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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Hussen BM, Najmadden ZB, Abdullah SR, Rasul MF, Mustafa SA, Ghafouri-Fard S, Taheri M. CRISPR/Cas9 gene editing: a novel strategy for fighting drug resistance in respiratory disorders. Cell Commun Signal 2024; 22:329. [PMID: 38877530 PMCID: PMC11179281 DOI: 10.1186/s12964-024-01713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024] Open
Abstract
Respiratory disorders are among the conditions that affect the respiratory system. The healthcare sector faces challenges due to the emergence of drug resistance to prescribed medications for these illnesses. However, there is a technology called CRISPR/Cas9, which uses RNA to guide DNA targeting. This technology has revolutionized our ability to manipulate and visualize the genome, leading to advancements in research and treatment development. It can effectively reverse epigenetic alterations that contribute to drug resistance. Some studies focused on health have shown that targeting genes using CRISPR/Cas9 can be challenging when it comes to reducing drug resistance in patients with respiratory disorders. Nevertheless, it is important to acknowledge the limitations of this technology, such as off-target effects, immune system reactions to Cas9, and challenges associated with delivery methods. Despite these limitations, this review aims to provide knowledge about CRISPR/Cas9 genome editing tools and explore how they can help overcome resistance in patients with respiratory disorders. Additionally, this study discusses concerns related to applications of CRISPR and provides an overview of successful clinical trial studies.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Biomedical Sciences, College of Science, Cihan University-Erbil, Erbil, 44001, Kurdistan Region, Iraq
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Zana Baqi Najmadden
- Research Center, University of Halabja, Halabja, 46018, Kurdistan region, Iraq
| | - Snur Rasool Abdullah
- Medical Laboratory Science, College of Health Sciences, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Tishk International University, Kurdistan Region, Iraq
| | - Suhad A Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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3
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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] [Grants] [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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4
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Tavakolidakhrabadi N, Aulicino F, May CJ, Saleem MA, Berger I, Welsh GI. Genome editing and kidney health. Clin Kidney J 2024; 17:sfae119. [PMID: 38766272 PMCID: PMC11099665 DOI: 10.1093/ckj/sfae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Indexed: 05/22/2024] Open
Abstract
Genome editing technologies, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas in particular, have revolutionized the field of genetic engineering, providing promising avenues for treating various genetic diseases. Chronic kidney disease (CKD), a significant health concern affecting millions of individuals worldwide, can arise from either monogenic or polygenic mutations. With recent advancements in genomic sequencing, valuable insights into disease-causing mutations can be obtained, allowing for the development of new treatments for these genetic disorders. CRISPR-based treatments have emerged as potential therapies, especially for monogenic diseases, offering the ability to correct mutations and eliminate disease phenotypes. Innovations in genome editing have led to enhanced efficiency, specificity and ease of use, surpassing earlier editing tools such as zinc-finger nucleases and transcription activator-like effector nucleases (TALENs). Two prominent advancements in CRISPR-based gene editing are prime editing and base editing. Prime editing allows precise and efficient genome modifications without inducing double-stranded DNA breaks (DSBs), while base editing enables targeted changes to individual nucleotides in both RNA and DNA, promising disease correction in the absence of DSBs. These technologies have the potential to treat genetic kidney diseases through specific correction of disease-causing mutations, such as somatic mutations in PKD1 and PKD2 for polycystic kidney disease; NPHS1, NPHS2 and TRPC6 for focal segmental glomerulosclerosis; COL4A3, COL4A4 and COL4A5 for Alport syndrome; SLC3A1 and SLC7A9 for cystinuria and even VHL for renal cell carcinoma. Apart from editing the DNA sequence, CRISPR-mediated epigenome editing offers a cost-effective method for targeted treatment providing new avenues for therapeutic development, given that epigenetic modifications are associated with the development of various kidney disorders. However, there are challenges to overcome, including developing efficient delivery methods, improving safety and reducing off-target effects. Efforts to improve CRISPR-Cas technologies involve optimizing delivery vectors, employing viral and non-viral approaches and minimizing immunogenicity. With research in animal models providing promising results in rescuing the expression of wild-type podocin in mouse models of nephrotic syndrome and successful clinical trials in the early stages of various disorders, including cancer immunotherapy, there is hope for successful translation of genome editing to kidney diseases.
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Affiliation(s)
| | - Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, Bristol Royal Hospital for Children
| | - Carl J May
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Gavin I Welsh
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
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5
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Bhattacharya S, Satpati P. Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes? J Chem Inf Model 2024; 64:3237-3247. [PMID: 38600752 DOI: 10.1021/acs.jcim.3c01515] [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: 04/12/2024]
Abstract
Popular RNA-guided DNA endonuclease Cas9 from Streptococcus pyogenes (SpCas9) recognizes the canonical 5'-NGG-3' protospacer adjacent motif (PAM) and triggers double-stranded DNA cleavage activity. Mutations in SpCas9 were demonstrated to expand the PAM readability and hold promise for therapeutic and genome editing applications. However, the energetics of the PAM recognition and its relation to the atomic structure remain unknown. Using the X-ray structure (precatalytic SpCas9:sgRNA:dsDNA) as a template, we calculated the change in the PAM binding affinity in response to SpCas9 mutations using computer simulations. The E1219V mutation in SpCas9 fine-tunes the water accessibility in the PAM binding pocket and promotes new interactions in the SpCas9:noncanonical T-rich PAM, thus weakening the PAM stringency. The nucleotide-specific interaction of two arginine residues (i.e., R1333 and R1335 of SpCas9) ensured stringent 5'-NGG-3' PAM recognition. R1335A substitution (SpCas9R1335A) completely disrupts the direct interaction between SpCas9 and PAM sequences (canonical or noncanonical), accounting for the loss of editing activity. Interestingly, the double mutant (SpCas9R1335A,E1219V) boosts DNA binding affinity by favoring protein:PAM electrostatic contact in a desolvated pocket. The underlying thermodynamics explain the varied DNA cleavage activity of SpCas9 variants. A direct link between the energetics, structures, and activity is highlighted, which can aid in the rational design of improved SpCas9-based genome editing tools.
