51
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Wimmer F, Englert F, Beisel CL. A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes. Methods Mol Biol 2022; 2433:391-411. [PMID: 34985758 DOI: 10.1007/978-1-0716-1998-8_24] [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] [Indexed: 06/14/2023]
Abstract
Type I CRISPR-Cas systems represent the most common and diverse type of these prokaryotic defense systems and are being harnessed for a growing set of applications. As these systems rely on multi-protein effector complexes, their characterization remains challenging. Here, we report a rapid and straightforward method to characterize these systems in a cell-free transcription-translation (TXTL) system. A ribonucleoprotein complex is produced and binds to its target next to a recognized PAM, thereby preventing the targeted sequence from being cleaved by a restriction enzyme. Selection for uncleaved targeted plasmids leads to an enrichment of recognized sequences within a PAM library. This assay will aid the exploration of CRISPR-Cas diversity and evolution and help contribute new systems for CRISPR technologies and applications.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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52
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Devi V, Harjai K, Chhibber S. Self-targeting spacers in CRISPR-array: Accidental occurrence or evolutionarily conserved phenomenon. J Basic Microbiol 2021; 62:4-12. [PMID: 34904260 DOI: 10.1002/jobm.202100514] [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: 09/22/2021] [Revised: 11/18/2021] [Accepted: 11/27/2021] [Indexed: 11/12/2022]
Abstract
In recent years, a tremendous amount of inquisitiveness among scientists in the clustered regularly interspaced short palindrome repeats (CRISPR)-CRISPR-associated proteins (Cas) has led to many studies to delineate their exact role in prokaryotes. CRISPR-Cas is an adaptive immune system that protects prokaryotes from phages and mobile genetic elements. It incorporates small DNA fragment of the invader in the CRISPR-array and protects the host from future invasion by them. In a few instances, the CRISPR-array also incorporates self-targeting spacers, most likely by accident or leaky incorporation. A significant number of spacers are found to match with the host genes across the species; however, self-targeting spacers have not been investigated in detail in most of the organisms. The presence of self-targeting spacers in the CRISPR-array led to speculation that the CRISPR-Cas system has a lot more to offer than just being the conventional adaptive immune system. It has been implicated in gene regulation and autoimmunity more or less equally. In this review, an attempt has been made to understand self-targeting spacers in the context of gene regulation, autoimmunity, and its avoidance strategies.
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Affiliation(s)
- Veena Devi
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India
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53
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Collette N, Dhungel P, Lund SJ, Schwedler JL, Saada EA, Light YK, Sinha A, Schoeniger JS, Negrete OA. Immunocompromised Cas9 transgenic mice for rapid in vivo assessment of host factors involved in highly pathogenic virus infection. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:286-295. [PMID: 34729376 PMCID: PMC8526419 DOI: 10.1016/j.omtm.2021.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/24/2021] [Indexed: 11/26/2022]
Abstract
Targeting host factors for anti-viral development offers several potential advantages over traditional countermeasures that include broad-spectrum activity and prevention of resistance. Characterization of host factors in animal models provides strong evidence of their involvement in disease pathogenesis, but the feasibility of performing high-throughput in vivo analyses on lists of genes is problematic. To begin addressing the challenges of screening candidate host factors in vivo, we combined advances in CRISPR-Cas9 genome editing with an immunocompromised mouse model used to study highly pathogenic viruses. Transgenic mice harboring a constitutively expressed Cas9 allele (Cas9tg/tg) with or without knockout of type I interferon receptors served to optimize in vivo delivery of CRISPR single-guide RNA (sgRNA) using Invivofectamine 3.0, a simple and easy-to-use lipid nanoparticle reagent. Invivofectamine 3.0-mediated liver-specific editing to remove activity of the critical Ebola virus host factor Niemann-Pick disease type C1 in an average of 74% of liver cells protected immunocompromised Cas9tg/tg mice from lethal surrogate Ebola virus infection. We envision that immunocompromised Cas9tg/tg mice combined with straightforward sgRNA in vivo delivery will enable efficient host factor loss-of-function screening in the liver and other organs to rapidly study their effects on viral pathogenesis and help initiate development of broad-spectrum, host-directed therapies against emerging pathogens.
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Affiliation(s)
- Nicole Collette
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Pragyesh Dhungel
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Sean J Lund
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Jennifer L Schwedler
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Edwin A Saada
- Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Yooli K Light
- Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Anupama Sinha
- Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Joseph S Schoeniger
- Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Oscar A Negrete
- Department of Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA 94550, USA
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54
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
- Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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55
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Zhang Y, Marchisio MA. Type II anti-CRISPR proteins as a new tool for synthetic biology. RNA Biol 2021; 18:1085-1098. [PMID: 32991234 PMCID: PMC8244766 DOI: 10.1080/15476286.2020.1827803] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/03/2020] [Accepted: 09/20/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) system represents, in prokaryotes, an adaptive and inheritable immune response against invading DNA. The discovery of anti-CRISPR proteins (Acrs), which are inhibitors of CRISPR-Cas, mainly encoded by phages and prophages, showed a co-evolution history between prokaryotes and phages. In the past decade, the CRISPR-Cas systems together with the corresponding Acrs have been turned into a genetic-engineering tool. Among the six types of CRISPR-Cas characterized so far, type II CRISPR-Cas system is the most popular in biotechnology. Here, we discuss about the discovery, the reported inhibitory mechanisms, and the applications in both gene editing and gene transcriptional regulation of type II Acrs. Moreover, we provide insights into future potential research and feasible applications.
