1
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Zhu H, Wang L, Wang Y, Jiang X, Qin Q, Song M, Huang Q. Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e. Cell Mol Life Sci 2024; 81:257. [PMID: 38874784 DOI: 10.1007/s00018-024-05263-7] [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: 03/01/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 06/15/2024]
Abstract
Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.
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Affiliation(s)
- Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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2
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Rosignoli S, Lustrino E, Conci A, Fabrizi A, Rinaldo S, Latella MC, Enzo E, Prosseda G, De Rosa L, De Luca M, Paiardini A. AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach. Nucleic Acids Res 2024:gkae419. [PMID: 38795068 DOI: 10.1093/nar/gkae419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/23/2024] [Accepted: 05/07/2024] [Indexed: 05/27/2024] Open
Abstract
Gene therapy of dominantly inherited genetic diseases requires either the selective disruption of the mutant allele or the editing of the specific mutation. The CRISPR-Cas system holds great potential for the genetic correction of single nucleotide variants (SNVs), including dominant mutations. However, distinguishing between single-nucleotide variations in a pathogenic genomic context remains challenging. The presence of a PAM in the disease-causing allele can guide its precise targeting, preserving the functionality of the wild-type allele. The AlPaCas (Aligning Patients to Cas) webserver is an automated pipeline for sequence-based identification and structural analysis of SNV-derived PAMs that satisfy this demand. When provided with a gene/SNV input, AlPaCas can: (i) identify SNV-derived PAMs; (ii) provide a list of available Cas enzymes recognizing the SNV (s); (iii) propose mutational Cas-engineering to enhance the selectivity towards the SNV-derived PAM. With its ability to identify allele-specific genetic variants that can be targeted using already available or engineered Cas enzymes, AlPaCas is at the forefront of advancements in genome editing. AlPaCas is open to all users without a login requirement and is freely available at https://schubert.bio.uniroma1.it/alpacas.
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Affiliation(s)
- Serena Rosignoli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome 00185, Italy
| | - Elisa Lustrino
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome 00185, Italy
| | - Alessio Conci
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alessandra Fabrizi
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome 00185, Italy
| | | | - Elena Enzo
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Gianni Prosseda
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome 00185, Italy
| | - Laura De Rosa
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Michele De Luca
- Centre for Regenerative Medicine "Stefano Ferrari", Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome 00185, Italy
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3
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Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. Cell 2024:S0092-8674(24)00457-4. [PMID: 38781968 DOI: 10.1016/j.cell.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/20/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity.
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Affiliation(s)
- Amy R Eggers
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kai Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Owen T Tuck
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Bryant Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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4
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Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun 2024; 15:3663. [PMID: 38688943 PMCID: PMC11061278 DOI: 10.1038/s41467-024-47830-3] [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: 02/21/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.
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Affiliation(s)
- Grace N Hibshman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| | - Matthew M Hooper
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hongshan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.
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5
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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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6
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Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- PpoI. Phys Chem Chem Phys 2024; 26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
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7
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Zhang F, Wang JY, Li CL, Zhang WG. HyCas9-12aGEP: an efficient genome editing platform for Corynebacterium glutamicum. Front Bioeng Biotechnol 2024; 12:1327172. [PMID: 38532881 PMCID: PMC10963414 DOI: 10.3389/fbioe.2024.1327172] [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: 10/24/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Corynebacterium glutamicum plays a crucial role as a significant industrial producer of metabolites. Despite the successful development of CRISPR-Cas9 and CRISPR-Cas12a-assisted genome editing technologies in C. glutamicum, their editing resolution and efficiency are hampered by the diverse on-target activities of guide RNAs (gRNAs). To address this problem, a hybrid CRISPR-Cas9-Cas12a genome editing platform (HyCas9-12aGEP) was developed in C. glutamicum in this study to co-express sgRNA (corresponding to SpCas9 guide RNA), crRNA (corresponding to FnCas12a guide RNA), or hfgRNA (formed by the fusion of sgRNA and crRNA). HyCas9-12aGEP improves the efficiency of mapping active gRNAs and outperforms both CRISPR-Cas9 and CRISPR-Cas12a in genome editing resolution and efficiency. In the experiment involving the deletion of the cg0697-0740 gene segment, an unexpected phenotype was observed, and HyCas9-12aGEP efficiently identified the responsible genotype from more than 40 genes. Here, HyCas9-12aGEP greatly improve our capability in terms of genome reprogramming in C. glutamicum.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | | | | | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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8
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Wang J, Maschietto F, Qiu T, Arantes PR, Skeens E, Palermo G, Lisi GP, Batista VS. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophys J 2023; 122:4635-4644. [PMID: 37936350 PMCID: PMC10754686 DOI: 10.1016/j.bpj.2023.11.005] [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: 07/13/2023] [Revised: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 11/09/2023] Open
Abstract
A hallmark of tightly regulated high-fidelity enzymes is that they become activated only after encountering cognate substrates, often by an induced-fit mechanism rather than conformational selection. Upon analysis of molecular dynamics trajectories, we recently discovered that the Cas9 HNH domain exists in three conformations: 1) Y836 (which is two residues away from the catalytic D839 and H840 residues) is hydrogen bonded to the D829 backbone amide, 2) Y836 is hydrogen bonded to the backbone amide of D861 (which is one residue away from the third catalytic residue N863), and 3) Y836 is not hydrogen bonded to either residue. Each of the three conformers differs from the active state of HNH. The conversion between the inactive and active states involves a local unfolding-refolding process that displaces the Cα and side chain of the catalytic N863 residue by ∼5 Å and ∼10 Å, respectively. In this study, we report the two largest principal components of coordinate variance of the HNH domain throughout molecular dynamics trajectories to establish the interconversion pathways of these conformations. We show that conformation 2 is an obligate step between conformations 1 and 3, which are not directly interconvertible without conformation 2. The loss of hydrogen bonding of the Y836 side chain in conformation 3 likely plays an essential role in activation during local unfolding-refolding of an α-helix containing the catalytic N863. Three single Lys-to-Ala mutants appear to eliminate this substrate-independent activation pathway of the wild-type HNH nuclease, thereby enhancing the fidelity of HNH cleavage.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
| | | | - Tianyin Qiu
- Department of Chemistry, Yale University, New Haven, Connecticut
| | - Pablo R Arantes
- Department of Bioengineering, University of California, Riverside, Riverside, California
| | - Erin Skeens
- Department of Chemistry, University of California, Riverside, Riverside, California
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, California; Department of Chemistry, University of California, Riverside, Riverside, California.
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut.
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9
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Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Thornton BW, Xu B, Trinidad MI, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571777. [PMID: 38168238 PMCID: PMC10760125 DOI: 10.1101/2023.12.14.571777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Thermostable CRISPR-Cas9 enzymes could improve genome editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold higher genome editing levels. Cryo-EM structures of the wildtype and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome editing activity.
