1
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Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Comput Struct Biotechnol J 2024; 23:537-548. [PMID: 38235361 PMCID: PMC10791570 DOI: 10.1016/j.csbj.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.
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Affiliation(s)
- Shuixiu Wen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Yuxin Zhao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Xinyu Qi
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Mingzhu Cai
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Kaisheng Huang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Hui Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
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2
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Zhao S, Liu J, Zuo Z. Secondary Conformational Checkpoint in CRISPR-Cas9. J Chem Theory Comput 2024; 20:3440-3448. [PMID: 38625092 DOI: 10.1021/acs.jctc.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
A specific checkpoint between target DNA binding and cleavage primarily governs the precision of Cas9 gene editing. Although various CRISPR-Cas9 variants have been developed to improve DNA cleavage accuracy, we still lack a comprehensive understanding of how they work at the molecular level. Herein, we have focused on studying the late-stage conformational transitions of Cas9 and an evolved Cas9 mutant (evoCas9) that start from the precleavage state. Our submilliseconds of dynamic simulations reveal that the presence of base mismatches leads the HNH nuclease domain of Cas9 to alter its principal functional modes of motion, thereby impairing its conformational activation. This observation suggests the existence of a secondary conformational checkpoint that fine-tunes the final DNA cleavage activation. Remarkably, evoCas9 is prone to deviating from the normal activation pathway with base mismatches. This is characterized by a noticeable shift in the positioning of the HNH domain and a significantly perturbed allosteric communication network within the enzyme. Therefore, the mutations evolved in evoCas9 also reinforce the secondary checkpoint in addition to the previously identified primary checkpoint, collectively ensuring this variant's high gene-editing accuracy. This mechanism should also apply to other Cas9-guide RNA variants with enhanced fidelity.
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Affiliation(s)
- Shuxin Zhao
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai 201620, China
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Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, Rajan R. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage. CRISPR J 2023; 6:527-542. [PMID: 38108519 PMCID: PMC10753984 DOI: 10.1089/crispr.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/10/2023] [Indexed: 12/19/2023] Open
Abstract
To protect against mobile genetic elements (MGEs), some bacteria and archaea have clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) adaptive immune systems. CRISPR RNAs (crRNAs) bound to Cas nucleases hybridize to MGEs based on sequence complementarity to guide the nucleases to cleave the MGEs. This programmable DNA cleavage has been harnessed for gene editing. Safety concerns include off-target and guide RNA (gRNA)-free DNA cleavages, both of which are observed in the Cas nuclease commonly used for gene editing, Streptococcus pyogenes Cas9 (SpyCas9). We developed a SpyCas9 variant (SpyCas9H982A) devoid of gRNA-free DNA cleavage activity that is more selective for on-target cleavage. The H982A substitution in the metal-dependent RuvC active site reduces Mn2+-dependent gRNA-free DNA cleavage by ∼167-fold. Mechanistic molecular dynamics analysis shows that Mn2+, but not Mg2+, produces a gRNA-free DNA cleavage competent state that is disrupted by the H982A substitution. Our study demonstrates the feasibility of modulating cation:protein interactions to engineer safer gene editing tools.
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Affiliation(s)
- Sydney N. Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Isabelle Schuster
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Yadin G. Joseph
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
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4
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Li Y, Cooper BH, Liu Y, Wu D, Zhang X, Rohs R, Qin PZ. CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid. Biochemistry 2023; 62:2541-2548. [PMID: 37552860 PMCID: PMC10578059 DOI: 10.1021/acs.biochem.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
CRISPR-Cas9 has been adapted as a readily programmable genome manipulation agent, and continuing technological advances rely on an in-depth mechanistic understanding of Cas9 target discrimination. Cas9 interrogates a target by unwinding the DNA duplex to form an R-loop, where the RNA guide hybridizes with one of the DNA strands. It has been shown that RNA guides shorter than the normal length of 20-nucleotide (-nt) support Cas9 cleavage activity by enabling partial unwinding beyond the RNA/DNA hybrid. To investigate whether DNA segment beyond the RNA/DNA hybrid can impact Cas9 target discrimination with truncated guides, Cas9 double-stranded DNA cleavage rates (kcat) were measured with 16-nt guides on targets with varying sequences at +17 to +20 positions distal to the protospacer-adjacent-motif (PAM). The data reveal a log-linear inverse correlation between kcat and the PAM+(17-20) DNA duplex dissociation free energy (ΔGNN(17-20)0), with sequences having smaller ΔGNN(17-20)0 showing faster cleavage and a higher degree of unwinding. The results indicate that, with a 16-nt guide, "peripheral" DNA sequences beyond the RNA/DNA hybrid contribute to target discrimination by tuning the cleavage reaction transition state through the modulation of PAM-distal unwinding. The finding provides mechanistic insights for the further development of strategies that use RNA guide truncation to enhance Cas9 specificity.