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Affiliation(s)
- Shreya Bhattacharya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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6
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Saha A, Ahsan M, Arantes PR, Schmitz M, Chanez C, Jinek M, Palermo G. An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nat Commun 2024; 15:1473. [PMID: 38368461 PMCID: PMC10874386 DOI: 10.1038/s41467-024-45762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential mechanism in which initial cleavage of the non-target strand is followed by target strand cleavage. How the spatially distant DNA target strand traverses toward the RuvC catalytic core is presently not understood. Here, continuous tens of microsecond-long molecular dynamics and free-energy simulations reveal that an α-helical lid, located within the RuvC domain, plays a pivotal role in the traversal of the DNA target strand by anchoring the crRNA:target strand duplex and guiding the target strand toward the RuvC core, as also corroborated by DNA cleavage experiments. In this mechanism, the REC2 domain pushes the crRNA:target strand duplex toward the core of the enzyme, while the Nuc domain aids the bending and accommodation of the target strand within the RuvC core by bending inward. Understanding of this critical process underlying Cas12a activity will enrich fundamental knowledge and facilitate further engineering strategies for genome editing.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Michael Schmitz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
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7
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Maghsoud Y, Jayasinghe-Arachchige VM, Kumari P, Cisneros GA, Liu J. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. J Chem Inf Model 2023; 63:6834-6850. [PMID: 37877218 DOI: 10.1021/acs.jcim.3c01284] [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: 10/26/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium-dependent nuclease domains of the Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH domain is believed to determine the DNA cleavage activity of both endonuclease domains and is sensitive to complementary RNA-DNA base pairing. However, the underlying molecular mechanisms of CRISPR-Cas9, by which it rebukes or accepts mismatches, are poorly understood. Thus, investigation of the structure and dynamics of the catalytic state of Cas9 with either matched or mismatched t-DNA can provide insights into improving its specificity by reducing off-target cleavages. Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical molecular dynamics and coupled quantum mechanics/molecular mechanics simulations to study two possible mechanisms of t-DNA cleavage reaction catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA structure called MM5 (C to G at the fifth position from the protospacer adjacent motif region), the impact of single-guide RNA (sgRNA) and t-DNA complementarity on the catalysis process was investigated. Based on these simulations, our calculated binding affinities, minimum energy paths, and analysis of catalytically important residues provide atomic-level details of the differences between matched and mismatched cleavage reactions. In addition, several residues exhibit significant differences in their catalytic roles for the two studied systems, including K253, K263, R820, K896, and K913.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Vindi M Jayasinghe-Arachchige
- 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
| | - Pratibha Kumari
- 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
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - 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
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8
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Noshay J, Walker T, Alexander W, Klingeman D, Romero J, Walker A, Prates E, Eckert C, Irle S, Kainer D, Jacobson D. Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering. Nucleic Acids Res 2023; 51:10147-10161. [PMID: 37738140 PMCID: PMC10602897 DOI: 10.1093/nar/gkad736] [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: 07/08/2022] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023] Open
Abstract
CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.
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Affiliation(s)
- Jaclyn M Noshay
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Tyler Walker
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - William G Alexander
- Synthetic Biology, Biosciences,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dawn M Klingeman
- Synthetic Biology, Biosciences,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jonathon Romero
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Angelica M Walker
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Erica Prates
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Carrie Eckert
- Synthetic Biology, Biosciences,Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stephan Irle
- Computational Sciences and Engineering, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David Kainer
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel A Jacobson
- Computational and Predictive Biology, Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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9
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Chen QH, Qian YD, Niu YJ, Hu CY, Meng YH. Characterization of an efficient CRISPR-iCas9 system in Yarrowia lipolytica for the biosynthesis of carotenoids. Appl Microbiol Biotechnol 2023; 107:6299-6313. [PMID: 37642716 DOI: 10.1007/s00253-023-12731-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/20/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas9) technology in the genetic modification of Yarrowia lipolytica is challenged by low efficiency and low throughput. Here, a highly efficient CRISPR-iCas9 (with D147Y and P411T mutants) genetic manipulation tool was established for Y. lipolytica, which was further utilized to integrate carotene synthetic key genes and significantly improve the target product yield. First, CRISPR-iCas9 could shorten the time of genetic modification and enable the rapid knockout of nonsense suppressors. iCas9 can lead to more than 98% knockout efficiency for NHEJ-mediated repair after optimal target disruption of a single gene, 100% knockout efficiency for a single gene-guided version, and more than 80% knockout efficiency for multiple genes simultaneously in Y. lipolytica. Subsequently, this technology allowed for rapid one-step integration of large fragments (up to 9902-bp) of genes into chromosomes. Finally, YL-ABTG and YL-ABTG2Z were further constructed through CRISPR-iCas9 integration of key genes in a one-step process, resulting in a maximum β-carotene and zeaxanthin content of 3.12 mg/g and 2.33 mg/g dry cell weight, respectively. Therefore, CRISPR-iCas9 technology provides a feasible approach to genetic modification for efficient biosynthesis of biological compounds in Y. lipolytica. KEY POINTS: • iCas9 with D147Y and P411T mutants improved the CRISPR efficiency in Y. lipolytica. • CRISPR-iCas9 achieved efficient gene knockout and integration in Y. lipolytica. • CRISPR-iCas9 rapidly modified Y. lipolytica for carotenoid bioproduction.
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Affiliation(s)
- Qi Hang Chen
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education; National Research & Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, Shaanxi, 710119, People's Republic of China
| | - Ya Dan Qian
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education; National Research & Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, Shaanxi, 710119, People's Republic of China
| | - Yong Jie Niu
- Xian Healthful Biotechnology Co, Ltd. Hangtuo Road, Xian, Shaanxi, 710100, People's Republic of China
| | - Ching Yuan Hu
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education; National Research & Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, Shaanxi, 710119, People's Republic of China
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Yong Hong Meng
- The Engineering Research Center for High-Valued Utilization of Fruit Resources in Western China, Ministry of Education; National Research & Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, Shaanxi, 710119, People's Republic of China.
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10
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Sun W, Cheng Z, Wang J, Yang J, Li X, Wang J, Chen M, Yang X, Sheng G, Lou J, Wang Y. AcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation. Proc Natl Acad Sci U S A 2023; 120:e2303675120. [PMID: 37494395 PMCID: PMC10400994 DOI: 10.1073/pnas.2303675120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023] Open
Abstract
Anti-CRISPR (Acr) proteins are encoded by phages and other mobile genetic elements and inhibit host CRISPR-Cas immunity using versatile strategies. AcrIIC4 is a broad-spectrum Acr that inhibits the type II-C CRISPR-Cas9 system in several species by an unknown mechanism. Here, we determined a series of structures of Haemophilus parainfluenzae Cas9 (HpaCas9)-sgRNA in complex with AcrIIC4 and/or target DNA, as well as the crystal structure of AcrIIC4 alone. We found that AcrIIC4 resides in the crevice between the REC1 and REC2 domains of HpaCas9, where its extensive interactions restrict the mobility of the REC2 domain and prevent the unwinding of target double-stranded (ds) DNA at the PAM-distal end. Therefore, the full-length guide RNA:target DNA heteroduplex fails to form in the presence of AcrIIC4, preventing Cas9 nuclease activation. Altogether, our structural and biochemical studies illuminate a unique Acr mechanism that allows DNA binding to the Cas9 effector complex but blocks its cleavage by preventing R-loop formation, a key step supporting DNA cleavage by Cas9.