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Affiliation(s)
- Yadan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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56
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Jia N, Patel DJ. Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins. Nat Rev Mol Cell Biol 2021; 22:563-579. [PMID: 34089013 DOI: 10.1038/s41580-021-00371-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
CRISPR loci and Cas proteins provide adaptive immunity in prokaryotes against invading bacteriophages and plasmids. In response, bacteriophages have evolved a broad spectrum of anti-CRISPR proteins (anti-CRISPRs) to counteract and overcome this immunity pathway. Numerous anti-CRISPRs have been identified to date, which suppress single-subunit Cas effectors (in CRISPR class 2, type II, V and VI systems) and multisubunit Cascade effectors (in CRISPR class 1, type I and III systems). Crystallography and cryo-electron microscopy structural studies of anti-CRISPRs bound to effector complexes, complemented by functional experiments in vitro and in vivo, have identified four major CRISPR-Cas suppression mechanisms: inhibition of CRISPR-Cas complex assembly, blocking of target binding, prevention of target cleavage, and degradation of cyclic oligonucleotide signalling molecules. In this Review, we discuss novel mechanistic insights into anti-CRISPR function that have emerged from X-ray crystallography and cryo-electron microscopy studies, and how these structures in combination with function studies provide valuable tools for the ever-growing CRISPR-Cas biotechnology toolbox, to be used for precise and robust genome editing and other applications.
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Affiliation(s)
- Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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57
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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58
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Kozovska Z, Rajcaniova S, Munteanu P, Dzacovska S, Demkova L. CRISPR: History and perspectives to the future. Biomed Pharmacother 2021; 141:111917. [PMID: 34328110 DOI: 10.1016/j.biopha.2021.111917] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022] Open
Abstract
This review summarizes the information about the history and future of the CRISPR/Cas9 method. Genome editing can be perceived as a group of technologies that allow scientists to change the DNA of an organism. These technologies involve the deletion, insertion, or modification of the genome at a specific site in a DNA sequence. Gene therapy in humans has a perspective to be used to eliminate the gene responsible for a particular genetic disorder. The review focuses on the key elements of this promising method and the possibility of its application in the treatment of cancer and genetic diseases.
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Affiliation(s)
- Z Kozovska
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia.
| | - S Rajcaniova
- Department of Cell and Molecular Biology of Drugs Faculty of Pharmacy, Comenius University, Odbojarov 10, 83232 Bratislava, Slovakia
| | - P Munteanu
- Institute of Biochemistry and Microbiology, Faculty of chemical and food technology, Slovak Technical University, Radlinského 9, 81237 Bratislava, Slovakia
| | - S Dzacovska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia
| | - L Demkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, University Science Park for Biomedicine, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
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59
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Barkau CL, O'Reilly D, Eddington SB, Damha MJ, Gagnon KT. Small nucleic acids and the path to the clinic for anti-CRISPR. Biochem Pharmacol 2021; 189:114492. [PMID: 33647260 PMCID: PMC8725204 DOI: 10.1016/j.bcp.2021.114492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.
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Affiliation(s)
- Christopher L Barkau
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Seth B Eddington
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA.
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60
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Gama-Brambila R, Chen J, Dabiri Y, Tascher G, Němec V, Münch C, Song G, Knapp S, Cheng X. A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins. JACS AU 2021; 1:777-785. [PMID: 34467332 PMCID: PMC8395650 DOI: 10.1021/jacsau.1c00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Indexed: 06/01/2023]
Abstract
The discovery of clustered regularly interspaced short palindromic repeats and their associated proteins (Cas) has revolutionized the field of genome and epigenome editing. A number of new methods have been developed to precisely control the function and activity of Cas proteins, including fusion proteins and small-molecule modulators. Proteolysis-targeting chimeras (PROTACs) represent a new concept using the ubiquitin-proteasome system to degrade a protein of interest, highlighting the significance of chemically induced protein-E3 ligase interaction in drug discovery. Here, we engineered Cas proteins (Cas9, dCas9, Cas12, and Cas13) by inserting a Phe-Cys-Pro-Phe (FCPF) amino acid sequence (known as the π-clamp system) and demonstrate that the modified CasFCPF proteins can be (1) labeled in live cells by perfluoroaromatics carrying the fluorescein or (2) degraded by a perfluoroaromatics-functionalized PROTAC (PROTAC-FCPF). A proteome-wide analysis of PROTAC-FCPF-mediated Cas9FCPF protein degradation revealed a high target specificity, suggesting a wide range of applications of perfluoroaromatics-induced proximity in the regulation of stability, activity, and functionality of any FCPF-tagging protein.
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Affiliation(s)
- Rodrigo
A. Gama-Brambila
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Jie Chen
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Yasamin Dabiri
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Georg Tascher
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt am Main, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | - Václav Němec
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Christian Münch
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt am Main, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | - Guangqi Song
- Department
of Gastroenterology, Zhongshan Hospital
of Fudan University, 180 Fenglin Road, Xuhui District, 200032 Shanghai, China
| | - Stefan Knapp
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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61
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Chen ZP, Zhang HM, Yang P, Yuan R, Li Y, Liang WB. No-nonspecific recognition-based amplification strategy for endonuclease activity screening with dual-color DNA nano-clew. Biosens Bioelectron 2021; 190:113446. [PMID: 34166945 DOI: 10.1016/j.bios.2021.113446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
The inevitable nonspecific recognition severely restricted widely used nucleic acid amplification strategies, which has become an urgent problem in current scientific research. Herein, we developed a novel no-nonspecific recognition-based amplification strategy to construct dual-color dye loaded nano-clew as ultrabright illuminant for screening endonuclease activity with Escherichia coliRY13 I (EcoR I) as a model, which overcame some major drawbacks such as nonspecific recognition and photobleaching. Typically, the target endonuclease induces cleavage of the customized dumbbell-shape substrate (DSS) to generate two same triggers that can initiate the rolling circle amplification (RCA) to prepare long single-strand DNA (lssDNA), which could self-assemble into irregular DNA nano-clew based on the electrostatic interactions with Mg2+ to furtherly capture the donor and accepter fluorophore proximately, constructing the dye loaded nano-clew with dual-color fluorescence (FL) emission to resist photobleaching. Importantly, in absence of EcoR I, even if the DSS could combine with circular template a little, the reaction system performed hardly RCA reaction due to no cohesive terminus, resulting an extremely low background fluorescence signal because of the prevention of nonspecific RCA reaction. As expected, the proposed sensing platform with a low limit of detection (LOD) of 3.4 × 10-7 U/μL was demonstrated to work well for endonuclease inhibitors screening also. Furthermore, the proposed no-nonspecific recognition strategy could be readily extended to various DNA or RNA enzymes such as DNA methyltransferase, DNA repair-related enzymes and polynucleotide kinase just by simply changing the recognition sequence in the DNA substrate, performing great potential of endonucleases-related clinical diagnosis and drugs discovery.
