1
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Bussi G, Bonomi M, Gkeka P, Sattler M, Al-Hashimi HM, Auffinger P, Duca M, Foricher Y, Incarnato D, Jones AN, Kirmizialtin S, Krepl M, Orozco M, Palermo G, Pasquali S, Salmon L, Schwalbe H, Westhof E, Zacharias M. RNA dynamics from experimental and computational approaches. Structure 2024; 32:1281-1287. [PMID: 39241758 DOI: 10.1016/j.str.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/21/2024] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
Conformational dynamics is crucial for the biological function of RNA molecules and for their potential as therapeutic targets. This meeting report outlines key "take-home" messages that emerged from the presentations and discussions during the CECAM workshop "RNA dynamics from experimental and computational approaches" in Paris, June 26-28, 2023.
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Affiliation(s)
- Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
| | - Massimiliano Bonomi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Molecular Design Sciences, Sanofi, Vitry-sur-Seine, France.
| | - Michael Sattler
- Technical University of Munich, Munich, Germany; Helmholtz Munich, Munich, Germany.
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Pascal Auffinger
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France
| | - Yann Foricher
- Integrated Drug Discovery, Small Molecules Medicinal Chemistry, Sanofi, Vitry-sur-Seine, France
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Alisha N Jones
- Department of Chemistry, New York University, New York, NY, USA
| | - Serdal Kirmizialtin
- Department of Chemistry, New York University, New York, NY, USA; Chemistry Program, Science Division, New York University, Abu Dhabi, United Arab Emirates
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 00, Czech Republic
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, and Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, The University of California, Riverside, Riverside, CA, USA
| | - Samuela Pasquali
- Laboratoire Biologie Fonctionnelle et Adaptative, CNRS UMR 8251 INSERM ERL 1133, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, UMR 5082 (CNRS, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), University of Lyon, 69100 Villeurbanne, France
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67084 Strasbourg, France
| | - Martin Zacharias
- Physics Department and Center of Protein Assemblies, Technical University of Munich, Munich, Germany
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2
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Strohkendl I, Saha A, Moy C, Nguyen AH, Ahsan M, Russell R, Palermo G, Taylor DW. Cas12a domain flexibility guides R-loop formation and forces RuvC resetting. Mol Cell 2024; 84:2717-2731.e6. [PMID: 38955179 PMCID: PMC11283365 DOI: 10.1016/j.molcel.2024.06.007] [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: 09/11/2023] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for biotechnology and therapeutic applications. To understand how R-loop formation within the compact Cas12a enables target recognition and nuclease activation, we used cryo-electron microscopy to capture wild-type Acidaminococcus sp. Cas12a R-loop intermediates and DNA delivery into the RuvC active site. Stages of Cas12a R-loop formation-starting from a 5-bp seed-are marked by distinct REC domain arrangements. Dramatic domain flexibility limits contacts until nearly complete R-loop formation, when the non-target strand is pulled across the RuvC nuclease and coordinated domain docking promotes efficient cleavage. Next, substantial domain movements enable target strand repositioning into the RuvC active site. Between cleavage events, the RuvC lid conformationally resets to occlude the active site, requiring re-activation. These snapshots build a structural model depicting Cas12a DNA targeting that rationalizes observed specificity and highlights mechanistic comparisons to other class 2 effectors.