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Affiliation(s)
- Wei Sun
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
| | - Zhi Cheng
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiuyu Wang
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
| | - Jing Yang
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
| | - Xueyan Li
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Jinlong Wang
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Minxuan Chen
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Xiaoqi Yang
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Gang Sheng
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing100049, China
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11
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Maschietto F, Allen B, Kyro GW, Batista VS. MDiGest: A Python package for describing allostery from molecular dynamics simulations. J Chem Phys 2023; 158:215103. [PMID: 37272574 PMCID: PMC10769569 DOI: 10.1063/5.0140453] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/04/2023] [Indexed: 06/06/2023] Open
Abstract
Many biological processes are regulated by allosteric mechanisms that communicate with distant sites in the protein responsible for functionality. The binding of a small molecule at an allosteric site typically induces conformational changes that propagate through the protein along allosteric pathways regulating enzymatic activity. Elucidating those communication pathways from allosteric sites to orthosteric sites is, therefore, essential to gain insights into biochemical processes. Targeting the allosteric pathways by mutagenesis can allow the engineering of proteins with desired functions. Furthermore, binding small molecule modulators along the allosteric pathways is a viable approach to target reactions using allosteric inhibitors/activators with temporal and spatial selectivity. Methods based on network theory can elucidate protein communication networks through the analysis of pairwise correlations observed in molecular dynamics (MD) simulations using molecular descriptors that serve as proxies for allosteric information. Typically, single atomic descriptors such as α-carbon displacements are used as proxies for allosteric information. Therefore, allosteric networks are based on correlations revealed by that descriptor. Here, we introduce a Python software package that provides a comprehensive toolkit for studying allostery from MD simulations of biochemical systems. MDiGest offers the ability to describe protein dynamics by combining different approaches, such as correlations of atomic displacements or dihedral angles, as well as a novel approach based on the correlation of Kabsch-Sander electrostatic couplings. MDiGest allows for comparisons of networks and community structures that capture physical information relevant to allostery. Multiple complementary tools for studying essential dynamics include principal component analysis, root mean square fluctuation, as well as secondary structure-based analyses.
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Affiliation(s)
- Federica Maschietto
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Brandon Allen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Gregory W. Kyro
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA
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12
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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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13
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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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14
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Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State. Int J Mol Sci 2023; 24:ijms24021204. [PMID: 36674715 PMCID: PMC9867433 DOI: 10.3390/ijms24021204] [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: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this structure, we build a full-length model for the ternary complex in cleavage state. This model enables identification of the residues for the interactions between the HNH domain and the WED and REC domains. Moreover, we found that the stem-loop 2 of the sgRNA tightly binds to the PI and RuvC domains and may also regulate the position shift of the RuvC domain. Further mutagenesis and molecular dynamics simulations supported the idea that the interactions of the HNH domain with the WED and REC domains play an important role in the DNA cleavage. Thus, this study provides new mechanistic insights into the DNA cleavage of SaCas9 and is also useful for guiding the future engineering of SaCas9-mediated gene editing systems.
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15
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Belato HB, Norbrun C, Luo J, Pindi C, Sinha S, D’Ordine AM, Jogl G, Palermo G, Lisi GP. Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage. J Chem Phys 2022; 157:225103. [PMID: 36546784 PMCID: PMC9759293 DOI: 10.1063/5.0128815] [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: 09/30/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Allosteric signaling within multidomain proteins is a driver of communication between spatially distant functional sites. Understanding the mechanism of allosteric coupling in large multidomain proteins is the most promising route to achieving spatial and temporal control of the system. The recent explosion of CRISPR-Cas9 applications in molecular biology and medicine has created a need to understand how the atomic level protein dynamics of Cas9, which are the driving force of its allosteric crosstalk, influence its biophysical characteristics. In this study, we used a synergistic approach of nuclear magnetic resonance (NMR) and computation to pinpoint an allosteric hotspot in the HNH domain of the thermostable GeoCas9. We show that mutation of K597 to alanine disrupts a salt-bridge network, which in turn alters the structure, the timescale of allosteric motions, and the thermostability of the GeoHNH domain. This homologous lysine-to-alanine mutation in the extensively studied mesophilic S. pyogenes Cas9 similarly alters the dynamics of the SpHNH domain. We have previously demonstrated that the alteration of allostery via mutations is a source for the specificity enhancement of SpCas9 (eSpCas9). Hence, this may also be true in GeoCas9.
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Affiliation(s)
- Helen B. Belato
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Carmelissa Norbrun
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Jinping Luo
- Brown University Transgenic Mouse and Gene Targeting Facility, Providence, Rhode Island 02903, USA
| | - Chinmai Pindi
- Departments of Bioengineering and Chemistry, University of California Riverside, Riverside, California 92521, USA
| | - Souvik Sinha
- Departments of Bioengineering and Chemistry, University of California Riverside, Riverside, California 92521, USA
| | - Alexandra M. D’Ordine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Giulia Palermo
- Departments of Bioengineering and Chemistry, University of California Riverside, Riverside, California 92521, USA
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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16
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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: 4] [Impact Index Per Article: 2.0] [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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17
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Wang JY, Pausch P, Doudna JA. Structural biology of CRISPR-Cas immunity and genome editing enzymes. Nat Rev Microbiol 2022; 20:641-656. [PMID: 35562427 DOI: 10.1038/s41579-022-00739-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2022] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. In this Review, we examine recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR-Cas immune systems and deployed for wide-ranging genome editing applications. We explore the adaptive and interference aspects of CRISPR-Cas function as well as open questions about the molecular mechanisms responsible for genome targeting. These structural insights reflect close evolutionary links between CRISPR-Cas systems and mobile genetic elements, including the origins and evolution of CRISPR-Cas systems from DNA transposons, retrotransposons and toxin-antitoxin modules. We discuss how the evolution and structural diversity of CRISPR-Cas systems explain their functional complexity and utility as genome editing tools.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick Pausch
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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18
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Mollica L, Cupaioli FA, Rossetti G, Chiappori F. An overview of structural approaches to study therapeutic RNAs. Front Mol Biosci 2022; 9:1044126. [PMID: 36387283 PMCID: PMC9649582 DOI: 10.3389/fmolb.2022.1044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2023] Open
Abstract
RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.