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10
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Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, Rajan R. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage. CRISPR J 2023; 6:527-542. [PMID: 38108519 PMCID: PMC10753984 DOI: 10.1089/crispr.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/10/2023] [Indexed: 12/19/2023] Open
Abstract
To protect against mobile genetic elements (MGEs), some bacteria and archaea have clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) adaptive immune systems. CRISPR RNAs (crRNAs) bound to Cas nucleases hybridize to MGEs based on sequence complementarity to guide the nucleases to cleave the MGEs. This programmable DNA cleavage has been harnessed for gene editing. Safety concerns include off-target and guide RNA (gRNA)-free DNA cleavages, both of which are observed in the Cas nuclease commonly used for gene editing, Streptococcus pyogenes Cas9 (SpyCas9). We developed a SpyCas9 variant (SpyCas9H982A) devoid of gRNA-free DNA cleavage activity that is more selective for on-target cleavage. The H982A substitution in the metal-dependent RuvC active site reduces Mn2+-dependent gRNA-free DNA cleavage by ∼167-fold. Mechanistic molecular dynamics analysis shows that Mn2+, but not Mg2+, produces a gRNA-free DNA cleavage competent state that is disrupted by the H982A substitution. Our study demonstrates the feasibility of modulating cation:protein interactions to engineer safer gene editing tools.
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Affiliation(s)
- Sydney N. Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Isabelle Schuster
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Yadin G. Joseph
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
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11
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Ding S, Liu J, Han X, Tang M. CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy. Int J Mol Sci 2023; 24:16325. [PMID: 38003514 PMCID: PMC10671490 DOI: 10.3390/ijms242216325] [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: 10/08/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system, an RNA-based adaptive immune system found in bacteria and archaea, has catalyzed the development and application of a new generation of gene editing tools. Numerous studies have shown that this system can precisely target a wide range of human genes, including those associated with diseases such as cancer. In cancer research, the intricate genetic mutations in tumors have promoted extensive utilization of the CRISPR/Cas9 system due to its efficient and accurate gene editing capabilities. This includes improvements in Chimeric Antigen Receptor (CAR)-T-cell therapy, the establishment of tumor models, and gene and drug target screening. Such progress has propelled the investigation of cancer molecular mechanisms and the advancement of precision medicine. However, the therapeutic potential of genome editing remains underexplored, and lingering challenges could elevate the risk of additional genetic mutations. Here, we elucidate the fundamental principles of CRISPR/Cas9 gene editing and its practical applications in tumor research. We also briefly discuss the primary challenges faced by CRISPR technology and existing solutions, intending to enhance the efficacy of this gene editing therapy and shed light on the underlying mechanisms of tumors.
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Affiliation(s)
- Shuai Ding
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Jinfeng Liu
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Xin Han
- Department of Biochemistry and Molecular Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Mengfan Tang
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
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12
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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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13
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Wang J, Le Gall J, Frock RL, Strick TR. Shifted PAMs generate DNA overhangs and enhance SpCas9 post-catalytic complex dissociation. Nat Struct Mol Biol 2023; 30:1707-1718. [PMID: 37828409 PMCID: PMC10643121 DOI: 10.1038/s41594-023-01104-6] [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: 03/30/2022] [Accepted: 08/21/2023] [Indexed: 10/14/2023]
Abstract
Using Sanger sequencing and high-throughput genome sequencing of DNA cleavage reactions, we find that the Streptococcus pyogenes SpCas9 complex responds to internal mechanical strain by robustly generating a distribution of overhanging, rather than blunt, DNA ends. Internal mechanical strain is generated by shifting (increasing or decreasing) the spacing between the RNA-DNA hybrid and the downstream canonical PAM. Up to 2-base 3' overhangs can be robustly generated via a 2-base increase in the distance between hybrid and PAM. We also use single-molecule experiments to reconstruct the full course of the CRISPR-SpCas9 reaction in real-time, structurally and kinetically monitoring and quantifying R-loop formation, the first and second DNA-incision events, and dissociation of the post-catalytic complex. Complex dissociation and release of broken DNA ends is a rate-limiting step of the reaction, and shifted SpCas9 is sufficiently destabilized so as to rapidly dissociate after formation of broken DNA ends.
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Affiliation(s)
- Jinglong Wang
- Institut Jacques Monod, Université de Paris Cité, Paris, France
- Institut de Biologie, Ecole Normale Supérieure, Université PSL, Paris, France
- Department of Radiation Oncology, School of Medicine, Stanford University, Stanford, CA, USA
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Julien Le Gall
- Institut de Biologie, Ecole Normale Supérieure, Université PSL, Paris, France
| | - Richard L Frock
- Programme « Equipe Labélisée » de la Ligue Nationale Contre le Cancer, Paris, France
| | - Terence R Strick
- Institut de Biologie, Ecole Normale Supérieure, Université PSL, Paris, France.
- Programme « Equipe Labélisée » de la Ligue Nationale Contre le Cancer, Paris, France.
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14
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O’Brien A, Bauer DC, Burgio G. Predicting CRISPR-Cas12a guide efficiency for targeting using machine learning. PLoS One 2023; 18:e0292924. [PMID: 37847697 PMCID: PMC10581463 DOI: 10.1371/journal.pone.0292924] [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: 06/22/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas technology has revolutionized many fields in biology. Beyond Cas9 nucleases, Cas12a (formerly Cpf1) has emerged as a promising alternative to Cas9 for editing AT-rich genomes. Despite the promises, guide RNA efficiency prediction through computational tools search still lacks accuracy. Through a computational meta-analysis, here we report that Cas12a target and off-target cleavage behavior are a factor of nucleotide bias combined with nucleotide mismatches relative to the protospacer adjacent motif (PAM) site. These features helped to train a Random Forest machine learning model to improve the accuracy by at least 15% over existing algorithms to predict guide RNA efficiency for the Cas12a enzyme. Despite the progresses, our report underscores the need for more representative datasets and further benchmarking to reliably and accurately predict guide RNA efficiency and off-target effects for Cas12a enzymes.