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Affiliation(s)
- Yue Li
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Brendon H Cooper
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Yukang Liu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Difei Wu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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Chenouard V, Leray I, Tesson L, Remy S, Allan A, Archer D, Caulder A, Fortun A, Bernardeau K, Cherifi Y, Teboul L, David L, Anegon I. Excess of guide RNA reduces knockin efficiency and drastically increases on-target large deletions. iScience 2023; 26:106399. [PMID: 37034986 PMCID: PMC10074149 DOI: 10.1016/j.isci.2023.106399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
CRISPR-Cas9 cleavage efficacy and accuracy are the main challenges gene editing faces, and they are particularly affected by the optimal formation of the ribonucleoprotein (RNP) complex. We used nano differential scanning fluorimetry, a label and immobilization-free assay, to demonstrate that an equimolar ratio of Cas9 and guide RNA (gRNA) is optimal for RNP complex formation. We almost achieved 50% of green fluorescent protein (GFP) to blue fluorescent protein (BFP) conversion using a biallelic homozygous GFP human induced pluripotent stem cell line, when 0.4 μM of Cas9, equimolar Cas9/gRNA ratio and 2 μM of single-stranded oligonucleotide, were used and showed that increasing Cas9/gRNA ratio did not further improve KI efficiency. Additionally, excess gRNA decreased point mutation KI efficiency in rat embryos and drastically increased the occurrence of on-target large deletions. These findings highlight the importance of CRISPR/Cas9 stoichiometric optimization to ensure efficient and accurate KI generation, which will be applicable to other in vitro as well as in vivo models.
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Affiliation(s)
- Vanessa Chenouard
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
- genOway, Lyon 69007, France
| | - Isabelle Leray
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Laurent Tesson
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| | - Severine Remy
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
| | - Alasdair Allan
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Daniel Archer
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Adam Caulder
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Agnès Fortun
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, Plateforme P2R, SFR Bonamy, F-44000 Nantes, France
- Cibles et Médicaments des Infections et du Cancer, IICiMed, Nantes Université, UR 1155, F-44000 Nantes, France
| | - Karine Bernardeau
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, US16, Plateforme P2R, SFR Bonamy, F-44000 Nantes, France
| | | | - Lydia Teboul
- Mary Lyon Centre, MRC Harwell Institute, Harwell Oxford, UK
| | - Laurent David
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
- Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Ignacio Anegon
- INSERM, Nantes Université, CHU Nantes, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France
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6
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Nierzwicki Ł, Ahsan M, Palermo G. The Electronic Structure of Genome Editors from the First Principles. ELECTRONIC STRUCTURE (BRISTOL, ENGLAND) 2023; 5:014003. [PMID: 36926635 PMCID: PMC10016068 DOI: 10.1088/2516-1075/acb410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
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7
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Bhattacharya S, Satpati P. Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:1817-1837. [PMID: 36687047 PMCID: PMC9850488 DOI: 10.1021/acsomega.2c05583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The CRISPR/Cas9 system is a popular genome-editing tool with immense therapeutic potential. It is a simple two-component system (Cas9 protein and RNA) that recognizes the DNA sequence on the basis of RNA:DNA complementarity, and the Cas9 protein catalyzes the double-stranded break in the DNA. In the past decade, near-atomic resolution structures at various stages of the CRISPR/Cas9 DNA editing pathway have been reported along with numerous experimental and computational studies. Such studies have boosted knowledge of the genome-editing mechanism. Despite such advancements, the application of CRISPR/Cas9 in therapeutics is still limited, primarily due to off-target effects. Several studies aim at engineering high-fidelity Cas9 to minimize the off-target effects. Molecular Dynamics (MD) simulations have been an excellent complement to the experimental studies for investigating the mechanism of CRISPR/Cas9 editing in terms of structure, thermodynamics, and kinetics. MD-based studies have uncovered several important molecular aspects of Cas9, such as nucleotide binding, catalytic mechanism, and off-target effects. In this Review, the contribution of MD simulation to understand the CRISPR/Cas9 mechanism has been discussed, preceded by an overview of the history, mechanism, and structural aspects of the CRISPR/Cas9 system. These studies are important for the rational design of highly specific Cas9 and will also be extremely promising for achieving more accurate genome editing in the future.