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Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Aakash Saha
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Catherine Moy
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Alexander-Hoi Nguyen
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA; Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; LIVESTRONG Cancer Institute, Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
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3
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Patel A, Sinha S, Arantes P, Palermo G. Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600075. [PMID: 38948825 PMCID: PMC11213026 DOI: 10.1101/2024.06.21.600075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cascade is a class 1, type 1 CRISPR-Cas system with a variety of roles in prokaryote defense, specifically against DNA-based viruses. The Vibrio Cholerae transposon, Tn6677, encodes a variant of the type 1F Cascade known as type 1F-3. This Cascade variant complexes with a homodimer of the transposition protein TniQ and leverages the sequence specificity of Cascade to direct the integration activity of the heteromeric transposase tnsA/B, resulting in site-specific transposition of Tn6677. We desire to uncover the molecular details behind R Loop formation of 'Cascade-TniQ.' Due to the lack of a complete model of Cascade-TniQ available at atom-level resolution, we first build a complete model using AlphaFold V2.1. We then simulate this model via classical molecular dynamics and umbrella sampling to study an important regulatory component within Cascade-TniQ, known as the Cas8 'bundle.' Particularly, we show that this alpha helical bundle experiences a free energy barrier to its large-scale translatory motions and relative free energies of its states primarily dependent on a loop within a Cas7 subunit in Cascade-TniQ. Further, we comment on additional structural and dynamical regulatory points of Cascade-TniQ during R Loop formation, such as Cascade-TniQ backbone rigidity, and the potential role TniQ plays in regulating bundle dynamics. In summary, our outcomes provide the first all-atom dynamic representation of one of the largest CRISPR systems, with information that can contribute to understanding the mechanism of nucleic acid binding and, eventually, to transposase recruitment itself. Such information may prove informative to advance genome engineering efforts.
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4
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Saha A, Ahsan M, Arantes PR, Schmitz M, Chanez C, Jinek M, Palermo G. An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nat Commun 2024; 15:1473. [PMID: 38368461 PMCID: PMC10874386 DOI: 10.1038/s41467-024-45762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/01/2024] [Indexed: 02/19/2024] Open
Abstract
CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-strand DNA breaks using its single RuvC nuclease domain by a sequential mechanism in which initial cleavage of the non-target strand is followed by target strand cleavage. How the spatially distant DNA target strand traverses toward the RuvC catalytic core is presently not understood. Here, continuous tens of microsecond-long molecular dynamics and free-energy simulations reveal that an α-helical lid, located within the RuvC domain, plays a pivotal role in the traversal of the DNA target strand by anchoring the crRNA:target strand duplex and guiding the target strand toward the RuvC core, as also corroborated by DNA cleavage experiments. In this mechanism, the REC2 domain pushes the crRNA:target strand duplex toward the core of the enzyme, while the Nuc domain aids the bending and accommodation of the target strand within the RuvC core by bending inward. Understanding of this critical process underlying Cas12a activity will enrich fundamental knowledge and facilitate further engineering strategies for genome editing.
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Affiliation(s)
- Aakash Saha
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Pablo R Arantes
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Michael Schmitz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA.
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5
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Palermo G, Soares TA. Editorial: Editing DNA and RNA through Computations. J Chem Inf Model 2023; 63:7603-7604. [PMID: 38143420 DOI: 10.1021/acs.jcim.3c01824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Affiliation(s)
- Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside 52512, California, United States
| | - Thereza A Soares
- Department of Chemistry, FFCLRP, University of São Paulo, Sao Paulo 05508-900, Brazil
- Department of Chemistry, University of Oslo, Oslo 0315, Norway
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6
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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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7
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Di Felice R, Mayes ML, Richard RM, Williams-Young DB, Chan GKL, de Jong WA, Govind N, Head-Gordon M, Hermes MR, Kowalski K, Li X, Lischka H, Mueller KT, Mutlu E, Niklasson AMN, Pederson MR, Peng B, Shepard R, Valeev EF, van Schilfgaarde M, Vlaisavljevich B, Windus TL, Xantheas SS, Zhang X, Zimmerman PM. A Perspective on Sustainable Computational Chemistry Software Development and Integration. J Chem Theory Comput 2023; 19:7056-7076. [PMID: 37769271 PMCID: PMC10601486 DOI: 10.1021/acs.jctc.3c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 09/30/2023]
Abstract
The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.