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Affiliation(s)
- Aidan O’Brien
- Division of Genome Science and Cancer and The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
- Commonwealth Scientific and Industrial Research (CSIRO) Health and Biosecurity, Adelaide, SA, Australia
| | - Denis C. Bauer
- Commonwealth Scientific and Industrial Research (CSIRO) Health and Biosecurity, Adelaide, SA, Australia
- Faculty of Medicine and Health Science, Department of Biomedical Sciences, Macquarie University, Macquarie Park, Australia
- Faculty of Science and Engineering, Applied BioSciences, Macquarie University, Macquarie Park, Australia
| | - Gaetan Burgio
- Division of Genome Science and Cancer and The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
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15
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Zhao L, Koseki SRT, Silverstein RA, Amrani N, Peng C, Kramme C, Savic N, Pacesa M, Rodríguez TC, Stan T, Tysinger E, Hong L, Yudistyra V, Ponnapati MR, Jacobson JM, Church GM, Jakimo N, Truant R, Jinek M, Kleinstiver BP, Sontheimer EJ, Chatterjee P. PAM-flexible genome editing with an engineered chimeric Cas9. Nat Commun 2023; 14:6175. [PMID: 37794046 PMCID: PMC10550912 DOI: 10.1038/s41467-023-41829-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
CRISPR enzymes require a defined protospacer adjacent motif (PAM) flanking a guide RNA-programmed target site, limiting their sequence accessibility for robust genome editing applications. In this study, we recombine the PAM-interacting domain of SpRY, a broad-targeting Cas9 possessing an NRN > NYN (R = A or G, Y = C or T) PAM preference, with the N-terminus of Sc + +, a Cas9 with simultaneously broad, efficient, and accurate NNG editing capabilities, to generate a chimeric enzyme with highly flexible PAM preference: SpRYc. We demonstrate that SpRYc leverages properties of both enzymes to specifically edit diverse PAMs and disease-related loci for potential therapeutic applications. In total, the approaches to generate SpRYc, coupled with its robust flexibility, highlight the power of integrative protein design for Cas9 engineering and motivate downstream editing applications that require precise genomic positioning.
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Affiliation(s)
- Lin Zhao
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Rachel A Silverstein
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Christina Peng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Christian Kramme
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Natasha Savic
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Tomás C Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Teodora Stan
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Emma Tysinger
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lauren Hong
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Vivian Yudistyra
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Joseph M Jacobson
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Noah Jakimo
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Cambridge, USA
| | - Pranam Chatterjee
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Computer Science, Duke University, Durham, NC, USA.
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16
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Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H. Coupled catalytic states and the role of metal coordination in Cas9. Nat Catal 2023; 6:969-977. [PMID: 38348449 PMCID: PMC10861241 DOI: 10.1038/s41929-023-01031-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/29/2023] [Indexed: 02/15/2024]
Abstract
Controlling the activity of the CRISPR-Cas9 system is essential to its safe adoption for clinical and research applications. Although the conformational dynamics of Cas9 are known to control its enzymatic activity, details of how Cas9 influences the catalytic processes at both nuclease domains remain elusive. Here we report five cryo-electron microscopy structures of the active Acidothermus cellulolyticus Cas9 complex along the reaction path at 2.2-2.9 Å resolution. We observed that a large movement in one nuclease domain, triggered by the cognate DNA, results in noticeable changes in the active site of the other domain that is required for metal coordination and catalysis. Furthermore, the conformations synchronize the reaction intermediates, enabling coupled cutting of the two DNA strands. Consistent with the roles of conformations in organizing the active sites, adjustments to the metal-coordination residues lead to altered metal specificity of A. cellulolyticus Cas9 and commonly used Streptococcus pyogenes Cas9 in cells.
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Affiliation(s)
- Anuska Das
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
- These authors contributed equally: Anuska Das, Jay Rai, Mitchell O. Roth
| | - Jay Rai
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
- Present address: Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA
- These authors contributed equally: Anuska Das, Jay Rai, Mitchell O. Roth
| | - Mitchell O. Roth
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
- These authors contributed equally: Anuska Das, Jay Rai, Mitchell O. Roth
| | - Yuerong Shu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
| | - Megan L. Medina
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Mackenzie R. Barakat
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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17
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Nguyen MT, Kim SA, Cheng YY, Hong SH, Jin YS, Han NS. A qPCR Method to Assay Endonuclease Activity of Cas9-sgRNA Ribonucleoprotein Complexes. J Microbiol Biotechnol 2023; 33:1228-1237. [PMID: 37415091 PMCID: PMC10580886 DOI: 10.4014/jmb.2305.05010] [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: 05/10/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
The CRISPR-Cas system has emerged as the most efficient genome editing technique for a wide range of cells. Delivery of the Cas9-sgRNA ribonucleoprotein complex (Cas9 RNP) has gained popularity. The objective of this study was to develop a quantitative polymerase chain reaction (qPCR)-based assay to quantify the double-strand break reaction mediated by Cas9 RNP. To accomplish this, the dextransucrase gene (dsr) from Leuconostoc citreum was selected as the target DNA. The Cas9 protein was produced using recombinant Escherichia coli BL21, and two sgRNAs were synthesized through in vitro transcription to facilitate binding with the dsr gene. Under optimized in vitro conditions, the 2.6 kb dsr DNA was specifically cleaved into 1.1 and 1.5 kb fragments by both Cas9-sgRNA365 and Cas9-sgRNA433. By monitoring changes in dsr concentration using qPCR, the endonuclease activities of the two Cas9 RNPs were measured, and their efficiencies were compared. Specifically, the specific activities of dsr365RNP and dsr433RNP were 28.74 and 34.48 (unit/μg RNP), respectively. The versatility of this method was also verified using different target genes, uracil phosphoribosyl transferase (upp) gene, of Bifidobacterium bifidum and specific sgRNAs. The assay method was also utilized to determine the impact of high electrical field on Cas9 RNP activity during an efficient electroporation process. Overall, the results demonstrated that the qPCR-based method is an effective tool for measuring the endonuclease activity of Cas9 RNP.
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Affiliation(s)
- Minh Tri Nguyen
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
- Faculty of Biology, Dalat University, 01- Phu Dong Thien Vuong, Dalat, Vietnam
| | - Seul-Ah Kim
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ya-Yun Cheng
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sung Hoon Hong
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Health Industry, Division of Animal, Horticultural, and Food Science, Chungbuk National University, Cheongju 28644, Republic of Korea
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18
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination. Nucleic Acids Res 2023; 51:8730-8743. [PMID: 37522352 PMCID: PMC10484686 DOI: 10.1093/nar/gkad636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The finding sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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Affiliation(s)
- Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Kevin G Liu
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Aleique Allen
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Jiang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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19
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Bestas B, Wimberger S, Degtev D, Madsen A, Rottner AK, Karlsson F, Naumenko S, Callahan M, Touza JL, Francescatto M, Möller CI, Badertscher L, Li S, Cerboni S, Selfjord N, Ericson E, Gordon E, Firth M, Chylinski K, Taheri-Ghahfarokhi A, Bohlooly-Y M, Snowden M, Pangalos M, Nuttall B, Akcakaya P, Sienski G, Maresca M. A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo. Nat Commun 2023; 14:5474. [PMID: 37673883 PMCID: PMC10482872 DOI: 10.1038/s41467-023-41240-7] [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: 10/03/2022] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes.