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Affiliation(s)
- Zhao-Peng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Hao-Min Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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62
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Yu L, Marchisio MA. Saccharomyces cerevisiae Synthetic Transcriptional Networks Harnessing dCas12a and Type V-A anti-CRISPR Proteins. ACS Synth Biol 2021; 10:870-883. [PMID: 33819020 DOI: 10.1021/acssynbio.1c00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Type V-A anti-CRISPR proteins (AcrVAs) represent the response from phages to the CRISPR-Cas12a prokaryotic immune system. CRISPR-Cas12a was repurposed, in high eukaryotes, to carry out gene editing and transcription regulation, the latter via a nuclease-dead Cas12a (dCas12a). Consequently, AcrVAs were adopted to regulate (d)Cas12a activity. However, the usage of both dCas12a-based transcription factors and AcrVAs in the yeast Saccharomyces cerevisiae has not been explored. In this work, we show that, in the baker's yeast, two dCas12a proteins (denAsCas12a and dLbCas12a) work both as activators (upon fusion to a strong activation domain) and repressors, whereas dMbCa12a is nonfunctional. The activation efficiency of dCas12a-ADs manifests a dependence on the number of crRNA binding sites, whereas it is not directly correlated to the amount of crRNA in the cells. Moreover, AcrVA1, AcrVA4, and AcrVA5 are able to inhibit dLbCa12a in yeast, and denAsCas12a is only inhibited by AcrVA1. However, AcrVA1 performs well at high concentration only. Coexpression of two or three AcrVAs does not enhance inhibition of dCas12a(-AD), suggesting a competition between different AcrVAs. Further, AcrVA4 significantly limits gene editing by LbCas12a. Overall, our results indicate that dCas12a:crRNA and AcrVA proteins are highly performant components in S. cerevisiae synthetic transcriptional networks.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
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63
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Hoffmann MD, Mathony J, Upmeier Zu Belzen J, Harteveld Z, Aschenbrenner S, Stengl C, Grimm D, Correia BE, Eils R, Niopek D. Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein. Nucleic Acids Res 2021; 49:e29. [PMID: 33330940 PMCID: PMC7969004 DOI: 10.1093/nar/gkaa1198] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 10/30/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Optogenetic control of CRISPR–Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and engineered, the need for straightforward strategies to control their activity via exogenous stimuli persists. The Cas9 from Neisseria meningitidis (Nme) is a particularly small and target-specific Cas9 orthologue, and thus of high interest for in vivo genome editing applications. Here, we report the first optogenetic tool to control NmeCas9 activity in mammalian cells via an engineered, light-dependent anti-CRISPR (Acr) protein. Building on our previous Acr engineering work, we created hybrids between the NmeCas9 inhibitor AcrIIC3 and the LOV2 blue light sensory domain from Avena sativa. Two AcrIIC3-LOV2 hybrids from our collection potently blocked NmeCas9 activity in the dark, while permitting robust genome editing at various endogenous loci upon blue light irradiation. Structural analysis revealed that, within these hybrids, the LOV2 domain is located in striking proximity to the Cas9 binding surface. Together, our work demonstrates optogenetic regulation of a type II-C CRISPR effector and might suggest a new route for the design of optogenetic Acrs.
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Affiliation(s)
- Mareike D Hoffmann
- Dept. of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, 69120 Heidelberg, Germany
| | - Jan Mathony
- Centre for Synthetic Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Department of Biology, Technical University of Darmstadt,64287 Darmstadt, Germany.,PhD Student, BZH graduate school, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Zander Harteveld
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Sabine Aschenbrenner
- Centre for Synthetic Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Department of Biology, Technical University of Darmstadt,64287 Darmstadt, Germany
| | | | - Dirk Grimm
- Dept. of Infectious Diseases/Virology, Medical Faculty, University of Heidelberg, 69120 Heidelberg, Germany.,BioQuant, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Heidelberg, 69120 Heidelberg, Germany
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Roland Eils
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin 10178, Germany.,Health Data Science Unit, BioQuant and Medical Faculty of Heidelberg University, Heidelberg 69120, Germany
| | - Dominik Niopek
- Centre for Synthetic Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany.,Department of Biology, Technical University of Darmstadt,64287 Darmstadt, Germany
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64
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Abstract
Glioblastoma is a highly lethal form of brain cancer with no current treatment options that substantially improve patient outcomes. A key therapeutic challenge is the identification of methods that reduce tumor burden while leaving normal cells unaffected. We show that TERT-promoter mutations, common in glioblastoma, lead to TERT reactivation through increased binding of GABPB1L-isoform–containing transcription factor complexes. In turn, we find that cancer-cell–specific inhibition of TERT through GABPB1L reduction results in near-term anti-growth effects and an impaired DNA damage response that profoundly increase the sensitivity of glioblastoma tumors to frontline chemotherapy. Our results thus provide rationale for GABPB1L inhibition combined with temozolomide chemotherapy treatment as a promising therapeutic strategy for glioblastoma. Most glioblastomas (GBMs) achieve cellular immortality by acquiring a mutation in the telomerase reverse transcriptase (TERT) promoter. TERT promoter mutations create a binding site for a GA binding protein (GABP) transcription factor complex, whose assembly at the promoter is associated with TERT reactivation and telomere maintenance. Here, we demonstrate increased binding of a specific GABPB1L-isoform–containing complex to the mutant TERT promoter. Furthermore, we find that TERT promoter mutant GBM cells, unlike wild-type cells, exhibit a critical near-term dependence on GABPB1L for proliferation, notably also posttumor establishment in vivo. Up-regulation of the protein paralogue GABPB2, which is normally expressed at very low levels, can rescue this dependence. More importantly, when combined with frontline temozolomide (TMZ) chemotherapy, inducible GABPB1L knockdown and the associated TERT reduction led to an impaired DNA damage response that resulted in profoundly reduced growth of intracranial GBM tumors. Together, these findings provide insights into the mechanism of cancer-specific TERT regulation, uncover rapid effects of GABPB1L-mediated TERT suppression in GBM maintenance, and establish GABPB1L inhibition in combination with chemotherapy as a therapeutic strategy for TERT promoter mutant GBM.