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Affiliation(s)
- Luca Mollica
- Department of Medical Biotechnologies and Translational Medicine, L.I.T.A/University of Milan, Milan, Italy
| | | | | | - Federica Chiappori
- National Research Council—Institute for Biomedical Technologies, Milan, Italy
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19
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Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FHT, Palermo G, Cameron P, Donohoue PD, Jinek M. Structural basis for Cas9 off-target activity. Cell 2022; 185:4067-4081.e21. [PMID: 36306733 PMCID: PMC10103147 DOI: 10.1016/j.cell.2022.09.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/01/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022]
Abstract
The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is determined by complementarity to a 20-nucleotide segment in its guide RNA. However, Cas9 can bind and cleave partially complementary off-target sequences, which raises safety concerns for its use in clinical applications. Here, we report crystallographic structures of Cas9 bound to bona fide off-target substrates, revealing that off-target binding is enabled by a range of noncanonical base-pairing interactions within the guide:off-target heteroduplex. Off-target substrates containing single-nucleotide deletions relative to the guide RNA are accommodated by base skipping or multiple noncanonical base pairs rather than RNA bulge formation. Finally, PAM-distal mismatches result in duplex unpairing and induce a conformational change in the Cas9 REC lobe that perturbs its conformational activation. Together, these insights provide a structural rationale for the off-target activity of Cas9 and contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
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Affiliation(s)
- Martin Pacesa
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Chun-Han Lin
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Antoine Cléry
- Institute of Biochemistry, ETH Zurich, Hönggerbergring 64, 8093 Zurich, Switzerland
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthew J Irby
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Frédéric H-T Allain
- Institute of Biochemistry, ETH Zurich, Hönggerbergring 64, 8093 Zurich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, USA
| | - Peter Cameron
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Paul D Donohoue
- Caribou Biosciences, 2929 Seventh Street Suite 105, Berkeley, CA 94710, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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20
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David SR, Maheshwaram SK, Shet D, Lakshminarayana MB, Soni GV. Temperature dependent in vitro binding and release of target DNA by Cas9 enzyme. Sci Rep 2022; 12:15243. [PMID: 36085316 PMCID: PMC9463129 DOI: 10.1038/s41598-022-19485-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
The CRISPR-associated protein 9 (Cas9) system has proven to be a powerful technology for genome editing in a wide variety of in vivo and in vitro applications. CRISPR-Cas9, when loaded with the guide RNA, cleaves the DNA at the target position as recognized by the guide RNA sequence. For successful application of this technology, it is important to study the biophysical parameters affecting its function. Temperature dependence of the Cas9 binding as well as energetics of product release after cleavage has not been well reported in the literature. In this work, we study the binding properties of Cas9 enzyme to the sequence specific target DNA at a range of temperatures and, surprisingly, find that the Cas9 enzyme, in our study, can find and bind its target DNA with 90 ± 20% efficiency at temperatures as low as 4 °C. Further, we show that the cleaved DNA products remain bound to the Cas9 enzyme strongly and is released from the enzyme only at higher temperatures. Using the gel shift assays, we quantify the rate of Cas9 binding to target DNA to be 0.8 ± 0.2 min-1 at 37 °C. We also tested denaturant (SDS) dependent release of cleaved product which showed a similar release pattern with a dissociation constant of 0.23 ± 0.04 mM. Our results of heat and denaturant dependence on Cas9-DNA binding and release mechanics will provide valuable insights for developing temperature dependent applications of the CRISPR-Cas9 technology.
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Affiliation(s)
| | | | - Divya Shet
- Raman Research Institute, Bangalore, Karnataka, 560080, India
| | | | - Gautam V Soni
- Raman Research Institute, Bangalore, Karnataka, 560080, India.
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21
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Zhdanova PV, Lomzov AA, Prokhorova DV, Stepanov GA, Chernonosov AA, Koval VV. Thermodynamic Swings: How Ideal Complex of Cas9-RNA/DNA Forms. Int J Mol Sci 2022; 23:8891. [PMID: 36012157 PMCID: PMC9408429 DOI: 10.3390/ijms23168891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 12/26/2022] Open
Abstract
Most processes of the recognition and formation of specific complexes in living systems begin with collisions in solutions or quasi-solutions. Then, the thermodynamic regulation of complex formation and fine tuning of complexes come into play. Precise regulation is very important in all cellular processes, including genome editing using the CRISPR-Cas9 tool. The Cas9 endonuclease is an essential component of the CRISPR-Cas-based genome editing systems. The attainment of high-specificity and -efficiency Cas9 during targeted DNA cleavage is the main problem that limits the practical application of the CRISPR-Cas9 system. In this study, we analyzed the thermodynamics of interaction of a complex's components of Cas9-RNA/DNA through experimental and computer simulation methods. We found that there is a small energetic preference during Cas9-RNA/DNA formation from the Cas9-RNA and DNA/DNA duplex. The small difference in binding energy is relevant for biological interactions and could be part of the sequence-specific recognition of double-stranded DNA by the CRISPR-Cas9 system.
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Affiliation(s)
- Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Daria V. Prokhorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia
| | - Grigory A. Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia
| | - Alexander A. Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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22
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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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23
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Panda G, Ray A. Comparative Structural and Dynamics Study of Free and gRNA-bound FnCas9 and SpCas9 Proteins. Comput Struct Biotechnol J 2022; 20:4172-4184. [PMID: 36016716 PMCID: PMC9389198 DOI: 10.1016/j.csbj.2022.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
gRNA binding caused Cas9 to open up, exposing hydrophobic residues. Concerted domain movement was observed in both SpCas9 and FnCas9. gRNA binding led to decrease in helicity and increase in structural transitions. High binding affinity of FnCas9 with gRNA is mostly due to electrostatic interaction. Arginine-helix has shown a pivotal role in the binding of gRNA in FnCas9 protein.
The introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation, hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates of on-target DNA cleavage. Here, we have compared the dynamics of a more specific naturally occurring Cas9 from Francisella novicida (FnCas9) to the most widely used, SpCas9 protein. Long-scale atomistic MD simulation of free and gRNA bound forms of both the Cas9 proteins was performed, and their domain rearrangements and binding affinity with gRNA were compared to decipher the possible reason behind the enhanced specificity of FnCas9 protein. The greater binding affinity with gRNA, high domain electrostatics, and more volatility of FnCas9 than SpCas9 may explain its increased specificity and lower tolerance for mismatches.
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24
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Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 2022; 50:8377-8391. [PMID: 35822842 PMCID: PMC9371913 DOI: 10.1093/nar/gkac578] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Danila Moscone
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Aakash Saha
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Ida Treglia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte Sant'Angelo, Ed. 7, Via Cintia 26, 80126 Naples, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
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25
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Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
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Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
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26
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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: 4] [Impact Index Per Article: 2.0] [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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27
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Mattiello L, Rütgers M, Sua-Rojas MF, Tavares R, Soares JS, Begcy K, Menossi M. Molecular and Computational Strategies to Increase the Efficiency of CRISPR-Based Techniques. FRONTIERS IN PLANT SCIENCE 2022; 13:868027. [PMID: 35712599 PMCID: PMC9194676 DOI: 10.3389/fpls.2022.868027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The prokaryote-derived Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas mediated gene editing tools have revolutionized our ability to precisely manipulate specific genome sequences in plants and animals. The simplicity, precision, affordability, and robustness of this technology have allowed a myriad of genomes from a diverse group of plant species to be successfully edited. Even though CRISPR/Cas, base editing, and prime editing technologies have been rapidly adopted and implemented in plants, their editing efficiency rate and specificity varies greatly. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9-derived technologies and their implications on enhancing editing efficiency. We highlight the major efforts of engineering Cas9, Cas12a, Cas12b, and Cas12f proteins aiming to improve their efficiencies. We also provide a perspective on the global future of agriculturally based products using DNA-free CRISPR/Cas techniques. The improvement of CRISPR-based technologies efficiency will enable the implementation of genome editing tools in a variety of crop plants, as well as accelerate progress in basic research and molecular breeding.