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Affiliation(s)
- Burcu Bestas
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Dmitrii Degtev
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Alexandra Madsen
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Antje K Rottner
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Sergey Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - Megan Callahan
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Julia Liz Touza
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Margherita Francescatto
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | - Carl Ivar Möller
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Songyuan Li
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Silvia Cerboni
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Niklas Selfjord
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Elke Ericson
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Firth
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Cambridge, UK
| | | | - Amir Taheri-Ghahfarokhi
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Mike Snowden
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Barrett Nuttall
- Translational Genomics, Translational Medicine, R&D Oncology, AstraZeneca, Waltham, MA, USA
| | - Pinar Akcakaya
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Grzegorz Sienski
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden.
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20
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Tanny T, Sallam M, Soda N, Nguyen NT, Alam M, Shiddiky MJA. CRISPR/Cas-Based Diagnostics in Agricultural Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11765-11788. [PMID: 37506507 DOI: 10.1021/acs.jafc.3c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.
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Affiliation(s)
- Tanzena Tanny
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mohamed Sallam
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Mayers Road, Nambour, QLD 4560, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, NSW 2800, Australia
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21
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Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541046. [PMID: 37292754 PMCID: PMC10245671 DOI: 10.1101/2023.05.16.541046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-associated proteins such as Cas9 and Cas12a are programable RNA-guided nucleases that have emerged as powerful tools for genome manipulation and molecular diagnostics. However, these enzymes are prone to cleaving off-target sequences that contain mismatches between the RNA guide and DNA protospacer. In comparison to Cas9, Cas12a has demonstrated distinct sensitivity to protospacer-adjacent-motif (PAM) distal mismatches, and the molecular basis of Cas12a's enhanced target discrimination is of great interest. In this study, we investigated the mechanism of Cas12a target recognition using a combination of site-directed spin labeling, fluorescent spectroscopy, and enzyme kinetics. With a fully matched RNA guide, the data revealed an inherent equilibrium between a DNA unwound state and a DNA-paired duplex-like state. Experiments with off-target RNA guides and pre-nicked DNA substrates identified the PAM-distal DNA unwinding equilibrium as a mismatch sensing checkpoint prior to the first step of DNA cleavage. The data sheds light on the distinct targeting mechanism of Cas12a and may better inform CRISPR based biotechnology developments.
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22
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van der Veer H, van Aalen EA, Michielsen CMS, Hanckmann ETL, Deckers J, van Borren MMGJ, Flipse J, Loonen AJM, Schoeber JPH, Merkx M. Glow-in-the-Dark Infectious Disease Diagnostics Using CRISPR-Cas9-Based Split Luciferase Complementation. ACS CENTRAL SCIENCE 2023; 9:657-667. [PMID: 37122471 PMCID: PMC10141630 DOI: 10.1021/acscentsci.2c01467] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Indexed: 05/03/2023]
Abstract
Nucleic acid detection methods based on CRISPR and isothermal amplification techniques show great potential for point-of-care diagnostic applications. However, most current methods rely on fluorescent or lateral flow assay readout, requiring external excitation or postamplification reaction transfer. Here, we developed a bioluminescent nucleic acid sensor (LUNAS) platform in which target dsDNA is sequence-specifically detected by a pair of dCas9-based probes mediating split NanoLuc luciferase complementation. LUNAS is easily integrated with recombinase polymerase amplification (RPA), providing attomolar sensitivity in a rapid one-pot assay. A calibrator luciferase is included for a robust ratiometric readout, enabling real-time monitoring of the RPA reaction using a simple digital camera. We designed an RT-RPA-LUNAS assay that allows SARS-CoV-2 RNA detection without the need for cumbersome RNA isolation and demonstrated its diagnostic performance for COVID-19 patient nasopharyngeal swab samples. Detection of SARS-CoV-2 from samples with viral RNA loads of ∼200 cp/μL was achieved within ∼20 min, showing that RPA-LUNAS is attractive for point-of-care infectious disease testing.
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Affiliation(s)
- Harmen
J. van der Veer
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Eva A. van Aalen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Claire M. S. Michielsen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Eva T. L. Hanckmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | - Jeroen Deckers
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
| | | | - Jacky Flipse
- Laboratory
for Medical Microbiology and Immunology, Rijnstate Hospital, P.O. Box 8, Velp 6880 AA, The Netherlands
| | - Anne J. M. Loonen
- Research
Group Applied Natural Sciences, Fontys University
of Applied Sciences, Eindhoven 5612 AP, The Netherlands
- Pathologie-DNA,
Lab for Molecular Diagnostics, Location
Jeroen Bosch Hospital, ’s-Hertogenbosch 5223 GZ, The Netherlands
| | - Joost P. H. Schoeber
- Research
Group Applied Natural Sciences, Fontys University
of Applied Sciences, Eindhoven 5612 AP, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
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23
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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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24
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Wan Y, Jiang Z. TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1518-1528. [PMID: 36006888 DOI: 10.1109/tcbb.2022.3201631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CRISPR/Cas9 is a widely used genome editing tool for site-directed modification of deoxyribonucleic acid (DNA) nucleotide sequences. However, how to accurately predict and evaluate the on- and off-target effects of single guide RNA (sgRNA) is one of the key problems for CRISPR/Cas9 system. Using computational methods to obtain high cell-specific sensitivity and specificity is a prerequisite for the optimal design of sgRNAs. Inspired by the work of predecessors, we found that sgRNA on-target knockout efficacy was not only related to the original sequence but also affected by important biological features. Hence, we introduce a novel approach called TransCrispr, which integrates Transformer and convolutional neural network (CNN) architecture to predict sgRNA knockout efficacy. Firstly, we encode the sequence data and send the transformed sgRNA sequence, positional information, and biological features into the network as input. Then, the convolutional neural network will automatically learn an appropriate feature representation for the sgRNA sequence and combine it with the positional information for self-attention learning of the Transformer. Finally, a regression score is generated by predicting biological features. Experiments on seven public datasets illustrate that TransCrispr outperforms state-of-the-art methods in terms of prediction accuracy and generalization ability.
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25
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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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26
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Huang X, Wang M, Wu X, Zou Y, Xu J, Cao C, Ma Q, Yu B, Liu Y, Gui Y. Screening DNA aptamers that control the DNA cleavage, homology-directed repair, and transcriptional regulation of the CRISPR-(d)Cas9 system. Mol Ther 2023; 31:260-268. [PMID: 36245127 PMCID: PMC9840146 DOI: 10.1016/j.ymthe.2022.10.009] [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: 09/14/2021] [Revised: 09/06/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Accurate genome editing based on various molecular tools has always been the focus of gene-editing research and the primary goal for therapeutic application. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system is a well-established gene-editing method that is preferred due to its simplicity and high efficiency. In this study, a group of single-stranded DNA aptamers with high affinity and high specificity for the Cas9 protein were obtained by the systematic evolution of ligands through the exponential enrichment method. Their binding affinity and possible binding domains to the Cas9 protein were analyzed. In addition, we demonstrated the effectiveness of aptamers in regulating dCas9-modulated gene transcription, in terms of both transcriptional activation and repression. Additionally, the aptamers successfully reduced the off-target effect and improved the efficiency of gene homologous recombination repair mediated by CRISPR-Cas9. The findings suggest a potential method to better control precise gene editing and enrich the diversity of modulating tools for the CRISPR-Cas9 system.