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65
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Molinari E, Sayer JA. Gene and epigenetic editing in the treatment of primary ciliopathies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:353-401. [PMID: 34175048 DOI: 10.1016/bs.pmbts.2021.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Primary ciliopathies are inherited human disorders that arise from mutations in ciliary genes. They represent a spectrum of severe, incurable phenotypes, differentially involving several organs, including the kidney and the eye. The development of gene-based therapies is opening up new avenues for the treatment of ciliopathies. Particularly attractive is the possibility of correcting in situ the causative genetic mutation, or pathological epigenetic changes, through the use of gene editing tools. Due to their versatility and efficacy, CRISPR/Cas-based systems represent the most promising gene editing toolkit for clinical applications. However, delivery and specificity issues have so far held back the translatability of CRISPR/Cas-based therapies into clinical practice, especially where systemic administration is required. The eye, with its characteristics of high accessibility and compartmentalization, represents an ideal target for in situ gene correction. Indeed, studies for the evaluation of a CRISPR/Cas-based therapy for in vivo gene correction to treat a retinal ciliopathy have reached the clinical stage. Further technological advances may be required for the development of in vivo CRISPR-based treatments for the kidney. We discuss here the possibilities and the challenges associated to the implementation of CRISPR/Cas-based therapies for the treatment of primary ciliopathies with renal and retinal phenotypes.
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Affiliation(s)
- Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom; Renal Services, The Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, United Kingdom.
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66
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Zhao J, Inomata R, Kato Y, Miyagishi M. Development of aptamer-based inhibitors for CRISPR/Cas system. Nucleic Acids Res 2021; 49:1330-1344. [PMID: 33123724 PMCID: PMC7897479 DOI: 10.1093/nar/gkaa865] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 09/17/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022] Open
Abstract
The occurrence of accidental mutations or deletions caused by genome editing with CRISPR/Cas9 system remains a critical unsolved problem of the technology. Blocking excess or prolonged Cas9 activity in cells is considered as one means of solving this problem. Here, we report the development of an inhibitory DNA aptamer against Cas9 by means of in vitro selection (systematic evolution of ligands by exponential enrichment) and subsequent screening with an in vitro cleavage assay. The inhibitory aptamer could bind to Cas9 at low nanomolar affinity and partially form a duplex with CRISPR RNA, contributing to its inhibitory activity. We also demonstrated that improving the inhibitory aptamer with locked nucleic acids efficiently suppressed Cas9-directed genome editing in cells and reduced off-target genome editing. The findings presented here might enable the development of safer and controllable genome editing for biomedical research and gene therapy.
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Affiliation(s)
- Jing Zhao
- Molecular Composite Physiology Research Group, Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8566, Japan.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Rika Inomata
- Molecular Composite Physiology Research Group, Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8566, Japan.,Program in Life Science Innovation, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Yoshio Kato
- Molecular Composite Physiology Research Group, Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8566, Japan
| | - Makoto Miyagishi
- Molecular Composite Physiology Research Group, Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8566, Japan.,Program in Life Science Innovation, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
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67
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Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg? Biochem Soc Trans 2021; 48:507-516. [PMID: 32196554 DOI: 10.1042/bst20190638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022]
Abstract
Bacteriophages (phages) and their preys are engaged in an evolutionary arms race driving the co-adaptation of their attack and defense mechanisms. In this context, phages have evolved diverse anti-CRISPR proteins to evade the bacterial CRISPR-Cas immune system, and propagate. Anti-CRISPR proteins do not share much resemblance with each other and with proteins of known function, which raises intriguing questions particularly relating to their modes of action. In recent years, there have been many structure-function studies shedding light on different CRISPR-Cas inhibition strategies. As the anti-CRISPR field of research is rapidly growing, it is opportune to review the current knowledge on these proteins, with particular emphasis on the molecular strategies deployed to inactivate distinct steps of CRISPR-Cas immunity. Anti-CRISPR proteins can be orthosteric or allosteric inhibitors of CRISPR-Cas machineries, as well as enzymes that irreversibly modify CRISPR-Cas components. This repertoire of CRISPR-Cas inhibition mechanisms will likely expand in the future, providing fundamental knowledge on phage-bacteria interactions and offering great perspectives for the development of biotechnological tools to fine-tune CRISPR-Cas-based gene edition.
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68
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Huang L, Yang B, Yi H, Asif A, Wang J, Lithgow T, Zhang H, Minhas FUAA, Yin Y. AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. Nucleic Acids Res 2021; 49:D622-D629. [PMID: 33068435 PMCID: PMC7778997 DOI: 10.1093/nar/gkaa857] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/10/2020] [Accepted: 09/22/2020] [Indexed: 11/17/2022] Open
Abstract
CRISPR–Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR–Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR–Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed Acr-Aca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.
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Affiliation(s)
- Le Huang
- Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Bowen Yang
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
| | - Haidong Yi
- Department of Computer Science, University of North Carolina at Chapel Hill, NC, USA
| | - Amina Asif
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), PO Nilore, Islamabad, Pakistan.,Department of Computer Science, National University of Computer and Emerging Sciences (NUCES), Islamabad, Pakistan
| | - Jiawei Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Han Zhang
- College of Artificial Intelligence, Nankai University, Tianjin, China
| | | | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
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69
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Abstract
Bacteriophages encode diverse anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas immunity during infection of their bacterial hosts. Although detailed mechanisms have been characterized for multiple Acr proteins, an understanding of their role in phage infection biology is just emerging. Here, we review recent work in this area and propose a framework of "phage autonomy" to evaluate CRISPR-immune evasion strategies. During phage infection, Acr proteins are deployed by a tightly regulated "fast on-fast off" transcriptional burst, which is necessary, but insufficient, for CRISPR-Cas inactivation. Instead of a single phage shutting down CRISPR-Cas immunity, a community of acr-carrying phages cooperate to suppress bacterial immunity, displaying low phage autonomy. Enzymatic Acr proteins with novel mechanisms have been recently revealed and are predicted to enhance phage autonomy, while phage DNA protective measures offer the highest phage autonomy observed. These varied Acr mechanisms and strengths also have unexpected impacts on the bacterial populations and competing phages.