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Affiliation(s)
- Lucia Mattiello
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Mark Rütgers
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Fernanda Sua-Rojas
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael Tavares
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - José Sérgio Soares
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL, United States
| | - Marcelo Menossi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
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28
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Chung Liang L, Sulaiman N, Yazid MD. A Decade of Progress in Gene Targeted Therapeutic Strategies in Duchenne Muscular Dystrophy: A Systematic Review. Front Bioeng Biotechnol 2022; 10:833833. [PMID: 35402409 PMCID: PMC8984139 DOI: 10.3389/fbioe.2022.833833] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/31/2022] [Indexed: 02/01/2023] Open
Abstract
As one of the most severe forms of muscle dystrophy, Duchenne muscular dystrophy (DMD) results in progressive muscle wasting, ultimately resulting in premature death due to cardiomyopathy. In the many years of research, the solution to DMD remains palliative. Although numerous studies including clinical trials have provided promising results, approved drugs, even, the therapeutic window is still minimal with many shortcomings to be addressed. Logically, to combat DMD that arose from a single genetic mutation with gene therapy made sense. However, gene-based strategies as a treatment option are no stranger to drawbacks and limitations such as the size of the dystrophin gene and possibilities of vectors to elicit immune responses. In this systematic review, we aim to provide a comprehensive compilation on gene-based therapeutic strategies and critically evaluate the approaches relative to its efficacy and feasibility while addressing their current limitations. With the keywords “DMD AND Gene OR Genetic AND Therapy OR Treatment,” we reviewed papers published in Science Direct, PubMed, and ProQuest over the past decade (2012–2021).
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Affiliation(s)
- Lam Chung Liang
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Nadiah Sulaiman
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Muhammad Dain Yazid
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
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29
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Belato HB, D'Ordine AM, Nierzwicki L, Arantes PR, Jogl G, Palermo G, Lisi GP. Structural and dynamic insights into the HNH nuclease of divergent Cas9 species. J Struct Biol 2022; 214:107814. [PMID: 34871741 PMCID: PMC8917064 DOI: 10.1016/j.jsb.2021.107814] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas9 is a widely used biochemical tool with applications in molecular biology and precision medicine. The RNA-guided Cas9 protein uses its HNH endonuclease domain to cleave the DNA strand complementary to its endogenous guide RNA. In this study, novel constructs of HNH from two divergent organisms, G. stearothermophilus (GeoHNH) and S. pyogenes (SpHNH) were engineered from their respective full-length Cas9 proteins. Despite low sequence similarity, the X-ray crystal structures of these constructs reveal that the core of HNH surrounding the active site is conserved. Structure prediction of the full-length GeoCas9 protein using Phyre2 and AlphaFold2 also showed that the crystallographic construct of GeoHNH represents the structure of the domain within the full-length GeoCas9 protein. However, significant differences are observed in the solution dynamics of structurally conserved regions of GeoHNH and SpHNH, the latter of which was shown to use such molecular motions to propagate the DNA cleavage signal. Indeed, molecular simulations show that the intradomain signaling pathways, which drive SpHNH function, are non-specific and poorly formed in GeoHNH. Taken together, these outcomes suggest mechanistic differences between mesophilic and thermophilic Cas9 species.
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Affiliation(s)
- Helen B Belato
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
| | - Alexandra M D'Ordine
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
| | - Lukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA; Department of Chemistry, University of California Riverside, Riverside, CA, USA.
| | - George P Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI, USA.
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30
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Zhdanova PV, Chernonosov AA, Prokhorova DV, Stepanov GA, Kanazhevskaya LY, Koval VV. Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry. Int J Mol Sci 2022; 23:1129. [PMID: 35163047 PMCID: PMC8834707 DOI: 10.3390/ijms23031129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
The Cas9 endonuclease is an essential component of the CRISPR-Cas-based genome editing tools. The attainment of high specificity and efficiency of Cas9 during targetted DNA cleavage is the main problem that limits the clinical application of the CRISPR-Cas9 system. A deep understanding of the Cas9 mechanism and its structural-functional relationships is required to develop strategies for precise gene editing. Here, we present the first attempt to describe the solution structure of Cas9 from S. pyogenes using hydrogen-deuterium exchange mass spectrometry (HDX-MS) coupled to molecular dynamics simulations. HDX data revealed multiple protein regions with deuterium uptake levels varying from low to high. By analysing the difference in relative deuterium uptake by apoCas9 and its complex with sgRNA, we identified peptides involved in the complex formation and possible changes in the protein conformation. The REC3 domain was shown to undergo the most prominent conformational change upon enzyme-RNA interactions. Detection of the HDX in two forms of the enzyme provided detailed information about changes in the Cas9 structure induced by sgRNA binding and quantified the extent of the changes. The study demonstrates the practical utility of HDX-MS for the elucidation of mechanistic aspects of Cas9 functioning.
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Affiliation(s)
- Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (P.V.Z.); (A.A.C.); (D.V.P.); (G.A.S.); (L.Y.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A. Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (P.V.Z.); (A.A.C.); (D.V.P.); (G.A.S.); (L.Y.K.)
| | - Daria V. Prokhorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (P.V.Z.); (A.A.C.); (D.V.P.); (G.A.S.); (L.Y.K.)
| | - Grigory A. Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (P.V.Z.); (A.A.C.); (D.V.P.); (G.A.S.); (L.Y.K.)
| | - Lyubov Yu. Kanazhevskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (P.V.Z.); (A.A.C.); (D.V.P.); (G.A.S.); (L.Y.K.)
