtype SpyCas9. We also validate at least six variant protospacer adjacent motifs (PAMs), in addition to the preferred consensus PAM (5'-N4GATT-3'), for NmeCas9 genome editing in human cells. CONCLUSIONS Our results show that NmeCas9 is a naturally high-fidelity genome-editing enzyme and suggest that additional Cas9 orthologs may prove to exhibit similarly high accuracy, even without extensive engineering.
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Affiliation(s)
- Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Xin D Gao
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Raed Ibraheim
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Present Address: Bluebird bio, Cambridge, MA, USA
| | - Kanae E Sasaki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Present Address: Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Tong Wu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Paul D Donohoue
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Alexander H Settle
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
- Present Address: Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra M Lied
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Kyle McGovern
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
- Present Address: Sangamo Therapeutics, Inc., Richmond, CA, USA
| | - Chris K Fuller
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Peter Cameron
- Caribou Biosciences, Inc., 2929 7th Street, Suite 105, Berkeley, CA, 94710, USA
| | - Thomas G Fazzio
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Lihua Julie Zhu
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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239
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Zhang Y, Zou J, Zhao X, Yuan Z, Yi Z. Hepatitis C virus NS5A inhibitor daclatasvir allosterically impairs NS4B-involved protein-protein interactions within the viral replicase and disrupts the replicase quaternary structure in a replicase assembly surrogate system. J Gen Virol 2018; 100:69-83. [PMID: 30516462 DOI: 10.1099/jgv.0.001180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Daclatasvir (DCV) is a highly potent direct-acting antiviral that targets the non-structural protein 5A (NS5A) of hepatitis C virus (HCV) and has been used with great clinical success. Previous studies have demonstrated its impact on viral replication complex assembly. However, the precise mechanisms by which DCV impairs the replication complex assembly remains elusive. In this study, by using HCV subgenomic replicons and a viral replicase assembly surrogate system in which the HCV NS3-5B polyprotein is expressed to mimic the viral replicase assembly, we assessed the impact of DCV on the aggregation and tertiary structure of NS5A, the protein-protein interactions within the viral replicase and the quaternary structure of the viral replicase. We found that DCV did not affect aggregation and tertiary structure of NS5A. DCV induced a quaternary structural change of the viral replicase, as evidenced by selective increase of NS4B's sensitivity to proteinase K digestion. Mechanically, DCV impaired the NS4B-involved protein-protein interactions within the viral replicase. These phenotypes were consistent with the phenotypes of several reported NS4B mutants that abolish the viral replicase assembly. The DCV-resistant mutant Y93H was refractory to the DCV-induced reduction of the NS4B-involved protein interactions and the quaternary structural change of the viral replicase. In addition, Y93H reduced NS4B-involved protein-protein interactions within the viral replicase and attenuated viral replication. We propose that DCV may induce a positional change of NS5A, which allosterically affects protein interactions within the replicase components and disrupts replicase assembly.
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Affiliation(s)
- Yang Zhang
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Jingyi Zou
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Xiaomin Zhao
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Zhenghong Yuan
- 1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Zhigang Yi
- 2Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Fudan University, Shanghai, PR China.,1Key Laboratory of Medical Molecular Virology and Department of Medical Microbiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
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240
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Mekler V, Kuznedelov K, Minakhin L, Murugan K, Sashital DG, Severinov K. CRISPR-Cas molecular beacons as tool for studies of assembly of CRISPR-Cas effector complexes and their interactions with DNA. Methods Enzymol 2018; 616:337-363. [PMID: 30691650 PMCID: PMC6930961 DOI: 10.1016/bs.mie.2018.10.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas systems protect prokaryotic cells from invading phages and plasmids by recognizing and cleaving foreign nucleic acid sequences specified by CRISPR RNA spacer sequences. Several CRISPR-Cas systems have been widely used as tool for genetic engineering. In DNA-targeting CRISPR-Cas nucleoprotein effector complexes, the CRISPR RNA forms a hybrid with the complementary strand of foreign DNA, displacing the noncomplementary strand to form an R-loop. The DNA interrogation and R-loop formation involve several distinct steps the molecular details of which are not fully understood. This chapter describes a recently developed fluorometric Cas beacon assay that may be used for measuring of specific affinity of various CRISPR-Cas complexes for unlabeled target DNA and model DNA probes. The Cas beacon approach also can provide a sensitive method for monitoring the kinetics of assembly of CRISPR-Cas complexes.