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8
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Bravo JP, Hibshman GN, Taylor DW. Constructing next-generation CRISPR-Cas tools from structural blueprints. Curr Opin Biotechnol 2022; 78:102839. [PMID: 36371895 DOI: 10.1016/j.copbio.2022.102839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats - CRISPR-associated protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive immune response. Since the discovery that they can be reengineered as programmable RNA-guided nucleases, there has been significant interest in using these systems to perform diverse and precise genetic manipulations. Here, we outline recent advances in the mechanistic understanding of CRISPR-Cas9, how these findings have been leveraged in the rational redesign of Cas9 variants with altered activities, and how these novel tools can be exploited for biotechnology and therapeutics. We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight how future structural studies will bolster these technologies.
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Affiliation(s)
- Jack Pk Bravo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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9
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Wang T, Wang Y, Chen P, Yin BC, Ye BC. An Ultrasensitive, One-Pot RNA Detection Method Based on Rationally Engineered Cas9 Nickase-Assisted Isothermal Amplification Reaction. Anal Chem 2022; 94:12461-12471. [DOI: 10.1021/acs.analchem.2c02617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ting Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinru Chen
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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10
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Panda G, Ray A. Decrypting the mechanistic basis of CRISPR/Cas9 protein. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 172:60-76. [PMID: 35577099 DOI: 10.1016/j.pbiomolbio.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/14/2022] [Accepted: 05/10/2022] [Indexed: 12/25/2022]
Abstract
CRISPR/Cas system, a newly but extensively investigated genome-editing method, harbors practical solutions for various genetic problems. It relies on short guide RNAs (gRNAs) to recruit the Cas9 protein, a DNA cleaving enzyme, to its genomic target DNAs. The Cas9 enzyme exhibits some unique properties, like the ability to differentiate self vs. non-self - DNA strands using the base-pairing potential of crRNA, i.e., only CRISPR DNA is entirely complementary to the CRISPR repeat sequences at the crRNA whereas the presence of mismatches in the upstream region of the spacer permit CRISPR interference which is inhibited in case of CRISPR-DNA, allosteric regulation in its domains, and domain reorientation on sgRNA binding. Several groups have contributed their efforts in understanding the functioning of the CRISPR/Cas system, but even then, there is a lot more to explore in this area. The structural and sequence-based understanding of the whole CRISPR-associated bacterial ortholog family landscape is still ambiguous. A better understanding of the underlying energetics of the CRISPR/Cas9 system should reveal critical parameters to design better CRISPR/Cas9s.