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (P.V.Z.); (A.A.C.); (D.V.P.); (G.A.S.); (L.Y.K.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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31
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Ergünay T, Ayhan Ö, Celen AB, Georgiadou P, Pekbilir E, Abaci YT, Yesildag D, Rettel M, Sobhiafshar U, Ogmen A, Emre NT, Sahin U. Sumoylation of Cas9 at lysine 848 regulates protein stability and DNA binding. Life Sci Alliance 2022; 5:5/4/e202101078. [PMID: 35022246 PMCID: PMC8761495 DOI: 10.26508/lsa.202101078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
Cas9 is sumoylated and ubiquitylated in human cells. K848 is the major SUMO2/3 modification site, but multiple lysines are ubiquitylated, precipitating proteasomal degradation. Preventing Cas9 sumoylation by K848 ablation or by pharmacologic means reduces Cas9 half-life and DNA binding ability. CRISPR/Cas9 is a popular genome editing technology. Although widely used, little is known about how this prokaryotic system behaves in humans. An unwanted consequence of eukaryotic Cas9 expression is off-target DNA binding leading to mutagenesis. Safer clinical implementation of CRISPR/Cas9 necessitates a finer understanding of the regulatory mechanisms governing Cas9 behavior in humans. Here, we report our discovery of Cas9 sumoylation and ubiquitylation, the first post-translational modifications to be described on this enzyme. We found that the major SUMO2/3 conjugation site on Cas9 is K848, a key positively charged residue in the HNH nuclease domain that is known to interact with target DNA and contribute to off-target DNA binding. Our results suggest that Cas9 ubiquitylation leads to decreased stability via proteasomal degradation. Preventing Cas9 sumoylation through conversion of K848 into arginine or pharmacologic inhibition of cellular sumoylation enhances the enzyme’s turnover and diminishes guide RNA-directed DNA binding efficacy, suggesting that sumoylation at this site regulates Cas9 stability and DNA binding. More research is needed to fully understand the implications of these modifications for Cas9 specificity.
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Affiliation(s)
- Tunahan Ergünay
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Özgecan Ayhan
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Arda B Celen
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Panagiota Georgiadou
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Emre Pekbilir
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Yusuf T Abaci
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Duygu Yesildag
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Mandy Rettel
- European Molecular Biology Laboratory, Proteomics Core Facility, Heidelberg, Germany
| | - Ulduz Sobhiafshar
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Anna Ogmen
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Nc Tolga Emre
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Umut Sahin
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
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32
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3D Modeling of Non-coding RNA Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:281-317. [DOI: 10.1007/978-3-031-08356-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Front Mol Biosci 2022; 9:1072733. [PMID: 36699705 PMCID: PMC9868570 DOI: 10.3389/fmolb.2022.1072733] [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: 10/17/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
The CRISPR-associated protein 9 (Cas9) has been engineered as a precise gene editing tool to make double-strand breaks. CRISPR-associated protein 9 binds the folded guide RNA (gRNA) that serves as a binding scaffold to guide it to the target DNA duplex via a RecA-like strand-displacement mechanism but without ATP binding or hydrolysis. The target search begins with the protospacer adjacent motif or PAM-interacting domain, recognizing it at the major groove of the duplex and melting its downstream duplex where an RNA-DNA heteroduplex is formed at nanomolar affinity. The rate-limiting step is the formation of an R-loop structure where the HNH domain inserts between the target heteroduplex and the displaced non-target DNA strand. Once the R-loop structure is formed, the non-target strand is rapidly cleaved by RuvC and ejected from the active site. This event is immediately followed by cleavage of the target DNA strand by the HNH domain and product release. Within CRISPR-associated protein 9, the HNH domain is inserted into the RuvC domain near the RuvC active site via two linker loops that provide allosteric communication between the two active sites. Due to the high flexibility of these loops and active sites, biophysical techniques have been instrumental in characterizing the dynamics and mechanism of the CRISPR-associated protein 9 nucleases, aiding structural studies in the visualization of the complete active sites and relevant linker structures. Here, we review biochemical, structural, and biophysical studies on the underlying mechanism with emphasis on how CRISPR-associated protein 9 selects the target DNA duplex and rejects non-target sequences.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Souvik Sinha
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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34
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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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35
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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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Li X, Wang C, Peng T, Chai Z, Ni D, Liu Y, Zhang J, Chen T, Lu S. Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Comput Struct Biotechnol J 2021; 19:6108-6124. [PMID: 34900128 PMCID: PMC8632846 DOI: 10.1016/j.csbj.2021.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immunity against invading phages and plasmids. Phages have evolved diverse protein inhibitors of CRISPR-Cas systems, called anti-CRISPR (Acr) proteins, to neutralize this CRISPR machinery. In response, bacteria have co-evolved Cas variants to escape phage's anti-CRISPR strategies, called anti-anti-CRISPR systems. Here we explore the anti-CRISPR allosteric inhibition and anti-anti-CRISPR rescue mechanisms between Streptococcus thermophilus Cas9 (St1Cas9) and the anti-CRISPR protein AcrIIA6 at the atomic level, by generating mutants of key residues in St1Cas9. Extensive unbiased molecular dynamics simulations show that the functional motions of St1Cas9 in the presence of AcrIIA6 differ substantially from those of St1Cas9 alone. AcrIIA6 binding triggers a shift of St1Cas9 conformational ensemble towards a less catalytically competent state; this state significantly compromises protospacer adjacent motif (PAM) recognition and nuclease activity by altering interdependently conformational dynamics and allosteric signals among nuclease domains, PAM-interacting (PI) regions, and AcrIIA6 binding motifs. Via in vitro DNA cleavage assays, we further elucidate the rescue mechanism of efficiently escaping AcrIIA6 inhibition harboring St1Cas9 triple mutations (G993K/K1008M/K1010E) in the PI domain and identify the evolutionary landscape of such mutational escape within species. Our results provide mechanistic insights into Acr proteins as natural brakes for the CRISPR-Cas systems and a promising potential for the design of allosteric Acr peptidomimetics.
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Affiliation(s)
- Xinyi Li
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Chengxiang Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ting Peng
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai 200438, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling. J Chem Inf Model 2021; 61:5172-5191. [PMID: 34551245 DOI: 10.1021/acs.jcim.1c00766] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed a computational framework for comprehensive and rapid mutational scanning of binding energetics and residue interaction networks in the SARS-CoV-2 spike protein complexes. Using this approach, we integrated atomistic simulations and conformational landscaping of the SARS-CoV-2 spike protein complexes with ensemble-based mutational screening and network modeling to characterize mechanisms of structure-functional mimicry and resilience toward mutational escape by the ACE2 protein decoy and de novo designed miniprotein inhibitors. A detailed analysis of structural plasticity of the SARS-CoV-2 spike proteins obtained from atomistic simulations of conformational landscapes and sequence-based profiling of the disorder propensities revealed the intrinsically flexible regions that harbor key functional sites targeted by circulating variants. The conservation of collective dynamics in the SARS-CoV-2 spike protein complexes showed that mutational escape positions are important for modulation of functional motions and that mutational changes in these sites can alter allosteric interaction networks. Through mutational profiling of binding and allosteric propensities in the SARS-CoV-2 spike protein complexes, we identified the key binding and regulatory hotspots that collectively determine functional response and resilience of miniproteins to mutational variants. The results suggest that binding affinities and allosteric signatures of the SARS-CoV-2 complexes can be determined by dynamic crosstalk between structurally stable regulatory centers and conformationally adaptable allosteric hotspots that collectively control the resilience toward mutational escape. This may underlie a mechanism in which moderate perturbations in the mutational escape positions can induce global allosteric changes and alter functional protein response by modulating signaling in the residue interaction networks.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Steve Agajanian
- Keck Center for Science and Engineering, Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Deniz Yasar Oztas
- Keck Center for Science and Engineering, Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
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38
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CRISPR/Cas9 Delivery System Engineering for Genome Editing in Therapeutic Applications. Pharmaceutics 2021; 13:pharmaceutics13101649. [PMID: 34683943 PMCID: PMC8538656 DOI: 10.3390/pharmaceutics13101649] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) systems have emerged as a robust and versatile genome editing platform for gene correction, transcriptional regulation, disease modeling, and nucleic acids imaging. However, the insufficient transfection and off-target risks have seriously hampered the potential biomedical applications of CRISPR/Cas9 technology. Herein, we review the recent progress towards CRISPR/Cas9 system delivery based on viral and non-viral vectors. We summarize the CRISPR/Cas9-inspired clinical trials and analyze the CRISPR/Cas9 delivery technology applied in the trials. The rational-designed non-viral vectors for delivering three typical forms of CRISPR/Cas9 system, including plasmid DNA (pDNA), mRNA, and ribonucleoprotein (RNP, Cas9 protein complexed with gRNA) were highlighted in this review. The vector-derived strategies to tackle the off-target concerns were further discussed. Moreover, we consider the challenges and prospects to realize the clinical potential of CRISPR/Cas9-based genome editing.