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Affiliation(s)
- Rosa Di Felice
- Departments
of Physics and Astronomy and Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- CNR-NANO
Modena, Modena 41125, Italy
| | - Maricris L. Mayes
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | | | | | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Wibe A. de Jong
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Niranjan Govind
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Martin Head-Gordon
- Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew R. Hermes
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Karol Kowalski
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Xiaosong Li
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Karl T. Mueller
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Erdal Mutlu
- Advanced
Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anders M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Mark R. Pederson
- Department
of Physics, The University of Texas at El
Paso, El Paso, Texas 79968, United States
| | - Bo Peng
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ron Shepard
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, United States
| | - Edward F. Valeev
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Bess Vlaisavljevich
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Theresa L. Windus
- Department
of Chemistry, Iowa State University and
Ames Laboratory, Ames, Iowa 50011, United States
| | - Sotiris S. Xantheas
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced
Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xing Zhang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Paul M. Zimmerman
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Sinha S, Pindi C, Ahsan M, Arantes PR, Palermo G. Machines on Genes through the Computational Microscope. J Chem Theory Comput 2023; 19:1945-1964. [PMID: 36947696 PMCID: PMC10104023 DOI: 10.1021/acs.jctc.2c01313] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Macromolecular machines acting on genes are at the core of life's fundamental processes, including DNA replication and repair, gene transcription and regulation, chromatin packaging, RNA splicing, and genome editing. Here, we report the increasing role of computational biophysics in characterizing the mechanisms of "machines on genes", focusing on innovative applications of computational methods and their integration with structural and biophysical experiments. We showcase how state-of-the-art computational methods, including classical and ab initio molecular dynamics to enhanced sampling techniques, and coarse-grained approaches are used for understanding and exploring gene machines for real-world applications. As this review unfolds, advanced computational methods describe the biophysical function that is unseen through experimental techniques, accomplishing the power of the "computational microscope", an expression coined by Klaus Schulten to highlight the extraordinary capability of computer simulations. Pushing the frontiers of computational biophysics toward a pragmatic representation of large multimegadalton biomolecular complexes is instrumental in bridging the gap between experimentally obtained macroscopic observables and the molecular principles playing at the microscopic level. This understanding will help harness molecular machines for medical, pharmaceutical, and biotechnological purposes.
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9
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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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10
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Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State. Int J Mol Sci 2023; 24:ijms24021204. [PMID: 36674715 PMCID: PMC9867433 DOI: 10.3390/ijms24021204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus Cas9 (SaCas9) is a widely used genome editing tool. Understanding its molecular mechanisms of DNA cleavage could effectively guide the engineering optimization of this system. Here, we determined the first cryo-electron microscopy structure of the SaCas9-sgRNA-DNA ternary complex. This structure reveals that the HNH nuclease domain is tightly bound to the cleavage site of the target DNA strand, and is in close contact with the WED and REC domains. Moreover, it captures the complete structure of the sgRNA, including the previously unresolved stem-loop 2. Based on this structure, we build a full-length model for the ternary complex in cleavage state. This model enables identification of the residues for the interactions between the HNH domain and the WED and REC domains. Moreover, we found that the stem-loop 2 of the sgRNA tightly binds to the PI and RuvC domains and may also regulate the position shift of the RuvC domain. Further mutagenesis and molecular dynamics simulations supported the idea that the interactions of the HNH domain with the WED and REC domains play an important role in the DNA cleavage. Thus, this study provides new mechanistic insights into the DNA cleavage of SaCas9 and is also useful for guiding the future engineering of SaCas9-mediated gene editing systems.
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11
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Bravo JP, Hibshman GN, Taylor DW. Constructing next-generation CRISPR-Cas tools from structural blueprints. Curr Opin Biotechnol 2022; 78:102839. [PMID: 36371895 DOI: 10.1016/j.copbio.2022.102839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats - CRISPR-associated protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive immune response. Since the discovery that they can be reengineered as programmable RNA-guided nucleases, there has been significant interest in using these systems to perform diverse and precise genetic manipulations. Here, we outline recent advances in the mechanistic understanding of CRISPR-Cas9, how these findings have been leveraged in the rational redesign of Cas9 variants with altered activities, and how these novel tools can be exploited for biotechnology and therapeutics. We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight how future structural studies will bolster these technologies.
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Affiliation(s)
- Jack Pk Bravo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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