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Affiliation(s)
- Xinbo Huang
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen 518000, China; Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518039, China; Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Mingxia Wang
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen 518000, China
| | - Xia Wu
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Yanfen Zou
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Jinming Xu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518039, China
| | - Congcong Cao
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen 518000, China; Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518039, China
| | - Qian Ma
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen 518000, China
| | - Bo Yu
- Department of Dermatology, Institute of Dermatology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China.
| | - Yuchen Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518039, China.
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen 518000, China.
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27
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Huang TP, Heins ZJ, Miller SM, Wong BG, Balivada PA, Wang T, Khalil AS, Liu DR. High-throughput continuous evolution of compact Cas9 variants targeting single-nucleotide-pyrimidine PAMs. Nat Biotechnol 2023; 41:96-107. [PMID: 36076084 PMCID: PMC9849140 DOI: 10.1038/s41587-022-01410-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/30/2022] [Indexed: 01/25/2023]
Abstract
Despite the availability of Cas9 variants with varied protospacer-adjacent motif (PAM) compatibilities, some genomic loci-especially those with pyrimidine-rich PAM sequences-remain inaccessible by high-activity Cas9 proteins. Moreover, broadening PAM sequence compatibility through engineering can increase off-target activity. With directed evolution, we generated four Cas9 variants that together enable targeting of most pyrimidine-rich PAM sequences in the human genome. Using phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution, we evolved Nme2Cas9, a compact Cas9 variant, into variants that recognize single-nucleotide pyrimidine-PAM sequences. We developed a general selection strategy that requires functional editing with fully specified target protospacers and PAMs. We applied this selection to evolve high-activity variants eNme2-T.1, eNme2-T.2, eNme2-C and eNme2-C.NR. Variants eNme2-T.1 and eNme2-T.2 offer access to N4TN PAM sequences with comparable editing efficiencies as existing variants, while eNme2-C and eNme2-C.NR offer less restrictive PAM requirements, comparable or higher activity in a variety of human cell types and lower off-target activity at N4CN PAM sequences.
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Affiliation(s)
- Tony P Huang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zachary J Heins
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Shannon M Miller
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Brandon G Wong
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Pallavi A Balivada
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Tina Wang
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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28
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RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2. Nature 2023; 613:582-587. [PMID: 36599980 PMCID: PMC9849127 DOI: 10.1038/s41586-022-05560-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2023]
Abstract
Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided, sequence-nonspecific degradation of single-stranded RNA, single-stranded DNA and double-stranded DNA following recognition of a complementary RNA target, culminating in abortive infection1. Here we report structures of Cas12a2 in binary, ternary and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of 'aromatic clamp' residues that are crucial for double-stranded DNA degradation and in vivo immune system function. Our work provides a structural basis for this mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.
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29
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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30
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Bravo JP, Hibshman GN, Taylor DW. Constructing next-generation CRISPR-Cas tools from structural blueprints. Curr Opin Biotechnol 2022; 78:102839. [PMID: 36371895 DOI: 10.1016/j.copbio.2022.102839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats - CRISPR-associated protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive immune response. Since the discovery that they can be reengineered as programmable RNA-guided nucleases, there has been significant interest in using these systems to perform diverse and precise genetic manipulations. Here, we outline recent advances in the mechanistic understanding of CRISPR-Cas9, how these findings have been leveraged in the rational redesign of Cas9 variants with altered activities, and how these novel tools can be exploited for biotechnology and therapeutics. We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight how future structural studies will bolster these technologies.
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Affiliation(s)
- Jack Pk Bravo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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31
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Baranova SV, Zhdanova PV, Lomzov AA, Koval VV, Chernonosov AA. Structure- and Content-Dependent Efficiency of Cas9-Assisted DNA Cleavage in Genome-Editing Systems. Int J Mol Sci 2022; 23:ijms232213889. [PMID: 36430368 PMCID: PMC9693425 DOI: 10.3390/ijms232213889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Genome-editing systems, being some of the key tools of molecular biologists, represent a reasonable hope for progress in the field of personalized medicine. A major problem with such systems is their nonideal accuracy and insufficient selectivity. The selectivity of CRISPR-Cas9 systems can be improved in several ways. One efficient way is the proper selection of the consensus sequence of the DNA to be cleaved. In the present work, we attempted to evaluate the effect of formed non-Watson-Crick pairs in a DNA duplex on the efficiency of DNA cleavage in terms of the influence of the structure of the formed partially complementary pairs. We also studied the effect of the location of such pairs in DNA relative to the PAM (protospacer-adjacent motif) on the cleavage efficiency. We believe that the stabilization of the Cas9-sgRNA complex with a DNA substrate containing noncomplementary pairs is due to loop reorganization in the RuvC domain of the enzyme. In addition, PAM-proximal mismatches in the DNA substrate lower enzyme efficiency because the "seed" region is involved in binding and cleavage, whereas PAM-distal mismatches have no significant impact on target DNA cleavage. Our data suggest that in the case of short duplexes with mismatches, the stages of recognition and binding of dsDNA substrates by the enzyme determine the reaction rate and time rather than the thermodynamic parameters affected by the "unwinding" of DNA. The results will provide a theoretical basis for predicting the efficiency and accuracy of CRISPR-Cas9 systems at cleaving target DNA.
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Affiliation(s)
- Svetlana V. Baranova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia
| | - Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
| | - Alexander A. Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia
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32
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Schmiderer L, Yudovich D, Oburoglu L, Hjort M, Larsson J. Site-specific CRISPR-based mitochondrial DNA manipulation is limited by gRNA import. Sci Rep 2022; 12:18687. [PMID: 36333335 PMCID: PMC9636205 DOI: 10.1038/s41598-022-21794-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Achieving CRISPR Cas9-based manipulation of mitochondrial DNA (mtDNA) has been a long-standing goal and would be of great relevance for disease modeling and for clinical applications. In this project, we aimed to deliver Cas9 into the mitochondria of human cells and analyzed Cas9-induced mtDNA cleavage and measured the resulting mtDNA depletion with multiplexed qPCR. In initial experiments, we found that measuring subtle effects on mtDNA copy numbers is challenging because of high biological variability, and detected no significant Cas9-caused mtDNA degradation. To overcome the challenge of being able to detect Cas9 activity on mtDNA, we delivered cytosine base editor Cas9-BE3 to mitochondria and measured its effect (C → T mutations) on mtDNA. Unlike regular Cas9-cutting, this leaves a permanent mark on mtDNA that can be detected with amplicon sequencing, even if the efficiency is low. We detected low levels of C → T mutations in cells that were exposed to mitochondrially targeted Cas9-BE3, but, surprisingly, these occurred regardless of whether a guide RNA (gRNA) specific to the targeted site, or non-targeting gRNA was used. This unspecific off-target activity shows that Cas9-BE3 can technically edit mtDNA, but also strongly indicates that gRNA import to mitochondria was not successful. Going forward mitochondria-targeted Cas9 base editors will be a useful tool for validating successful gRNA delivery to mitochondria without the ambiguity of approaches that rely on quantifying mtDNA copy numbers.