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Affiliation(s)
- Yuping Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94403, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94403, USA; Innovative Genomics Institute, Berkeley, CA, USA.
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70
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Nobrega FL, Walinga H, Dutilh BE, Brouns SJJ. Prophages are associated with extensive CRISPR-Cas auto-immunity. Nucleic Acids Res 2020; 48:12074-12084. [PMID: 33219687 PMCID: PMC7708048 DOI: 10.1093/nar/gkaa1071] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS has been suggested to reflect potential auto-immunity as an unwanted side effect of CRISPR-Cas defense, or a regulatory mechanism for gene expression. Here we investigated the incidence, distribution, and evasion of STS in over 100 000 bacterial genomes. We found STS in all CRISPR-Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR-Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR-Cas systems appears to be rare, suggesting a level of escape from the potentially deleterious effects of STS by other mechanisms such as anti-CRISPR proteins and CRISPR target mutations. We propose a scenario where it is common to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects as mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages.
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Affiliation(s)
- Franklin L Nobrega
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Hielke Walinga
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
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71
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Westra ER, Levin BR. It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements. Proc Natl Acad Sci U S A 2020; 117:27777-27785. [PMID: 33122438 PMCID: PMC7668106 DOI: 10.1073/pnas.1915966117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.
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Affiliation(s)
- Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE Cornwall, United Kingdom;
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA 30307
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72
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Pinilla-Redondo R, Shehreen S, Marino ND, Fagerlund RD, Brown CM, Sørensen SJ, Fineran PC, Bondy-Denomy J. Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nat Commun 2020; 11:5652. [PMID: 33159058 PMCID: PMC7648647 DOI: 10.1038/s41467-020-19415-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas). We uncover 11 type I-F and/or I-E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.
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Affiliation(s)
- Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- University College Copenhagen, Copenhagen, Denmark
| | - Saadlee Shehreen
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Bio-protection Research Centre, University of Otago, Dunedin, New Zealand.
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.
- Quantitative Biosciences Institute, UCSF, San Francisco, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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73
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Kaul T, Sony SK, Verma R, Motelb KFA, Prakash AT, Eswaran M, Bharti J, Nehra M, Kaul R. Revisiting CRISPR/Cas-mediated crop improvement: Special focus on nutrition. J Biosci 2020. [DOI: 10.1007/s12038-020-00094-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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74
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Matsumoto D, Tamamura H, Nomura W. A cell cycle-dependent CRISPR-Cas9 activation system based on an anti-CRISPR protein shows improved genome editing accuracy. Commun Biol 2020; 3:601. [PMID: 33097793 PMCID: PMC7584632 DOI: 10.1038/s42003-020-01340-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022] Open
Abstract
The development of genome editing systems based on the Cas9 endonuclease has greatly facilitated gene knockouts and targeted genetic alterations. Precise editing of target genes without off-target effects is crucial to prevent adverse effects in clinical applications. Although several methods have been reported to result in less off-target effects associated with the CRISPR technology, these often exhibit lower editing efficiency. Therefore, efficient, accurate, and innocuous CRISPR technology is still required. Anti-CRISPR proteins are natural inhibitors of CRISPR-Cas systems derived from bacteriophages. Here, the anti-CRISPR protein, AcrIIA4, was fused with the N terminal region of human Cdt1 that is degraded specifically in S and G2, the phases of the cell cycle when homology-directed repair (HDR) is dominant. Co-expression of SpyCas9 and AcrIIA4-Cdt1 not only increases the frequency of HDR but also suppress off-targets effects. Thus, the combination of SpyCas9 and AcrIIA4-Cdt1 is a cell cycle-dependent Cas9 activation system for accurate and efficient genome editing.
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Affiliation(s)
- Daisuke Matsumoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
- Daisuke Matsumoto, Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan.
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, 734-8553, Japan.
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75
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Lenskaia T, Boley D. Prokaryote autoimmunity in the context of self-targeting by CRISPR-Cas systems. J Bioinform Comput Biol 2020; 18:2050033. [PMID: 33078994 DOI: 10.1142/s021972002050033x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Prokaryote adaptive immunity (CRISPR-Cas systems) can be a threat to its carriers. We analyze the risks of autoimmune reactions related to adaptive immunity in prokaryotes by computational methods. We found important differences between bacteria and archaea with respect to autoimmunity potential. According to the results of our analysis, CRISPR-Cas systems in bacteria are more prone to self-targeting even though they possess fewer spacers per organism on average than archaea. The results of our study provide opportunities to use self-targeting in prokaryotes for biological and medical applications.
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Affiliation(s)
- Tatiana Lenskaia
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union Street SE, Minneapolis, Minnesota 55455, USA
| | - Daniel Boley
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union Street SE, Minneapolis, Minnesota 55455, USA
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76
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Song G, Zhang F, Zhang X, Gao X, Zhu X, Fan D, Tian Y. AcrIIA5 Inhibits a Broad Range of Cas9 Orthologs by Preventing DNA Target Cleavage. Cell Rep 2020; 29:2579-2589.e4. [PMID: 31775029 DOI: 10.1016/j.celrep.2019.10.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/15/2019] [Accepted: 10/18/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 is an adaptive immune system for prokaryotes to defend against invasive genetic elements such as phages and has been used as a powerful tool for genome editing and modulation. To overcome CRISPR immunity, phages encode anti-CRISPR proteins (Acrs) to inhibit Cas9, providing an efficient "off-switch" tool for Cas9-based applications. Here, we characterized AcrIIA5, which is a Cas9 inhibitor discovered in a virulent phage of Streptococcus thermophilus. We found that AcrIIA5 is a potent and broad-spectrum inhibitor of CRISPR-Cas9, which can inhibit diverse Cas9 orthologs of type II-A, type II-B, and type II-C. AcrIIA5 inhibits Cas9 by preventing DNA target cleavage, but DNA target binding of Cas9 is unaffected. Importantly, it can affect the activity of the RuvC nuclease domain of Cas9 independent of the HNH nuclease domain. Our work expands the diversity of the inhibitory mechanisms used by Acrs and provides the guidance for developing controlling tools in Cas9-based applications.
