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Sinan S, Appleby NM, Russell R. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. bioRxiv 2023:2023.07.25.550589. [PMID: 37546762 PMCID: PMC10402064 DOI: 10.1101/2023.07.25.550589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (Kd = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the affinities of both the precursor and mature forms of the crRNA, while deletion of an upstream sequence had no significant effect on affinity of the pre-crRNA. After processing, the mature crRNA remains very tightly bound to Cas12a, with a half-life of ~1 day and a Kd value of 60 pM. Addition of a 5'-phosphoryl group, which is normally lost during the processing reaction as the scissile phosphate, tightens binding of the mature crRNA by ~10-fold by accelerating binding and slowing dissociation. Using a direct competition assay, we found that pre-crRNA binding specificity is robust to other changes in RNA sequence, including tested changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. Together our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in some genome editing applications.
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Affiliation(s)
- Selma Sinan
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Nathan M. Appleby
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
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2
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Vasileva A, Selkova P, Arseniev A, Abramova M, Shcheglova N, Musharova O, Mizgirev I, Artamonova T, Khodorkovskii M, Severinov K, Fedorova I. Characterization of CoCas9 nuclease from Capnocytophaga ochracea. RNA Biol 2023; 20:750-759. [PMID: 37743659 PMCID: PMC10521337 DOI: 10.1080/15476286.2023.2256578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 09/26/2023] Open
Abstract
Cas9 nucleases are widely used for genome editing and engineering. Cas9 enzymes encoded by CRISPR-Cas defence systems of various prokaryotic organisms possess different properties such as target site preferences, size, and DNA cleavage efficiency. Here, we biochemically characterized CoCas9 from Capnocytophaga ochracea, a bacterium that inhabits the oral cavity of humans and contributes to plaque formation on teeth. CoCas9 recognizes a novel 5'-NRRWC-3' PAM and efficiently cleaves DNA in vitro. Functional characterization of CoCas9 opens ways for genetic engineering of C. ochracea using its endogenous CRISPR-Cas system. The novel PAM requirement makes CoCas9 potentially useful in genome editing applications.
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Affiliation(s)
- A. Vasileva
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - P. Selkova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - A. Arseniev
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - M. Abramova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - N. Shcheglova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - O. Musharova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - I. Mizgirev
- Laboratory of Carcinogenesis and Aging, N.N. Petrov National Medical Research Center of Oncology, St. Petersburg, Russia
| | - T. Artamonova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - M. Khodorkovskii
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - K. Severinov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - I. Fedorova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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3
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Abstract
High-resolution structures solved by Schuler et al. shed light on how Cas9's evolutionary ancestor IscB operates as an RNA-guided nuclease. With only two-fifths the size of Cas9, IscB holds great promise for alleviating the cargo size constraint of in vivo CRISPR delivery.
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Affiliation(s)
- Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Renke Tan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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4
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Urbaitis T, Gasiunas G, Young JK, Hou Z, Paulraj S, Godliauskaite E, Juskeviciene MM, Stitilyte M, Jasnauskaite M, Mabuchi M, Robb GB, Siksnys V. A new family of CRISPR-type V nucleases with C-rich PAM recognition. EMBO Rep 2022; 23:e55481. [PMID: 36268581 PMCID: PMC9724661 DOI: 10.15252/embr.202255481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 12/12/2022] Open
Abstract
Most CRISPR-type V nucleases are stimulated to cleave double-stranded (ds) DNA targets by a T-rich PAM, which restricts their targeting range. Here, we identify and characterize a new family of type V RNA-guided nuclease, Cas12l, that exclusively recognizes a C-rich (5'-CCY-3') PAM. The organization of genes within its CRISPR locus is similar to type II-B CRISPR-Cas9 systems, but both sequence analysis and functional studies establish it as a new family of type V effector. Biochemical experiments show that Cas12l nucleases function optimally between 37 and 52°C, depending on the ortholog, and preferentially cut supercoiled DNA. Like other type V nucleases, it exhibits collateral nonspecific ssDNA and ssRNA cleavage activity that is triggered by ssDNA or dsDNA target recognition. Finally, we show that one family member, Asp2Cas12l, functions in a heterologous cellular environment, altogether, suggesting that this new group of CRISPR-associated nucleases may be harnessed as genome editing reagents.