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Affiliation(s)
- Gayatri Panda
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
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Liu H, Zhou Y, Song Y, Zhang Q, Kan Y, Tang X, Xiao Q, Xiang Q, Liu H, Luo Y, Bao R. Structural and Dynamics Studies of the Spcas9 Variant Provide Insights into the Regulatory Role of the REC1 Domain. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Huayi Liu
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yi Zhou
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qianqian Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yeyi Kan
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinyue Tang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qingjie Xiao
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), Chinese Academy of Sciences, Shanghai 200135, China
| | - Qianyin Xiang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huanxiang Liu
- Faculty of Applied Science, Macao Polytechnic University, Macao, SAR 999078, China
| | - Yunzi Luo
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Frontiers Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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12
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Kang M, Zuo Z, Yin Z, Gu J. Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition. J Chem Inf Model 2022; 62:3057-3066. [PMID: 35666156 DOI: 10.1021/acs.jcim.1c01562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The off-target effects of Streptococcus pyogenes Cas9 (SpCas9) pose a significant challenge to harness it as a therapeutical approach. Two major factors can result in SpCas9 off-targeting: tolerance to target DNA-guide RNA (gRNA) mismatch and less stringent recognition of protospacer adjacent motif (PAM) flanking the target DNA. Despite the abundance of engineered SpCas9-gRNA variants with improved sensitivity to target DNA-gRNA mismatch, studies focusing on enhancing SpCas9 PAM recognition stringency are quite few. A recent pioneering study identified a D1135E variant of SpCas9 that exhibits much-reduced editing activity at the noncanonical NAG/NGA PAM sites while preserving robust on-target activity at the canonical NGG-flanking sites (N is any nucleobase). Herein, we aim to clarify the molecular mechanism by which this single D1135E mutation confers on SpCas9 enhanced specificity for PAM recognition by molecular dynamics simulations. The results suggest that the variant maintains the base-specific recognition for the canonical NGG PAM via four hydrogen bonds, akin to that in the wild type (WT) SpCas9. While the noncanonical NAG PAM is engaged to the two PAM-interacting arginine residues (i.e., R1333 and R1335) in WT SpCas9 via two to three hydrogen bonds, the D1135E variant prefers to establish two hydrogen bonds with the PAM bases, accounting for its minimal editing activity on the off-target sites with an NAG PAM. The impaired NAG recognition by D1135E SpCas9 results from the PAM duplex displacement such that the hydrogen bond of R1333 to the second PAM base is disfavored. We further propose a mechanistic model to delineate how the mutation perturbs the noncanonical PAM recognition. We anticipate that the mechanistic knowledge could be leveraged for continuous optimization of SpCas9 PAM recognition specificity toward high-precision demanding applications.
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Affiliation(s)
- Minjie Kang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
- Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Zhixiang Yin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jianrong Gu
- Informatization Office, Shanghai University of Engineering Science, Shanghai 201620, China
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13
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Zuo Z, Babu K, Ganguly C, Zolekar A, Newsom S, Rajan R, Wang YC, Liu J. Rational Engineering of CRISPR-Cas9 Nuclease to Attenuate Position-Dependent Off-Target Effects. CRISPR J 2022; 5:329-340. [PMID: 35438515 PMCID: PMC9271410 DOI: 10.1089/crispr.2021.0076] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The RNA-guided Cas9 nuclease from Streptococcus pyogenes has become an important gene-editing tool. However, its intrinsic off-target activity is a major challenge for biomedical applications. Distinct from some reported engineering strategies that specifically target a single domain, we rationally introduced multiple amino acid substitutions across multiple domains in the enzyme to create potential high-fidelity variants, considering the Cas9 specificity is synergistically determined by various domains. We also exploited our previously derived atomic model of activated Cas9 complex structure for guiding new modifications. This approach has led to the identification of the HSC1.2 Cas9 variant with enhanced specificity for DNA cleavage. While the enhanced specificity associated with the HSC1.2 variant appeared to be position-dependent in the in vitro cleavage assays, the frequency of off-target DNA editing with this Cas9 variant is much less than that of the wild-type Cas9 in human cells. The potential mechanisms causing the observed position-dependent effect were investigated through molecular dynamics simulation. Our discoveries establish a solid foundation for leveraging structural and dynamic information to develop Cas9-like enzymes with high specificity in gene editing.
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Affiliation(s)
- Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, People's Republic of China; Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, People's Republic of China; Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ashwini Zolekar
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sydney Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yu-Chieh Wang
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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14
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Li Y, Liu Y, Singh J, Tangprasertchai NS, Trivedi R, Fang Y, Qin PZ. Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM. CRISPR J 2022; 5:341-352. [PMID: 35352981 DOI: 10.1089/crispr.2021.0100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CRISPR-Cas9 is an RNA-guided nuclease that has been widely adapted for genome engineering. A key determinant in Cas9 target selection is DNA duplex unwinding to form an R-loop, in which the single-stranded RNA guide hybridizes with one of the DNA strands. To advance understanding on DNA unwinding by Cas9, we combined two types of spectroscopic label, 2-aminopurine and nitroxide spin-label, to investigate unwinding at a specific DNA base pair induced by Streptococcus pyogenes Cas9. Data obtained with RNA guide lengths varying from 13 to 20 nucleotide revealed that the DNA segment distal to the protospacer adjacent motif can adopt a "partial unwinding" state, in which a mixture of DNA-paired and DNA-unwound populations exist in equilibrium. Significant unwinding can occur at positions not supported by RNA/DNA pairing, and the degree of unwinding depends on RNA guide length and modulates DNA cleavage activity. The results shed light on Cas9 target selection and may inform developments of genome-engineering strategies.