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Affiliation(s)
- Ludwig Schmiderer
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, 221 00, Lund, Sweden.
- BMC A12, Lund University, 221 84, Lund, Sweden.
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, 221 00, Lund, Sweden
| | - Leal Oburoglu
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, 221 00, Lund, Sweden
| | - Martin Hjort
- Chemical Biology and Therapeutics, Department of Experimental Medical Science, Lund University, 221 00, Lund, Sweden
- MBC Biolabs, Navan Technologies, San Carlos, CA, 94070, USA
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, Lund University, 221 00, Lund, Sweden.
- BMC A12, Lund University, 221 84, Lund, Sweden.
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33
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Shi YJ, Duan M, Ding JM, Wang FQ, Bi LL, Zhang CX, Zhang YZ, Duan JY, Huang AH, Lei XL, Yin H, Zhang Y. DNA topology regulates PAM-Cas9 interaction and DNA unwinding to enable near-PAMless cleavage by thermophilic Cas9. Mol Cell 2022; 82:4160-4175.e6. [DOI: 10.1016/j.molcel.2022.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/04/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
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34
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Vos PD, Filipovska A, Rackham O. Frankenstein Cas9: engineering improved gene editing systems. Biochem Soc Trans 2022; 50:1505-1516. [PMID: 36305591 DOI: 10.1042/bst20220873] [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: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 01/05/2024]
Abstract
The discovery of CRISPR-Cas9 and its widespread use has revolutionised and propelled research in biological sciences. Although the ability to target Cas9's nuclease activity to specific sites via an easily designed guide RNA (gRNA) has made it an adaptable gene editing system, it has many characteristics that could be improved for use in biotechnology. Cas9 exhibits significant off-target activity and low on-target nuclease activity in certain contexts. Scientists have undertaken ambitious protein engineering campaigns to bypass these limitations, producing several promising variants of Cas9. Cas9 variants with improved and alternative activities provide exciting new tools to expand the scope and fidelity of future CRISPR applications.
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Affiliation(s)
- Pascal D Vos
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009, Australia
| | - Oliver Rackham
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009, Australia
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35
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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: 47] [Impact Index Per Article: 23.5] [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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36
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Abstract
At the core of the CRISPR-Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorating Cas9 function is still missing. Here, multi-microsecond molecular dynamics, free-energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation of an active HNH nuclease is tightly dependent on the catalytic Mg2+, unveiling its cardinal structural role. This activated Mg2+-bound HNH is consistently described through molecular simulations, solution NMR and DNA cleavage assays, revealing also that the protonation state of the catalytic H840 is strongly affected by active site mutations. Finally, ab-initio QM(DFT)/MM simulations and metadynamics establish the catalytic mechanism, showing that the catalysis is activated by H840 and completed by K866, rationalising DNA cleavage experiments. This information is critical to enhance the enzymatic function of CRISPR-Cas9 toward improved genome-editing.
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37
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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: 0] [Impact Index Per Article: 0] [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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38
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Karn V, Sandhya S, Hsu W, Parashar D, Singh HN, Jha NK, Gupta S, Dubey NK, Kumar S. CRISPR/Cas9 system in breast cancer therapy: advancement, limitations and future scope. Cancer Cell Int 2022; 22:234. [PMID: 35879772 PMCID: PMC9316746 DOI: 10.1186/s12935-022-02654-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/12/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer is one of the major causes of mortality worldwide, therefore it is considered a major health concern. Breast cancer is the most frequent type of cancer which affects women on a global scale. Various current treatment strategies have been implicated for breast cancer therapy that includes surgical removal, radiation therapy, hormonal therapy, chemotherapy, and targeted biological therapy. However, constant effort is being made to introduce novel therapies with minimal toxicity. Gene therapy is one of the promising tools, to rectify defective genes and cure various cancers. In recent years, a novel genome engineering technology, namely the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-9 (Cas9) has emerged as a gene-editing tool and transformed genome-editing techniques in a wide range of biological domains including human cancer research and gene therapy. This could be attributed to its versatile characteristics such as high specificity, precision, time-saving and cost-effective methodologies with minimal risk. In the present review, we highlight the role of CRISPR/Cas9 as a targeted therapy to tackle drug resistance, improve immunotherapy for breast cancer.
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Affiliation(s)
- Vamika Karn
- Department of Biotechnology, Amity University, Mumbai, 410221, India
| | - Sandhya Sandhya
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Wayne Hsu
- Division of General Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, 110, Taiwan
| | - Deepak Parashar
- Department of Obstetrics and Gynaecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Himanshu Narayan Singh
- Department of System Biology, Columbia University Irving Medical Centre, New York, NY, 10032, USA
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, 201310, India.,Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, 248007, India.,Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Navneet Kumar Dubey
- Victory Biotechnology Co., Ltd., Taipei, 114757, Taiwan. .,ShiNeo Technology Co., Ltd., New Taipei City, 24262, Taiwan.
| | - Sanjay Kumar
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, India.
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39
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Schuler G, Hu C, Ke A. Structural basis for RNA-guided DNA cleavage by IscB-ωRNA and mechanistic comparison with Cas9. Science 2022; 376:1476-1481. [PMID: 35617371 PMCID: PMC10041819 DOI: 10.1126/science.abq7220] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Class 2 CRISPR effectors Cas9 and Cas12 may have evolved from nucleases in IS200/IS605 transposons. IscB is about two-fifths the size of Cas9 but shares a similar domain organization. The associated ωRNA plays the combined role of CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA) to guide double-stranded DNA (dsDNA) cleavage. Here we report a 2.78-angstrom cryo-electron microscopy structure of IscB-ωRNA bound to a dsDNA target, revealing the architectural and mechanistic similarities between IscB and Cas9 ribonucleoproteins. Target-adjacent motif recognition, R-loop formation, and DNA cleavage mechanisms are explained at high resolution. ωRNA plays the equivalent function of REC domains in Cas9 and contacts the RNA-DNA heteroduplex. The IscB-specific PLMP domain is dispensable for RNA-guided DNA cleavage. The transition from ancestral IscB to Cas9 involved dwarfing the ωRNA and introducing protein domain replacements.