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Affiliation(s)
- Tomas Urbaitis
- CasZymeVilniusLithuania,Institute of BiotechnologyVilnius UniversityVilniusLithuania
| | | | | | - Zhenglin Hou
- Farming Solutions & DigitalCorteva Agriscience™JohnstonIAUSA
| | | | | | | | - Migle Stitilyte
- CasZymeVilniusLithuania,Institute of BiotechnologyVilnius UniversityVilniusLithuania
| | - Monika Jasnauskaite
- CasZymeVilniusLithuania,Present address:
LSC‐EMBL Partnership Institute for Genome Technologies Editing, Life Sciences CenterVilnius UniversityVilniusLithuania
| | | | | | - Virginijus Siksnys
- CasZymeVilniusLithuania,Institute of BiotechnologyVilnius UniversityVilniusLithuania
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5
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Seher TD, Nguyen N, Ramos D, Bapat P, Nobile CJ, Sindi SS, Hernday AD. AddTag, a two-step approach with supporting software package that facilitates CRISPR/Cas-mediated precision genome editing. G3 (Bethesda) 2021; 11:jkab216. [PMID: 34544122 PMCID: PMC8496238 DOI: 10.1093/g3journal/jkab216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/13/2021] [Indexed: 12/22/2022]
Abstract
CRISPR/Cas-induced genome editing is a powerful tool for genetic engineering, however, targeting constraints limit which loci are editable with this method. Since the length of a DNA sequence impacts the likelihood it overlaps a unique target site, precision editing of small genomic features with CRISPR/Cas remains an obstacle. We introduce a two-step genome editing strategy that virtually eliminates CRISPR/Cas targeting constraints and facilitates precision genome editing of elements as short as a single base-pair at virtually any locus in any organism that supports CRISPR/Cas-induced genome editing. Our two-step approach first replaces the locus of interest with an "AddTag" sequence, which is subsequently replaced with any engineered sequence, and thus circumvents the need for direct overlap with a unique CRISPR/Cas target site. In this study, we demonstrate the feasibility of our approach by editing transcription factor binding sites within Candida albicans that could not be targeted directly using the traditional gene-editing approach. We also demonstrate the utility of the AddTag approach for combinatorial genome editing and gene complementation analysis, and we present a software package that automates the design of AddTag editing.
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Affiliation(s)
- Thaddeus D Seher
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA 95343, USA
| | - Namkha Nguyen
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA 95343, USA
| | - Diana Ramos
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Priyanka Bapat
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA 95343, USA
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California, Merced, Merced, CA 95343, USA
| | - Suzanne S Sindi
- Health Sciences Research Institute, University of California, Merced, Merced, CA 95343, USA
- Department of Applied Mathematics, School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Aaron D Hernday
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California, Merced, Merced, CA 95343, USA
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6
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Strohkendl I, Saifuddin FA, Rybarski JR, Finkelstein IJ, Russell R. Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a. Mol Cell 2018; 71:816-824.e3. [PMID: 30078724 PMCID: PMC6679935 DOI: 10.1016/j.molcel.2018.06.043] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 12/26/2022]
Abstract
Class 2 CRISPR-Cas nucleases are programmable genome editing tools with promising applications in human health and disease. However, DNA cleavage at off-target sites that resemble the target sequence is a pervasive problem that remains poorly understood mechanistically. Here, we use quantitative kinetics to dissect the reaction steps of DNA targeting by Acidaminococcus sp Cas12a (also known as Cpf1). We show that Cas12a binds DNA tightly in two kinetically separable steps. Protospacer-adjacent motif (PAM) recognition is followed by rate-limiting R-loop propagation, leading to inevitable DNA cleavage of both strands. Despite functionally irreversible binding, Cas12a discriminates strongly against mismatches along most of the DNA target sequence. This result implies substantial reversibility during R-loop formation-a late transition state-and defies common descriptions of a "seed" region. Our results provide a quantitative basis for the DNA cleavage patterns measured in vivo and observations of greater reported target specificity for Cas12a than for the Cas9 nuclease.