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Affiliation(s)
- Guoxu Song
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Zhang
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuewen Zhang
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xing Gao
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxiao Zhu
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongdong Fan
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Tian
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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77
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Niu Y, Yang L, Gao T, Dong C, Zhang B, Yin P, Hopp AK, Li D, Gan R, Wang H, Liu X, Cao X, Xie Y, Meng X, Deng H, Zhang X, Ren J, Hottiger MO, Chen Z, Zhang Y, Liu X, Feng Y. A Type I-F Anti-CRISPR Protein Inhibits the CRISPR-Cas Surveillance Complex by ADP-Ribosylation. Mol Cell 2020; 80:512-524.e5. [PMID: 33049228 DOI: 10.1016/j.molcel.2020.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/11/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
CRISPR-Cas systems are bacterial anti-viral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here, we report a novel mechanism by which AcrIF11 inhibits the type I-F CRISPR system. Our structural and biochemical studies demonstrate that AcrIF11 functions as a novel mono-ADP-ribosyltransferase (mART) to modify N250 of the Cas8f subunit, a residue required for recognition of the protospacer-adjacent motif, within the crRNA-guided surveillance (Csy) complex from Pseudomonas aeruginosa. The AcrIF11-mediated ADP-ribosylation of the Csy complex results in complete loss of its double-stranded DNA (dsDNA) binding activity. Biochemical studies show that AcrIF11 requires, besides Cas8f, the Cas7.6f subunit for binding to and modifying the Csy complex. Our study not only reveals an unprecedented mechanism of type I CRISPR-Cas inhibition and the evolutionary arms race between phages and bacteria but also suggests an approach for designing highly potent regulatory tools in the future applications of type I CRISPR-Cas systems.
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Affiliation(s)
- Yiying Niu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingguang Yang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Teng Gao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Changpeng Dong
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China
| | - Buyu Zhang
- Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peipei Yin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ann-Katrin Hopp
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Dongdong Li
- The Protein Preparation and Characterization Core Facility of Tsinghua University, The China National Center for Protein Sciences (Beijing) Tsinghua University Branch, Beijing 100084, China
| | - Rui Gan
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Hongou Wang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xi Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yongchao Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohui Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Zeliang Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Liaoning Province, Shenyang 110866, China.
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Xiaoyun Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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78
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Wang J, Dai W, Li J, Xie R, Dunstan RA, Stubenrauch C, Zhang Y, Lithgow T. PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins. Nucleic Acids Res 2020; 48:W348-W357. [PMID: 32459325 PMCID: PMC7319593 DOI: 10.1093/nar/gkaa432] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/22/2020] [Accepted: 05/13/2020] [Indexed: 01/09/2023] Open
Abstract
Anti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR–Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR–Cas machineries for the development of new CRISPR–Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensemble learning based predictor, PaCRISPR, to accurately identify anti-CRISPRs from protein datasets derived from genome and metagenome sequencing projects. PaCRISPR employs different types of feature recognition united within an ensemble framework. Extensive cross-validation and independent tests show that PaCRISPR achieves a significantly more accurate performance compared with homology-based baseline predictors and an existing toolkit. The performance of PaCRISPR was further validated in discovering anti-CRISPRs that were not part of the training for PaCRISPR, but which were recently demonstrated to function as anti-CRISPRs for phage infections. Data visualization on anti-CRISPR relationships, highlighting sequence similarity and phylogenetic considerations, is part of the output from the PaCRISPR toolkit, which is freely available at http://pacrispr.erc.monash.edu/.
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Affiliation(s)
- Jiawei Wang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Wei Dai
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Jiahui Li
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Ruopeng Xie
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Rhys A Dunstan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Christopher Stubenrauch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, VIC 3800, Australia
| | - Yanju Zhang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Trevor Lithgow
- To whom correspondence should be addressed. Tel: +61 3 9902 9217; Fax: +61 3 9905 3726;
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79
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Yu L, Marchisio MA. Types I and V Anti-CRISPR Proteins: From Phage Defense to Eukaryotic Synthetic Gene Circuits. Front Bioeng Biotechnol 2020; 8:575393. [PMID: 33102460 PMCID: PMC7556299 DOI: 10.3389/fbioe.2020.575393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins), a prokaryotic RNA-mediated adaptive immune system, has been repurposed for gene editing and synthetic gene circuit construction both in bacterial and eukaryotic cells. In the last years, the emergence of the anti-CRISPR proteins (Acrs), which are natural OFF-switches for CRISPR-Cas, has provided a new means to control CRISPR-Cas activity and promoted a further development of CRISPR-Cas-based biotechnological toolkits. In this review, we focus on type I and type V-A anti-CRISPR proteins. We first narrate Acrs discovery and analyze their inhibitory mechanisms from a structural perspective. Then, we describe their applications in gene editing and transcription regulation. Finally, we discuss the potential future usage-and corresponding possible challenges-of these two kinds of anti-CRISPR proteins in eukaryotic synthetic gene circuits.
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80
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Eitzinger S, Asif A, Watters KE, Iavarone AT, Knott GJ, Doudna JA, Minhas FUAA. Machine learning predicts new anti-CRISPR proteins. Nucleic Acids Res 2020; 48:4698-4708. [PMID: 32286628 PMCID: PMC7229843 DOI: 10.1093/nar/gkaa219] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 01/30/2023] Open
Abstract
The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.