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Affiliation(s)
- Vladimir Mekler
- Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ, United States.
| | - Konstantin Kuznedelov
- Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ, United States
| | - Leonid Minakhin
- Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ, United States
| | - Karthik Murugan
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Ames, IA, United States
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Ames, IA, United States
| | - Konstantin Severinov
- Waksman Institute of Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, State University of New Jersey, Piscataway, NJ, United States; Center for Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
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241
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Zhu Y, Huang Z. Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools. Natl Sci Rev 2018; 6:438-451. [PMID: 34691893 PMCID: PMC8291651 DOI: 10.1093/nsr/nwy150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.
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Affiliation(s)
- Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
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242
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A CRISPR-Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 2018; 9:5012. [PMID: 30479331 PMCID: PMC6258682 DOI: 10.1038/s41467-018-07324-5] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 12/26/2022] Open
Abstract
Although polymerase chain reaction (PCR) is the most widely used method for DNA amplification, the requirement of thermocycling limits its non-laboratory applications. Isothermal DNA amplification techniques are hence valuable for on-site diagnostic applications in place of traditional PCR. Here we describe a true isothermal approach for amplifying and detecting double-stranded DNA based on a CRISPR–Cas9-triggered nicking endonuclease-mediated Strand Displacement Amplification method (namely CRISDA). CRISDA takes advantage of the high sensitivity/specificity and unique conformational rearrangements of CRISPR effectors in recognizing the target DNA. In combination with a peptide nucleic acid (PNA) invasion-mediated endpoint measurement, the method exhibits attomolar sensitivity and single-nucleotide specificity in detection of various DNA targets under a complex sample background. Additionally, by integrating the technique with a Cas9-mediated target enrichment approach, CRISDA exhibits sub-attomolar sensitivity. In summary, CRISDA is a powerful isothermal tool for ultrasensitive and specific detection of nucleic acids in point-of-care diagnostics and field analyses. Isothermal DNA amplification techniques are useful for diagnostic applications in place of traditional PCR. Here the authors describe CRISDA, which combines CRISPR–Cas9 with strand displacement amplification and exhibits attomolar sensitivity and single-nucleotide specificity in DNA detection.
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243
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Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nat Methods 2018; 15:947-954. [PMID: 30377372 PMCID: PMC6636682 DOI: 10.1038/s41592-018-0172-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022]
Abstract
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Shiheng Liu
- Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Kevin P Larsen
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Z Hong Zhou
- Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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244
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Guzina J, Chen WH, Stankovic T, Djordjevic M, Zdobnov E, Djordjevic M. In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence. Front Genet 2018; 9:474. [PMID: 30386377 PMCID: PMC6199352 DOI: 10.3389/fgene.2018.00474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023] Open
Abstract
In addition to its well-established defense function, CRISPR/Cas can also exhibit crucial non-canonical activity through endogenous gene expression regulation, which was found to mainly affect bacterial virulence. These non-canonical functions depend on scaRNA, which is a small RNA encoded outside of CRISPR array, that is typically flanked by a transcription start site (TSS) and a terminator, and is in part complementary to another small CRISPR/Cas-associated RNA (tracrRNAs). Identification of scaRNAs is however largely complicated by the scarcity of RNA-Seq data across different bacteria, so that they were identified only in a relatively rare CRISPR/Cas subtype (IIB), and the possibility of finding them in other Type II systems is currently unclear. This study presents the first effort toward systematic detection of small CRISPR/Cas-associated regulatory RNAs, where obtained predictions can guide future experiments. The core of our approach is ab initio detection of small RNAs from bacterial genome, which is based on jointly predicting transcription signals - TSS and terminators - and homology to CRISPR array repeat. Particularly, we employ our improved approach for detecting bacterial TSS, since accurate TSS detection is the main limiting factor for accurate small RNA prediction. We also explore how our predictions match to available RNA-Seq data and