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Affiliation(s)
- Gabriel Schuler
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
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40
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Saha A, Arantes PR, Palermo G. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Curr Opin Struct Biol 2022; 75:102400. [PMID: 35689914 DOI: 10.1016/j.sbi.2022.102400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/25/2022] [Accepted: 05/07/2022] [Indexed: 12/24/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) genome-editing revolution established the beginning of a new era in life sciences. Here, we review the role of state-of-the-art computations in the CRISPR-Cas9 revolution, from the early refinement of cryo-EM data to enhanced simulations of large-scale conformational transitions. Molecular simulations reported a mechanism for RNA binding and the formation of a catalytically competent Cas9 enzyme, in agreement with subsequent structural studies. Inspired by single-molecule experiments, molecular dynamics offered a rationale for the onset of off-target effects, while graph theory unveiled the allosteric regulation. Finally, the use of a mixed quantum-classical approach established the catalytic mechanism of DNA cleavage. Overall, molecular simulations have been instrumental in understanding the dynamics and mechanism of CRISPR-Cas9, contributing to understanding function, catalysis, allostery, and specificity.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States. https://twitter.com/@aakashsahha
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, United States. https://twitter.com/@pablitoarantes
| | - 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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41
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Vos PD, Rossetti G, Mantegna JL, Siira SJ, Gandadireja AP, Bruce M, Raven SA, Khersonsky O, Fleishman SJ, Filipovska A, Rackham O. Computationally designed hyperactive Cas9 enzymes. Nat Commun 2022; 13:3023. [PMID: 35641498 PMCID: PMC9156780 DOI: 10.1038/s41467-022-30598-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/10/2022] [Indexed: 12/01/2022] Open
Abstract
The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. However, this promise has long been limited by the technical challenges involved in genetic engineering. Recent advances in gene editing have bypassed some of these challenges but they are still far from ideal. Here we use FuncLib to computationally design Cas9 enzymes with substantially higher donor-independent editing activities. We use genetic circuits linked to cell survival in yeast to quantify Cas9 activity and discover synergistic interactions between engineered regions. These hyperactive Cas9 variants function efficiently in mammalian cells and introduce larger and more diverse pools of insertions and deletions into targeted genomic regions, providing tools to enhance and expand the possible applications of CRISPR-based gene editing. The ability to alter the genomes of living cells is key to understanding how genes influence the functions of organisms and will be critical to modify living systems for useful purposes. Here, the authors use computational design to discover Cas9 enzymes with increased activity.
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Affiliation(s)
- Pascal D Vos
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Jessica L Mantegna
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Andrianto P Gandadireja
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
| | - Mitchell Bruce
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Samuel A Raven
- Curtin Medical School, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia
| | - Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Nedlands, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Oliver Rackham
- Curtin Medical School, Curtin University, Bentley, WA, Australia. .,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia. .,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia. .,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia.
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42
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Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
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Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
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43
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Tao R, Wang Y, Hu Y, Jiao Y, Zhou L, Jiang L, Li L, He X, Li M, Yu Y, Chen Q, Yao S. WT-PE: Prime editing with nuclease wild-type Cas9 enables versatile large-scale genome editing. Signal Transduct Target Ther 2022; 7:108. [PMID: 35440051 PMCID: PMC9018734 DOI: 10.1038/s41392-022-00936-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 02/08/2023] Open
Abstract
Large scale genomic aberrations including duplication, deletion, translocation, and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer. The current prime editor, PE2, consisting of Cas9-nickase and reverse transcriptase enables efficient editing of genomic deletion and insertion, however, at small scale. Here, we designed a novel prime editor by fusing reverse transcriptase (RT) to nuclease wild-type Cas9 (WT-PE) to edit large genomic fragment. WT-PE system simultaneously introduced a double strand break (DSB) and a single 3' extended flap in the target site. Coupled with paired prime editing guide RNAs (pegRNAs) that have complementary sequences in their 3' terminus while target different genomic regions, WT-PE produced bi-directional prime editing, which enabled efficient and versatile large-scale genome editing, including large fragment deletion up to 16.8 megabase (Mb) pairs and chromosomal translocation. Therefore, our WT-PE system has great potential to model or treat diseases related to large-fragment aberrations.
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Affiliation(s)
- Rui Tao
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yanhong Wang
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yun Hu
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yaoge Jiao
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Lifang Zhou
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Lurong Jiang
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Li Li
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Xingyu He
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Min Li
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yamei Yu
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Qiang Chen
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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44
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Zuo Z, Babu K, Ganguly C, Zolekar A, Newsom S, Rajan R, Wang YC, Liu J. Rational Engineering of CRISPR-Cas9 Nuclease to Attenuate Position-Dependent Off-Target Effects. CRISPR J 2022; 5:329-340. [PMID: 35438515 PMCID: PMC9271410 DOI: 10.1089/crispr.2021.0076] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The RNA-guided Cas9 nuclease from Streptococcus pyogenes has become an important gene-editing tool. However, its intrinsic off-target activity is a major challenge for biomedical applications. Distinct from some reported engineering strategies that specifically target a single domain, we rationally introduced multiple amino acid substitutions across multiple domains in the enzyme to create potential high-fidelity variants, considering the Cas9 specificity is synergistically determined by various domains. We also exploited our previously derived atomic model of activated Cas9 complex structure for guiding new modifications. This approach has led to the identification of the HSC1.2 Cas9 variant with enhanced specificity for DNA cleavage. While the enhanced specificity associated with the HSC1.2 variant appeared to be position-dependent in the in vitro cleavage assays, the frequency of off-target DNA editing with this Cas9 variant is much less than that of the wild-type Cas9 in human cells. The potential mechanisms causing the observed position-dependent effect were investigated through molecular dynamics simulation. Our discoveries establish a solid foundation for leveraging structural and dynamic information to develop Cas9-like enzymes with high specificity in gene editing.