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Affiliation(s)
- Simon Eitzinger
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Amina Asif
- Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), PO Nilore, Islamabad, Pakistan.,FAST School of Computing, National University of Computer and Emerging Sciences (NUCES), Islamabad, Pakistan
| | - Kyle E Watters
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, 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.,Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA.,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158.,Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Fayyaz Ul Amir Afsar Minhas
- Department of Computer and Information Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), PO Nilore, Islamabad, Pakistan.,Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK
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81
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Jacobsen T, Ttofali F, Liao C, Manchalu S, Gray BN, Beisel CL. Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs. Nucleic Acids Res 2020; 48:5624-5638. [PMID: 32329776 PMCID: PMC7261169 DOI: 10.1093/nar/gkaa272] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems comprise diverse adaptive immune systems in prokaryotes whose RNA-directed nucleases have been co-opted for various technologies. Recent efforts have focused on expanding the number of known CRISPR-Cas subtypes to identify nucleases with novel properties. However, the functional diversity of nucleases within each subtype remains poorly explored. Here, we used cell-free transcription-translation systems and human cells to characterize six Cas12a single-effector nucleases from the V-A subtype, including nucleases sharing high sequence identity. While these nucleases readily utilized each other's guide RNAs, they exhibited distinct PAM profiles and apparent targeting activities that did not track based on phylogeny. In particular, two Cas12a nucleases encoded by Prevotella ihumii (PiCas12a) and Prevotella disiens (PdCas12a) shared over 95% amino-acid identity yet recognized distinct PAM profiles, with PiCas12a but not PdCas12a accommodating multiple G's in PAM positions -2 through -4 and T in position -1. Mutational analyses transitioning PiCas12a to PdCas12a resulted in PAM profiles distinct from either nuclease, allowing more flexible editing in human cells. Cas12a nucleases therefore can exhibit widely varying properties between otherwise related orthologs, suggesting selective pressure to diversify PAM recognition and supporting expansion of the CRISPR toolbox through ortholog mining and PAM engineering.
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Affiliation(s)
- Thomas Jacobsen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Fani Ttofali
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Srinivas Manchalu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | | | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany.,Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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82
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Gussow AB, Park AE, Borges AL, Shmakov SA, Makarova KS, Wolf YI, Bondy-Denomy J, Koonin EV. Machine-learning approach expands the repertoire of anti-CRISPR protein families. Nat Commun 2020; 11:3784. [PMID: 32728052 PMCID: PMC7391736 DOI: 10.1038/s41467-020-17652-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/08/2020] [Indexed: 11/28/2022] Open
Abstract
The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including diverse anti-CRISPR proteins (Acrs) that specifically inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small and highly variable proteins which makes their bioinformatic prediction a formidable task. We present a machine-learning approach for comprehensive Acr prediction. The model shows high predictive power when tested against an unseen test set and was employed to predict 2,500 candidate Acr families. Experimental validation of top candidates revealed two unknown Acrs (AcrIC9, IC10) and three other top candidates were coincidentally identified and found to possess anti-CRISPR activity. These results substantially expand the repertoire of predicted Acrs and provide a resource for experimental Acr discovery.
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Affiliation(s)
- Ayal B Gussow
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Allyson E Park
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Adair L Borges
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Sergey A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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83
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Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA. A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Science 2020; 369:54-59. [PMID: 32467331 PMCID: PMC7975689 DOI: 10.1126/science.abb6151] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022]
Abstract
The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. However, how viruses can counteract this immunity is not known. We describe a listeriaphage (ϕLS46) encoding an anti-CRISPR protein (AcrVIA1) that inactivates the type VI-A CRISPR system of Listeria seeligeri Using genetics, biochemistry, and structural biology, we found that AcrVIA1 interacts with the guide-exposed face of Cas13a, preventing access to the target RNA and the conformational changes required for nuclease activation. Unlike inhibitors of DNA-cleaving Cas nucleases, which cause limited immunosuppression and require multiple infections to bypass CRISPR defenses, a single dose of AcrVIA1 delivered by an individual virion completely dismantles type VI-A CRISPR-mediated immunity.
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Affiliation(s)
- Alexander J Meeske
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alice K Cassel
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Albina Kozlova
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, NY 14583, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14583, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14583, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14583, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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84
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Yi H, Huang L, Yang B, Gomez J, Zhang H, Yin Y. AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. Nucleic Acids Res 2020; 48:W358-W365. [PMID: 32402073 PMCID: PMC7319584 DOI: 10.1093/nar/gkaa351] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/09/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Anti-CRISPR (Acr) proteins encoded by (pro)phages/(pro)viruses have a great potential to enable a more controllable genome editing. However, genome mining new Acr proteins is challenging due to the lack of a conserved functional domain and the low sequence similarity among experimentally characterized Acr proteins. We introduce here AcrFinder, a web server (http://bcb.unl.edu/AcrFinder) that combines three well-accepted ideas used by previous experimental studies to pre-screen genomic data for Acr candidates. These ideas include homology search, guilt-by-association (GBA), and CRISPR-Cas self-targeting spacers. Compared to existing bioinformatics tools, AcrFinder has the following unique functions: (i) it is the first online server specifically mining genomes for Acr-Aca operons; (ii) it provides a most comprehensive Acr and Aca (Acr-associated regulator) database (populated by GBA-based Acr and Aca datasets); (iii) it combines homology-based, GBA-based, and self-targeting approaches in one software package; and (iv) it provides a user-friendly web interface to take both nucleotide and protein sequence files as inputs, and output a result page with graphic representation of the genomic contexts of Acr-Aca operons. The leave-one-out cross-validation on experimentally characterized Acr-Aca operons showed that AcrFinder had a 100% recall. AcrFinder will be a valuable web resource to help experimental microbiologists discover new Anti-CRISPRs.
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Affiliation(s)
- Haidong Yi
- Department of Computer Science, University of North Carolina at Chapel Hill, NC, USA
- College of Computer Science, Nankai University, Tianjin, China
| | - Le Huang
- College of Computer Science, Nankai University, Tianjin, China
| | - Bowen Yang
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Javi Gomez
- Department of Computer Science, Northern Illinois University, DeKalb, IL, USA
| | - Han Zhang
- College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA
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85
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Mathony J, Harteveld Z, Schmelas C, Upmeier Zu Belzen J, Aschenbrenner S, Sun W, Hoffmann MD, Stengl C, Scheck A, Georgeon S, Rosset S, Wang Y, Grimm D, Eils R, Correia BE, Niopek D. Computational design of anti-CRISPR proteins with improved inhibition potency. Nat Chem Biol 2020; 16:725-730. [PMID: 32284602 DOI: 10.1038/s41589-020-0518-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 02/12/2020] [Accepted: 03/12/2020] [Indexed: 11/09/2022]
Abstract
Anti-CRISPR (Acr) proteins are powerful tools to control CRISPR-Cas technologies. However, the available Acr repertoire is limited to naturally occurring variants. Here, we applied structure-based design on AcrIIC1, a broad-spectrum CRISPR-Cas9 inhibitor, to improve its efficacy on different targets. We first show that inserting exogenous protein domains into a selected AcrIIC1 surface site dramatically enhances inhibition of Neisseria meningitidis (Nme)Cas9. Then, applying structure-guided design to the Cas9-binding surface, we converted AcrIIC1 into AcrIIC1X, a potent inhibitor of the Staphylococcus aureus (Sau)Cas9, an orthologue widely applied for in vivo genome editing. Finally, to demonstrate the utility of AcrIIC1X for genome engineering applications, we implemented a hepatocyte-specific SauCas9 ON-switch by placing AcrIIC1X expression under regulation of microRNA-122. Our work introduces designer Acrs as important biotechnological tools and provides an innovative strategy to safeguard CRISPR technologies.