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Affiliation(s)
- Yue Li
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yukang Liu
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | | | - Ravi Trivedi
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yun Fang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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15
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Liu X, Kang X, Lei C, Ren W, Liu C. Programming the trans-cleavage Activity of CRISPR-Cas13a by Single-Strand DNA Blocker and Its Biosensing Application. Anal Chem 2022; 94:3987-3996. [PMID: 35193353 DOI: 10.1021/acs.analchem.1c05124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The precise and controllable programming of the trans-cleavage activity of the CRISPR-Cas13a systems is significant but challenging for fabricating high-performance biosensing systems toward various kinds of biomolecule targets. In this work, we have demonstrated that under a critical low Mg2+ concentration, a simple and short single-stranded DNA (ssDNA) probe free of any modification can efficiently prevent the assembly of crRNA and LwaCas13a only by partially binding with the crRNA repeat region, thereby blocking the trans-cleavage activity of the LwaCas13a system. Furthermore, we have demonstrated that the blocked trans-cleavage activity of the LwaCas13a system can be recovered by various kinds of biologically important substances as long as they could specifically release the blocker DNA from the crRNA in a target-responsive manner, providing a facile route for the quantification of diverse biomarkers such as enzymes, antigens/proteins, and exosomes. To the best of our knowledge, this is reported for the first time that a simple ssDNA can be employed as the switch element to control the crRNA structure and regulate the trans-cleavage activity of Cas13a, which has enriched the CRISPR-Cas13a sensing toolbox and will greatly expand its application scope.
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Affiliation(s)
- Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Xinyue Kang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
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16
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Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids. J Mol Biol 2022; 434:167518. [DOI: 10.1016/j.jmb.2022.167518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/11/2022] [Accepted: 02/23/2022] [Indexed: 11/19/2022]
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17
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Nierzwicki L, East KW, Morzan UN, Arantes PR, Batista VS, Lisi GP, Palermo G. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9. eLife 2021; 10:e73601. [PMID: 34908530 PMCID: PMC8741213 DOI: 10.7554/elife.73601] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/14/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing capabilities. At the molecular level, an intricate allosteric signaling is critical for DNA cleavage, but its role in the specificity enhancement of the Cas9 endonuclease is poorly understood. Here, multi-microsecond molecular dynamics is combined with solution NMR and graph theory-derived models to probe the allosteric role of key specificity-enhancing mutations. We show that mutations responsible for increasing the specificity of Cas9 alter the allosteric structure of the catalytic HNH domain, impacting the signal transmission from the DNA recognition region to the catalytic sites for cleavage. Specifically, the K855A mutation strongly disrupts the allosteric connectivity of the HNH domain, exerting the highest perturbation on the signaling transfer, while K810A and K848A result in more moderate effects on the allosteric communication. This differential perturbation of the allosteric signal correlates to the order of specificity enhancement (K855A > K848A ~ K810A) observed in biochemical studies, with the mutation achieving the highest specificity most strongly perturbing the signaling transfer. These findings suggest that alterations of the allosteric communication from DNA recognition to cleavage are critical to increasing the specificity of Cas9 and that allosteric hotspots can be targeted through mutational studies for improving the system's function.