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Affiliation(s)
- Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, People's Republic of China; Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Shanghai Frontiers Science Research Center for Druggability of Cardiovascular noncoding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, People's Republic of China; Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ashwini Zolekar
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sydney Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA; and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yu-Chieh Wang
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA; Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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45
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Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry 2022; 61:785-794. [PMID: 35420793 DOI: 10.1021/acs.biochem.2c00127] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many bacteria possess type-II immunity against invading phages or plasmids known as the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) system to detect and degrade the foreign DNA sequences. The Cas9 protein has two endonucleases responsible for double-strand breaks (the HNH domain for cleaving the target strand of DNA duplexes and RuvC domain for the nontarget strand, respectively) and a single-guide RNA-binding domain where the RNA and target DNA strands are base-paired. Three engineered single Lys-to-Ala HNH mutants (K810A, K848A, and K855A) exhibit an enhanced substrate specificity for cleavage of the target DNA strand. We report in this study that in the wild-type (wt) enzyme, D835, Y836, and D837 within the Y836-containing loop (comprising E827-D837) adjacent to the catalytic site have uncharacterizable broadened 1H15N nuclear magnetic resonance (NMR) features, whereas remaining residues in the loop have different extents of broadened NMR spectra. We find that this loop in the wt enzyme exhibits three distinct conformations over the duration of the molecular dynamics simulations, whereas the three Lys-to-Ala mutants retain only one conformation. The versatility of multiple alternate conformations of this loop in the wt enzyme could help to recruit noncognate DNA substrates into the HNH active site for cleavage, thereby reducing its substrate specificity relative to the three mutants. Our study provides further experimental and computational evidence that Lys-to-Ala substitutions reduce dynamics of proteins and thus increase their stability.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Erin Skeens
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521-9800, United States
| | - Federica Maschietto
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Brandon Allen
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - Gregory W Kyro
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521-9800, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06511-8499, United States
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46
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A tweak and a peek: How Cas9 pries open double-stranded DNA to check its sequence. Nat Struct Mol Biol 2022; 29:286-288. [PMID: 35422517 DOI: 10.1038/s41594-022-00763-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Li Y, Liu Y, Singh J, Tangprasertchai NS, Trivedi R, Fang Y, Qin PZ. Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM. CRISPR J 2022; 5:341-352. [PMID: 35352981 DOI: 10.1089/crispr.2021.0100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CRISPR-Cas9 is an RNA-guided nuclease that has been widely adapted for genome engineering. A key determinant in Cas9 target selection is DNA duplex unwinding to form an R-loop, in which the single-stranded RNA guide hybridizes with one of the DNA strands. To advance understanding on DNA unwinding by Cas9, we combined two types of spectroscopic label, 2-aminopurine and nitroxide spin-label, to investigate unwinding at a specific DNA base pair induced by Streptococcus pyogenes Cas9. Data obtained with RNA guide lengths varying from 13 to 20 nucleotide revealed that the DNA segment distal to the protospacer adjacent motif can adopt a "partial unwinding" state, in which a mixture of DNA-paired and DNA-unwound populations exist in equilibrium. Significant unwinding can occur at positions not supported by RNA/DNA pairing, and the degree of unwinding depends on RNA guide length and modulates DNA cleavage activity. The results shed light on Cas9 target selection and may inform developments of genome-engineering strategies.
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Affiliation(s)
- Yue Li
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yukang Liu
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | | | - Ravi Trivedi
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yun Fang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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48
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Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW. Structural basis for mismatch surveillance by CRISPR–Cas9. Nature 2022. [DOI: 10.1038/s41586-022-04470-1 (2022)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AbstractCRISPR–Cas9 as a programmable genome editing tool is hindered by off-target DNA cleavage1–4, and the underlying mechanisms by which Cas9 recognizes mismatches are poorly understood5–7. Although Cas9 variants with greater discrimination against mismatches have been designed8–10, these suffer from substantially reduced rates of on-target DNA cleavage5,11. Here we used kinetics-guided cryo-electron microscopy to determine the structure of Cas9 at different stages of mismatch cleavage. We observed a distinct, linear conformation of the guide RNA–DNA duplex formed in the presence of mismatches, which prevents Cas9 activation. Although the canonical kinked guide RNA–DNA duplex conformation facilitates DNA cleavage, we observe that substrates that contain mismatches distal to the protospacer adjacent motif are stabilized by reorganization of a loop in the RuvC domain. Mutagenesis of mismatch-stabilizing residues reduces off-target DNA cleavage but maintains rapid on-target DNA cleavage. By targeting regions that are exclusively involved in mismatch tolerance, we provide a proof of concept for the design of next-generation high-fidelity Cas9 variants.
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49
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Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW. Structural basis for mismatch surveillance by CRISPR-Cas9. Nature 2022; 603:343-347. [PMID: 35236982 PMCID: PMC8907077 DOI: 10.1038/s41586-022-04470-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/25/2022] [Indexed: 11/09/2022]
Abstract
CRISPR-Cas9 as a programmable genome editing tool is hindered by off-target DNA cleavage1-4, and the underlying mechanisms by which Cas9 recognizes mismatches are poorly understood5-7. Although Cas9 variants with greater discrimination against mismatches have been designed8-10, these suffer from substantially reduced rates of on-target DNA cleavage5,11. Here we used kinetics-guided cryo-electron microscopy to determine the structure of Cas9 at different stages of mismatch cleavage. We observed a distinct, linear conformation of the guide RNA-DNA duplex formed in the presence of mismatches, which prevents Cas9 activation. Although the canonical kinked guide RNA-DNA duplex conformation facilitates DNA cleavage, we observe that substrates that contain mismatches distal to the protospacer adjacent motif are stabilized by reorganization of a loop in the RuvC domain. Mutagenesis of mismatch-stabilizing residues reduces off-target DNA cleavage but maintains rapid on-target DNA cleavage. By targeting regions that are exclusively involved in mismatch tolerance, we provide a proof of concept for the design of next-generation high-fidelity Cas9 variants.
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Affiliation(s)
- Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Mu-Sen Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Grace N Hibshman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA
| | - Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA
| | - Kyungseok Jung
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Ryan S McCool
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA.
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
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50
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Singh M, Bindal G, Misra CS, Rath D. The era of Cas12 and Cas13 CRISPR-based disease diagnosis. Crit Rev Microbiol 2022; 48:714-729. [PMID: 35164636 DOI: 10.1080/1040841x.2021.2025041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein (Cas) systems, since their discovery, have found growing applications in cell imaging, transcription modulation, therapeutics and diagnostics. Discovery of Cas12 and Cas13 have brought a new dimension to the field of disease diagnosis. These endonucleases have been extensively used for diagnosis of viral diseases in humans and animals and to a lesser extent in plants. The exigency of SARS-CoV-2 pandemic has highlighted the potential of CRISPR-Cas systems and sparked the development of innovative point-of-care diagnostic technologies. Rapid adaptation of CRISPR-chemistry combined with sensitive read-outs for emerging pathogens make them ideal candidates for detection and management of diseases in future. CRISPR-based approaches have been recruited for the challenging task of cancer detection and prognosis. It stands to reason that the field of CRISPR-Cas-based diagnosis is likely to expand with Cas12 and Cas13 playing a pivotal role. Here we focus exclusively on Cas12- and Cas13-based molecular diagnosis in humans, animals and plants including the detection of SARS-coronavirus. The CRISPR-based diagnosis of plant and animal diseases have not found adequate mention in previous reviews. We discuss various advancements, the potential shortfalls and challenges in the widespread adaptation of this technology for disease diagnosis.
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Affiliation(s)
- Mandeep Singh
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, India
| | - Gargi Bindal
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | | | - Devashish Rath
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
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