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Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YMM, Palermo G, Miao Y. Gaussian accelerated molecular dynamics (GaMD): principles and applications. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2021; 11:e1521. [PMID: 34899998 PMCID: PMC8658739 DOI: 10.1002/wcms.1521] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 12/20/2022]
Abstract
Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., "Gaussian approximation"). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica exchange GaMD (rex-GaMD) and replica exchange umbrella sampling GaMD (GaREUS), have also been introduced, further improving sampling and free energy calculations. Recently, new "selective GaMD" algorithms including the ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD) enabled microsecond simulations to capture repetitive dissociation and binding of small-molecule ligands and highly flexible peptides. The simulations then allowed highly efficient quantitative characterization of the ligand/peptide binding thermodynamics and kinetics. Taken together, GaMD and its innovative variants are applicable to simulate a wide variety of biomolecular dynamics, including protein folding, conformational changes and allostery, ligand binding, peptide binding, protein-protein/nucleic acid/carbohydrate interactions, and carbohydrate/nucleic acid interactions. In this review, we present principles of the GaMD algorithms and recent applications in biomolecular simulations and drug design.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, United States
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr, Lawrence, KS, 66047, United States
| | - Rohaine V Hsu
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, KS, 66047, United States
| | - Yu-Ming M Huang
- Department of Physics & Astronomy, Wayne State University, 666 W Hancock St, Detroit, MI 48207, USA
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 92512, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, 2030 Becker Dr., Lawrence, Kansas 66047, United States
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40
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Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations. Biochemistry 2021; 60:1459-1484. [PMID: 33900725 PMCID: PMC8098775 DOI: 10.1021/acs.biochem.1c00139] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/12/2021] [Indexed: 12/11/2022]
Abstract
In this study, we used an integrative computational approach to examine molecular mechanisms and determine functional signatures underlying the role of functional residues in the SARS-CoV-2 spike protein that are targeted by novel mutational variants and antibody-escaping mutations. Atomistic simulations and functional dynamics analysis are combined with alanine scanning and mutational sensitivity profiling of the SARS-CoV-2 spike protein complexes with the ACE2 host receptor and the REGN-COV2 antibody cocktail(REG10987+REG10933). Using alanine scanning and mutational sensitivity analysis, we have shown that K417, E484, and N501 residues correspond to key interacting centers with a significant degree of structural and energetic plasticity that allow mutants in these positions to afford the improved binding affinity with ACE2. Through perturbation-based network modeling and community analysis of the SARS-CoV-2 spike protein complexes with ACE2, we demonstrate that E406, N439, K417, and N501 residues serve as effector centers of allosteric interactions and anchor major intermolecular communities that mediate long-range communication in the complexes. The results provide support to a model according to which mutational variants and antibody-escaping mutations constrained by the requirements for host receptor binding and preservation of stability may preferentially select structurally plastic and energetically adaptable allosteric centers to differentially modulate collective motions and allosteric interactions in the complexes with the ACE2 enzyme and REGN-COV2 antibody combination. This study suggests that the SARS-CoV-2 spike protein may function as a versatile and functionally adaptable allosteric machine that exploits the plasticity of allosteric regulatory centers to fine-tune response to antibody binding without compromising the activity of the spike protein.
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Affiliation(s)
- Gennady M. Verkhivker
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
- Depatment of Biomedical and Pharmaceutical Sciences,
Chapman University School of Pharmacy, Irvine, California
92618, United States
| | - Steve Agajanian
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
| | - Deniz Yazar Oztas
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid
College of Science and Technology, Chapman University, One
University Drive, Orange, California 92866, United States
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41
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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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Nierzwicki Ł, Palermo G. Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Front Mol Biosci 2021; 8:641208. [PMID: 33884260 PMCID: PMC8053777 DOI: 10.3389/fmolb.2021.641208] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today's cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution density maps obtained for protein flexible domains, as well as the ensemble of coexisting conformational states arising from cryo-EM, poses new challenges and opportunities for Molecular Dynamics (MD) simulations. With the ability to describe the biomolecular dynamics at the atomic level, MD can extend the capabilities of cryo-EM, capturing the conformational variability and predicting biologically relevant short-lived conformational states. Here, we report about the state-of-the-art MD procedures that are currently used to refine, reconstruct and interpret cryo-EM maps. We show the capability of MD to predict short-lived conformational states, finding remarkable confirmation by cryo-EM structures subsequently solved. This has been the case of the CRISPR-Cas9 genome editing machinery, whose catalytically active structure has been predicted through both long-time scale MD and enhanced sampling techniques 2 years earlier than cryo-EM. In summary, this contribution remarks the ability of MD to complement cryo-EM, describing conformational landscapes and relating structural transitions to function, ultimately discerning relevant short-lived conformational states and providing mechanistic knowledge of biological function.
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Affiliation(s)
- Łukasz Nierzwicki
- Department of Bioengineering, University of California, Riverside, CA, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, CA, United States
- Department of Chemistry, University of California, Riverside, CA, United States
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43
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Skeens E, East KW, Lisi GP. 1H, 13C, 15 N backbone resonance assignment of the recognition lobe subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:25-28. [PMID: 32935194 PMCID: PMC8635283 DOI: 10.1007/s12104-020-09977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
Rec3 is a subdomain of the recognition (Rec) lobe within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated protein Cas9 that is involved in nucleic acid binding and is critical to HNH endonuclease activation. Here, we report the backbone resonance assignments of an engineered construct of the Rec3 subdomain from Streptococcus pyogenes Cas9. We also analyze backbone chemical shift data to predict secondary structure and an overall fold that is consistent with that of Rec3 from the full-length S. pyogenes Cas9 protein.