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Affiliation(s)
- Lukasz Nierzwicki
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
| | - Kyle W East
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Uriel N Morzan
- International Centre for Theoretical PhysicsTriesteItaly
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
| | | | - George P Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversityProvidenceUnited States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, RiversideRiversideUnited States
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18
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Babu K, Kathiresan V, Kumari P, Newsom S, Parameshwaran HP, Chen X, Liu J, Qin PZ, Rajan R. Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence. Biochemistry 2021; 60:3783-3800. [PMID: 34757726 PMCID: PMC8675354 DOI: 10.1021/acs.biochem.1c00354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/23/2021] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection in bacteria and archaea against intruding genomic materials. Cas9, a type-II CRISPR effector protein, is widely used for gene editing applications since a single guide RNA can direct Cas9 to cleave specific genomic targets. The conformational changes associated with RNA/DNA binding are being modulated to develop Cas9 variants with reduced off-target cleavage. Previously, we showed that proline substitutions in the arginine-rich bridge helix (BH) of Streptococcus pyogenes Cas9 (SpyCas9-L64P-K65P, SpyCas92Pro) improve target DNA cleavage selectivity. In this study, we establish that kinetic analysis of the cleavage of supercoiled plasmid substrates provides a facile means to analyze the use of two parallel routes for DNA linearization by SpyCas9: (i) nicking by HNH followed by RuvC cleavage (the TS (target strand) pathway) and (ii) nicking by RuvC followed by HNH cleavage (the NTS (nontarget strand) pathway). BH substitutions and DNA mismatches alter the individual rate constants, resulting in changes in the relative use of the two pathways and the production of nicked and linear species within a given pathway. The results reveal coordinated actions between HNH and RuvC to linearize DNA, which is modulated by the integrity of the BH and the position of the mismatch in the substrate, with each condition producing distinct conformational energy landscapes as observed by molecular dynamics simulations. Overall, our results indicate that BH interactions with RNA/DNA enable target DNA discrimination through the differential use of the parallel sequential pathways driven by HNH/RuvC coordination.
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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, Oklahoma 73019, United States
| | - Venkatesan Kathiresan
- Department
of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, California 90089, United States
| | - Pratibha Kumari
- Department
of Pharmaceutical Sciences, University of North Texas System College
of Pharmacy, University of North Texas Health
Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United
States
| | - Sydney Newsom
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Hari Priya Parameshwaran
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Xiongping Chen
- Department
of Pharmaceutical Sciences, University of North Texas System College
of Pharmacy, University of North Texas Health
Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United
States
| | - Jin Liu
- Department
of Pharmaceutical Sciences, University of North Texas System College
of Pharmacy, University of North Texas Health
Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United
States
| | - Peter Z. Qin
- Department
of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, California 90089, United States
| | - 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, Oklahoma 73019, United States
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19
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Zheng Y, Hong K, Wang B, Liu D, Chen T, Wang Z. Genetic Diversity for Accelerating Microbial Adaptive Laboratory Evolution. ACS Synth Biol 2021; 10:1574-1586. [PMID: 34129323 DOI: 10.1021/acssynbio.0c00589] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Adaptive laboratory evolution (ALE) is a widely used and highly effective tool for improving microbial phenotypes and investigating the evolutionary roots of biological phenomena. Serving as the raw materials of evolution, mutations have been extensively utilized to increase the chances of engineering molecules or microbes with tailor-made functions. The generation of genetic diversity is therefore a core technology for accelerating ALE, and a high-quality mutant library is crucial to its success. Because of its importance, technologies for generating genetic diversity have undergone rapid development in recent years. Here, we review the existing techniques for the construction of mutant libraries, briefly introduce their mechanisms and applications, discuss ongoing and emerging efforts to apply engineering technologies in the construction of mutant libraries, and suggest future perspectives for library construction.
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Affiliation(s)
- Yangyang Zheng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Kunqiang Hong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Baowei Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dingyu Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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20
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Nierzwicki Ł, Arantes PR, Saha A, Palermo G. Establishing the allosteric mechanism in CRISPR-Cas9. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1503. [PMID: 34322166 PMCID: PMC8315640 DOI: 10.1002/wcms.1503] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR-Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three steps of the CRISPR-Cas9 function: affecting DNA recognition, mediating the cleavage and interfering with the off-target activity. An allosteric communication that activates concerted DNA cleavages was found to led through the L1/L2 loops, which connect the HNH and RuvC catalytic domains. The identification of these "allosteric transducers" inspired the development of novel variants of the Cas9 protein with improved specificity, opening a new avenue for controlling the CRISPR-Cas9 activity. Discussed studies also highlight the critical role of the recognition lobe in the conformational activation of the catalytic HNH domain. Specifically, the REC3 region was found to modulate the dynamics of HNH by sensing the formation of the RNA:DNA hybrid. The role of REC3 was revealed to be particularly relevant in the presence of DNA mismatches. Indeed, interference of REC3 with the RNA:DNA hybrid containing mismatched pairs at specific positions resulted in locking HNH in an inactive "conformational checkpoint" conformation, thereby hampering off-target cleavages. Overall, MD simulations established the fundamental mechanisms underlying the allosterism of CRISPR-Cas9, aiding engineering strategies to develop new CRISPR-Cas9 variants for improved genome editing.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Pablo Ricardo Arantes