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Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, 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 and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Rick Russell
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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7
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Pauwels L, De Clercq R, Goossens J, Iñigo S, Williams C, Ron M, Britt A, Goossens A. A Dual sgRNA Approach for Functional Genomics in Arabidopsis thaliana. G3 (Bethesda) 2018; 8:2603-2615. [PMID: 29884615 PMCID: PMC6071589 DOI: 10.1534/g3.118.200046] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/30/2018] [Indexed: 12/25/2022]
Abstract
Reverse genetics uses loss-of-function alleles to interrogate gene function. The advent of CRISPR/Cas9-based gene editing now allows the generation of knock-out alleles for any gene and entire gene families. Even in the model plant Arabidopsis thaliana, gene editing is welcomed as T-DNA insertion lines do not always generate null alleles. Here, we show efficient generation of heritable mutations in Arabidopsis using CRISPR/Cas9 with a workload similar to generating overexpression lines. We obtain for several different genes Cas9 null-segregants with bi-allelic mutations in the T2 generation. While somatic mutations were predominantly generated by the canonical non-homologous end joining (cNHEJ) pathway, we observed inherited mutations that were the result of synthesis-dependent microhomology-mediated end joining (SD-MMEJ), a repair pathway linked to polymerase θ (PolQ). We also demonstrate that our workflow is compatible with a dual sgRNA approach in which a gene is targeted by two sgRNAs simultaneously. This paired nuclease method results in more reliable loss-of-function alleles that lack a large essential part of the gene. The ease of the CRISPR/Cas9 workflow should help in the eventual generation of true null alleles of every gene in the Arabidopsis genome, which will advance both basic and applied plant research.
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Affiliation(s)
- Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Rebecca De Clercq
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jonas Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Sabrina Iñigo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Clara Williams
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Mily Ron
- UC Davis, Department of Plant Biology, Davis, CA 95616, US
| | - Anne Britt
- UC Davis, Department of Plant Biology, Davis, CA 95616, US
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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8
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Abstract
In the postgenomic era, the ability to quickly, efficiently, and inexpensively assign function to the zebrafish proteome is critical. Clustered regularly interspaced short palindromic repeats (CRISPRs) have revolutionized the ability to perform reverse genetics because of its simplicity and broad applicability. The CRISPR system is composed of an engineered, gene-specific single guide RNA (sgRNA) and a Cas9 enzyme that causes double-stranded breaks in DNA at the targeted site. This simple, two-part system, when injected into one-cell stage zebrafish embryos, efficiently mutates target loci at a frequency such that injected embryos phenocopy known mutant phenotypes. This property allows for CRISPR-based F0 screening in zebrafish, which provides a means to screen through a large number of candidate genes for their role in a phenotype of interest. While there are important considerations for any successful genetic screen, CRISPR screening has significant benefits over conventional methods and can be accomplished in any lab with modest molecular biology experience.
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Affiliation(s)
- A N Shah
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - C B Moens
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - A C Miller
- University of Oregon, Eugene, OR, United States
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9
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Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is poised to transform developmental biology by providing a simple, efficient method to precisely manipulate the genome of virtually any developing organism. This RNA-guided nuclease (RGN)-based approach already has been effectively used to induce targeted mutations in multiple genes simultaneously, create conditional alleles, and generate endogenously tagged proteins. Illustrating the adaptability of RGNs, the genomes of >20 different plant and animal species as well as multiple cell lines and primary cells have been successfully modified. Here we review the current and potential uses of RGNs to investigate genome function during development.
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Affiliation(s)
- Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Brian V Jenkins
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate M O'Connor-Giles
- Laboratory of Genetics, Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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