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Affiliation(s)
- Erin Skeens
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Kyle W East
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA
| | - George P Lisi
- Department of Molecular Biology, Cellular Biology & Biochemistry, Brown University, Providence, RI, 02903, USA.
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Hand TH, Roth MO, Smith CL, Shiel E, Klein KN, Gilbert DM, Li H. Catalytically Enhanced Cas9 through Directed Protein Evolution. CRISPR J 2021; 4:223-232. [PMID: 33876948 PMCID: PMC8182482 DOI: 10.1089/crispr.2020.0092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Guided by the extensive knowledge of CRISPR-Cas9 molecular mechanisms, protein engineering can be an effective method in improving CRISPR-Cas9 toward desired traits different from those of their natural forms. Here, we describe a directed protein evolution method that enables selection of catalytically enhanced CRISPR-Cas9 variants (CECas9) by targeting a shortened protospacer within a toxic gene. We demonstrate the effectiveness of this method with a previously characterized Type II-C Cas9 from Acidothermus cellulolyticus (AceCas9) and show by enzyme kinetics an up to fourfold improvement of the in vitro catalytic efficiency by AceCECas9. We further evolved the more widely used Streptococcus pyogenes Cas9 (SpyCas9) and demonstrated a noticeable improvement in the SpyCECas9-facilitated homology directed repair-based gene insertion in human colon cancer cells.
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Affiliation(s)
- Travis H. Hand
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA; Florida State University, Tallahassee, Florida, USA
| | - Mitchell O. Roth
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA; Florida State University, Tallahassee, Florida, USA
| | - Chardasia L. Smith
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, USA; and Florida State University, Tallahassee, Florida, USA
| | - Emily Shiel
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, USA; and Florida State University, Tallahassee, Florida, USA
| | - Kyle N. Klein
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - David M. Gilbert
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA; Florida State University, Tallahassee, Florida, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, USA; and Florida State University, Tallahassee, Florida, USA
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Xu CF, Chen GJ, Luo YL, Zhang Y, Zhao G, Lu ZD, Czarna A, Gu Z, Wang J. Rational designs of in vivo CRISPR-Cas delivery systems. Adv Drug Deliv Rev 2021; 168:3-29. [PMID: 31759123 DOI: 10.1016/j.addr.2019.11.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/09/2019] [Accepted: 11/19/2019] [Indexed: 02/08/2023]
Abstract
The CRISPR-Cas system initiated a revolution in genome editing when it was, for the first time, demonstrated success in the mammalian cells. Today, scientists are able to readily edit genomes, regulate gene transcription, engineer posttranscriptional events, and image nucleic acids using CRISPR-Cas-based tools. However, to efficiently transport CRISPR-Cas into target tissues/cells remains challenging due to many extra- and intra-cellular barriers, therefore largely limiting the applications of CRISPR-based therapeutics in vivo. In this review, we summarize the features of plasmid-, RNA- and ribonucleoprotein (RNP)-based CRISPR-Cas therapeutics. Then, we survey the current in vivo delivery systems. We specify the requirements for efficient in vivo delivery in clinical settings, and highlight both efficiency and safety for different CRISPR-Cas tools.
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46
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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: 36] [Impact Index Per Article: 9.0] [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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47
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Casalino L, Nierzwicki Ł, Jinek M, Palermo G. Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics. ACS Catal 2020; 10:13596-13605. [PMID: 33520346 PMCID: PMC7842700 DOI: 10.1021/acscatal.0c03566] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum-classical molecular dynamics (MD) and free energy methods are used to disclose the two-metal-dependent mechanism of phosphodiester bond cleavage in CRISPR-Cas9. Ab initio MD reveals a conformational rearrangement of the Mg2+-bound RuvC active site, which entails the relocation of H983 to act as a general base. Then, the DNA cleavage proceeds through a concerted associative pathway fundamentally assisted by the joint dynamics of the two Mg2+ ions. This clarifies previous controversial experimental evidence, which could not fully establish the catalytic role of the conserved H983 and the metal cluster conformation. The comparison with other two-metal-dependent enzymes supports the identified mechanism and suggests a common catalytic strategy for genome editing and recombination. Overall, the non-target DNA cleavage catalysis described here resolves a fundamental open question in the CRISPR-Cas9 biology and provides valuable insights for improving the catalytic efficiency and the metal-dependent function of the Cas9 enzyme, which are at the basis of the development of genome editing tools.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
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49
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Newman A, Starrs L, Burgio G. Cas9 Cuts and Consequences; Detecting, Predicting, and Mitigating CRISPR/Cas9 On- and Off-Target Damage: Techniques for Detecting, Predicting, and Mitigating the On- and off-target Effects of Cas9 Editing. Bioessays 2020; 42:e2000047. [PMID: 32643177 DOI: 10.1002/bies.202000047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Large deletions and genomic re-arrangements are increasingly recognized as common products of double-strand break repair at Clustered Regularly Interspaced, Short Palindromic Repeats - CRISPR associated protein 9 (CRISPR/Cas9) on-target sites. Together with well-known off-target editing products from Cas9 target misrecognition, these are important limitations, that need to be addressed. Rigorous assessment of Cas9-editing is necessary to ensure validity of observed phenotypes in Cas9-edited cell-lines and model organisms. Here the mechanisms of Cas9 specificity, and strategies to assess and mitigate unwanted effects of Cas9 editing are reviewed; covering guide-RNA design, RNA modifications, Cas9 modifications, control of Cas9 activity; computational prediction for off-targets, and experimental methods for detecting Cas9 cleavage. Although recognition of the prevalence of on- and off-target effects of Cas9 editing has increased in recent years, broader uptake across the gene editing community will be important in determining the specificity of Cas9 across diverse applications and organisms.
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Affiliation(s)
- Anthony Newman
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Lora Starrs
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Diseases, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
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50
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Zuo Z, Liu J. Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage. Curr Opin Struct Biol 2020; 62:166-174. [PMID: 32070859 PMCID: PMC7308215 DOI: 10.1016/j.sbi.2020.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/29/2022]
Abstract
The CRISPR-Cas9 system from Streptococcus pyogenes has been exploited as a programmable RNA-guided DNA-targeting and DNA-editing platform. This evolutionary tool enables diverse genetic manipulations with unprecedented precision and ease. Cas9 is an allosteric enzyme, which is allosterically regulated in conformational activation, target recognition, and DNA cleavage. Here, we outline the underlying allosteric control over the Cas9 complex assembly and targeting specificity. We further review the strategies for mitigating intrinsic Cas9 off-target effects through allosteric modulations and the advances in engineering controllable Cas9 systems that are responsive to external allosteric signals. Future development of highly specific, tunable CRISPR-Cas9 systems through allosteric modulations would greatly benefit applications that require both conditional control and high precision.
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Affiliation(s)
- Zhicheng Zuo
- College of Chemistry and Chemical Engineering, 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, TX 76107, USA.
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