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, Riverside, California
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California
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21
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Behl T, Sehgal A, Bala R, Chadha S. Understanding the molecular mechanisms and role of autophagy in obesity. Mol Biol Rep 2021; 48:2881-2895. [PMID: 33797660 DOI: 10.1007/s11033-021-06298-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022]
Abstract
Vital for growth, proliferation, subsistence, and thermogenesis, autophagy is the biological cascade, which confers defence against aging and various pathologies. Current research has demonstrated de novo activity of autophagy in stimulation of biological events. There exists a significant association between autophagy activation and obesity, encompassing expansion of adipocytes which facilitates β cell activity. The main objective of the manuscript is to enumerate intrinsic role of autophagy in obesity and associated complications. The peer review articles published till date were searched using medical databases like PubMed and MEDLINE for research, primarily in English language. Obesity is characterized by adipocytic hypertrophy and hyperplasia, which leads to imbalance of lipid absorption, free fatty acid release, and mitochondrial activity. Detailed evaluation of obesity progression is necessary for its treatment and related comorbidities. Data collected in regard to etiological sustaining of obesity, has revealed hypothesized energy misbalance and neuro-humoral dysfunction, which is stimulated by autophagy. Autophagy regulates chief salvaging events for protein clustering, excessive triglycerides, and impaired mitochondria which is accompanied by oxidative and genotoxic stress in mammals. Autophagy is a homeostatic event, which regulates biological process by eliminating lethal cells and reprocessing physiological constituents, comprising of proteins and fat. Unquestionably, autophagy impairment is involved in metabolic syndromes, like obesity. According to an individual's metabolic outline, autophagy activation is essential for metabolism and activity of the adipose tissue and to retard metabolic syndrome i.e. obesity. The manuscript summarizes the perception of current knowledge on autophagy stimulation and its effect on the obesity.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Rajni Bala
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Swati Chadha
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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22
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Saha A, Arantes PR, Hsu RV, Narkhede YB, Jinek M, Palermo G. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. J Chem Inf Model 2020; 60:6427-6437. [PMID: 33107304 PMCID: PMC7605327 DOI: 10.1021/acs.jcim.0c00929] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Indexed: 02/06/2023]
Abstract
CRISPR-Cas12a is a genome-editing system, recently also harnessed for nucleic acid detection, which is promising for the diagnosis of the SARS-CoV-2 coronavirus through the DETECTR technology. Here, a collective ensemble of multimicrosecond molecular dynamics characterizes the key dynamic determinants allowing nucleic acid processing in CRISPR-Cas12a. We show that DNA binding induces a switch in the conformational dynamics of Cas12a, which results in the activation of the peripheral REC2 and Nuc domains to enable cleavage of nucleic acids. The simulations reveal that large-amplitude motions of the Nuc domain could favor the conformational activation of the system toward DNA cleavages. In this process, the REC lobe plays a critical role. Accordingly, the joint dynamics of REC and Nuc shows the tendency to prime the conformational transition of the DNA target strand toward the catalytic site. Most notably, the highly coupled dynamics of the REC2 region and Nuc domain suggests that REC2 could act as a regulator of the Nuc function, similar to what was observed previously for the HNH domain in the CRISPR-associated nuclease Cas9. These mutual domain dynamics could be critical for the nonspecific binding of DNA and thereby for the underlying mechanistic functioning of the DETECTR technology. Considering that REC is a key determinant in the system's specificity, our findings provide a rational basis for future biophysical studies aimed at characterizing its function in CRISPR-Cas12a. Overall, our outcomes advance our mechanistic understanding of CRISPR-Cas12a and provide grounds for novel engineering efforts to improve genome editing and viral detection.
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Affiliation(s)
- Aakash Saha
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Pablo R. Arantes
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Rohaine V. Hsu
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Yogesh B. Narkhede
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Martin Jinek
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Giulia Palermo
- Department
of Bioengineering, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
- Department
of Chemistry, University of California,
Riverside, 900 University Avenue, Riverside, California 92521, United States
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23
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Liu J, Lai L. Editorial overview: Allosteric assemblies. Curr Opin Struct Biol 2020; 62:vi-vii. [DOI: 10.1016/j.sbi.2020.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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