analyze their conservation across related bacterial species. In Type IIB systems, our predictions are consistent with experimental data, and we systematically identify scaRNAs throughout this subtype. Furthermore, we identify scaRNA:tracrRNA pairs in a number of IIA/IIC systems, where the appearance of scaRNAs co-occurs with the strains being pathogenic. RNA-Seq and conservation analysis show that our method is well suited for predicting CRISPR/Cas-associated small RNAs. We also find possible existence of a modified mechanism of CRISPR-associated small RNA action, which, interestingly, closely resembles the setup employed in biotechnological applications. Overall, our findings indicate that scaRNA:tracrRNA pairs are present in all subtypes of Type II systems, and point to an underlying connection with bacterial virulence. In addition to formulating these hypotheses, careful manual curation that we performed, makes an important first step toward fully automated predictor of CRISPR/Cas-associated small RNAs, which will allow their large scale analysis across diverse bacterial genomes.
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Affiliation(s)
- Jelena Guzina
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Wei-Hua Chen
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Tamara Stankovic
- Multidisciplinary PhD Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | | | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marko Djordjevic
- Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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245
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Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol 2018; 3:135-149. [PMID: 30345399 PMCID: PMC6190536 DOI: 10.1016/j.synbio.2018.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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246
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Chatterjee P, Jakimo N, Jacobson JM. Minimal PAM specificity of a highly similar SpCas9 ortholog. SCIENCE ADVANCES 2018; 4:eaau0766. [PMID: 30397647 PMCID: PMC6200363 DOI: 10.1126/sciadv.aau0766] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 09/17/2018] [Indexed: 05/03/2023]
Abstract
RNA-guided DNA endonucleases of the CRISPR-Cas system are widely used for genome engineering and thus have numerous applications in a wide variety of fields. CRISPR endonucleases, however, require a specific protospacer adjacent motif (PAM) flanking the target site, thus constraining their targetable sequence space. In this study, we demonstrate the natural PAM plasticity of a highly similar, yet previously uncharacterized, Cas9 from Streptococcus canis (ScCas9) through rational manipulation of distinguishing motif insertions. To this end, we report affinity to minimal 5'-NNG-3' PAM sequences and demonstrate the accurate editing capabilities of the ortholog in both bacterial and human cells. Last, we build an automated bioinformatics pipeline, the Search for PAMs by ALignment Of Targets (SPAMALOT), which further explores the microbial PAM diversity of otherwise overlooked Streptococcus Cas9 orthologs. Our results establish that ScCas9 can be used both as an alternative genome editing tool and as a functional platform to discover novel Streptococcus PAM specificities.
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Affiliation(s)
- Pranam Chatterjee
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Corresponding author.
| | - Noah Jakimo
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph M. Jacobson
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
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She W, Ni J, Shui K, Wang F, He R, Xue J, Reetz MT, Li A, Ma L. Rapid and Error-Free Site-Directed Mutagenesis by a PCR-Free In Vitro CRISPR/Cas9-Mediated Mutagenic System. ACS Synth Biol 2018; 7:2236-2244. [PMID: 30075075 DOI: 10.1021/acssynbio.8b00245] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The quality and efficiency of any PCR-based mutagenesis technique may not be optimal due to, among other things, amino acid bias, which means that the development of efficient PCR-free methods is desirable. Here, we present a highly efficient in vitro CRISPR/Cas9-mediated mutagenic (ICM) system that allows rapid construction of designed mutants in a PCR-free manner. First, it involves plasmid digestion by utilizing a complex of Cas9 with specific single guide RNA (sgRNA) followed by degradation with T5 exonuclease to generate a 15 nt homologous region. Second, primers containing the desired mutations are annealed to form the double-stranded DNA fragments, which are then ligated into the linearized plasmid. In theory, neither the size of the target plasmid nor the unavailable restriction enzyme site poses any problems that may arise in traditional techniques. In this study, single and multiple site-directed mutagenesis were successfully performed even for a large size plasmid (up to 9.0 kb). Moreover, a PCR-free site-saturation mutagenesis library on single site and two adjacent sites of a green fluorescent protein was also generated with promising results. This demonstrates the great potential of the ICM system for creating high-quality mutant libraries in directed evolution as an alternative to PCR-based saturation mutagenesis, thus facilitating research on synthetic biology.
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Affiliation(s)
- Wenwen She
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jing Ni
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Fei Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Ruyi He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Jinhui Xue
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Aitao Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 434200, China
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248
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Lone BA, Karna SKL, Ahmad F, Shahi N, Pokharel YR. CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering. GENETICS RESEARCH INTERNATIONAL 2018; 2018:3797214. [PMID: 30319822 PMCID: PMC6167567 DOI: 10.1155/2018/3797214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/19/2018] [Indexed: 12/26/2022]
Abstract
Microbes use diverse defence strategies that allow them to withstand exposure to a variety of genome invaders such as bacteriophages and plasmids. One such defence strategy is the use of RNA guided endonuclease called CRISPR-associated (Cas) 9 protein. The Cas9 protein, derived from type II CRISPR/Cas system, has been adapted as a versatile tool for genome targeting and engineering due to its simplicity and high efficiency over the earlier tools such as ZFNs and TALENs. With recent advancements, CRISPR/Cas9 technology has emerged as a revolutionary tool for modulating the genome in living cells and inspires innovative translational applications in different fields. In this paper we review the developments and its potential uses in the CRISPR/Cas9 technology as well as recent advancements in genome engineering using CRISPR/Cas9.
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Affiliation(s)
- Bilal Ahmad Lone
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Shibendra Kumar Lal Karna
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Faiz Ahmad
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Nerina Shahi
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
| | - Yuba Raj Pokharel
- Faculty of Life science and Biotechnology, South Asian University, Akbar Bhawan Chanakyapuri, New Delhi 110021, India
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249
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Raper AT, Stephenson AA, Suo Z. Sharpening the Scissors: Mechanistic Details of CRISPR/Cas9 Improve Functional Understanding and Inspire Future Research. J Am Chem Soc 2018; 140:11142-11152. [PMID: 30160947 DOI: 10.1021/jacs.8b05469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interest in CRISPR/Cas9 remains high level as new applications of the revolutionary gene-editing tool continue to emerge. While key structural and biochemical findings have illuminated major steps in the enzymatic mechanism of Cas9, several important details remain unidentified or poorly characterized that may contribute to known functional limitations. Here we describe the foundation of research that has led to a fundamental understanding of Cas9 and address mechanistic uncertainties that restrict continued development of this gene-editing platform, including specificity for the protospacer adjacent motif, propensity for off-target binding and cleavage, as well as interactions with cellular components during gene editing. Discussion of these topics and considerations should inspire future research to hone this remarkable technology and advance CRISPR/Cas9 to new heights.
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Affiliation(s)
- Austin T Raper
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Anthony A Stephenson
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Zucai Suo
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States.,The James Comprehensive Cancer Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Department of Biomedical Sciences , College of Medicine, Florida State University , Tallahassee , Florida 32306 , United States
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250
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Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys 2018; 51:e91. [PMID: 30555184 PMCID: PMC6292676 DOI: 10.1017/s0033583518000070] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 - a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution - reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1-3 regions 'sense' nucleic acids, 'regulate' the HNH conformational transition, and ultimately 'lock' the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1-3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.
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Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, University of California, Riverside, CA 92507
| | - Janice S. Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Clarisse G. Ricci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure (ENS) de Lyon, CNRS, Lyon 1, France
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8107, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
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