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Affiliation(s)
- Jan Mathony
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
| | - Zander Harteveld
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Carolin Schmelas
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, Germany
| | - Julius Upmeier Zu Belzen
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany
| | - Sabine Aschenbrenner
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mareike D Hoffmann
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Stengl
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sandrine Georgeon
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dirk Grimm
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- BioQuant Center and Cluster of Excellence CellNetworks at Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany
| | - Roland Eils
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Dominik Niopek
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany.
- Health Data Science Unit, University Hospital Heidelberg, Heidelberg, Germany.
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86
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Trasanidou D, Gerós AS, Mohanraju P, Nieuwenweg AC, Nobrega FL, Staals RHJ. Keeping crispr in check: diverse mechanisms of phage-encoded anti-crisprs. FEMS Microbiol Lett 2020; 366:5488435. [PMID: 31077304 PMCID: PMC6538845 DOI: 10.1093/femsle/fnz098] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
CRISPR-Cas represents the only adaptive immune system of prokaryotes known to date. These immune systems are widespread among bacteria and archaea, and provide protection against invasion of mobile genetic elements, such as bacteriophages and plasmids. As a result of the arms-race between phages and their prokaryotic hosts, phages have evolved inhibitors known as anti-CRISPR (Acr) proteins to evade CRISPR immunity. In the recent years, several Acr proteins have been described in both temperate and virulent phages targeting diverse CRISPR-Cas systems. Here, we describe the strategies of Acr discovery and the multiple molecular mechanisms by which these proteins operate to inhibit CRISPR immunity. We discuss the biological relevance of Acr proteins and speculate on the implications of their activity for the development of improved CRISPR-based research and biotechnological tools.
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Affiliation(s)
- Despoina Trasanidou
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Ana Sousa Gerós
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Anna Cornelia Nieuwenweg
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Franklin L Nobrega
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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87
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Davidson AR, Lu WT, Stanley SY, Wang J, Mejdani M, Trost CN, Hicks BT, Lee J, Sontheimer EJ. Anti-CRISPRs: Protein Inhibitors of CRISPR-Cas Systems. Annu Rev Biochem 2020; 89:309-332. [PMID: 32186918 PMCID: PMC9718424 DOI: 10.1146/annurev-biochem-011420-111224] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) together with their accompanying cas (CRISPR-associated) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA, such as viral genomes. CRISPR-Cas systems provide a uniquely powerful defense because they can adapt to newly encountered genomes. The adaptive ability of these systems has been exploited, leading to their development as highly effective tools for genome editing. The widespread use of CRISPR-Cas systems has driven a need for methods to control their activity. This review focuses on anti-CRISPRs (Acrs), proteins produced by viruses and other mobile genetic elements that can potently inhibit CRISPR-Cas systems. Discovered in 2013, there are now 54 distinct families of these proteins described, and the functional mechanisms of more than a dozen have been characterized in molecular detail. The investigation of Acrs is leading to a variety of practical applications and is providing exciting new insight into the biology of CRISPR-Cas systems.
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Affiliation(s)
- Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Wang-Ting Lu
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Sabrina Y Stanley
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Jingrui Wang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Marios Mejdani
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Chantel N Trost
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , , ,
| | - Brian T Hicks
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada; , ,
| | - Jooyoung Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; ,
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; ,
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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88
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Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B. Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression. Annu Rev Microbiol 2020; 74:21-37. [PMID: 32503371 DOI: 10.1146/annurev-micro-020518-120107] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
More than 50 protein families have been identified that inhibit CRISPR (clustered regularly interspaced short palindromic repeats)-Cas-mediated adaptive immune systems. Here, we analyze the available anti-CRISPR (Acr) structures and describe common themes and unique mechanisms of stoichiometric and enzymatic suppressors of CRISPR-Cas. Stoichiometric inhibitors often function as molecular decoys of protein-binding partners or nucleic acid targets, while enzymatic suppressors covalently modify Cas ribonucleoprotein complexes or degrade immune signaling molecules. We review mechanistic insights that have been revealed by structures of Acrs, discuss some of the trade-offs associated with each of these strategies, and highlight how Acrs are regulated and deployed in the race to overcome adaptive immunity.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
| | - Shweta Karambelkar
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
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89
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Peng X, Mayo-Muñoz D, Bhoobalan-Chitty Y, Martínez-Álvarez L. Anti-CRISPR Proteins in Archaea. Trends Microbiol 2020; 28:913-921. [PMID: 32499102 DOI: 10.1016/j.tim.2020.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022]
Abstract
Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR-Cas immunity through direct interaction with the large subunit Cas10d of the effector complex, and AcrIIIB1 inhibits subtype III-B CRISPR-Cas immunity through a mechanism interfering with middle/late gene targeting. Future development of efficient screening methods will be key to uncovering the diversity of archaeal Acrs.
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Affiliation(s)
- Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
| | - David Mayo-Muñoz
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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90
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CRISPR-Cas13 Inhibitors Block RNA Editing in Bacteria and Mammalian Cells. Mol Cell 2020; 78:850-861.e5. [PMID: 32348779 DOI: 10.1016/j.molcel.2020.03.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/10/2020] [Accepted: 03/25/2020] [Indexed: 02/08/2023]
Abstract
Cas13 has demonstrated unique and broad utility in RNA editing, nucleic acid detection, and disease diagnosis; however, a constantly active Cas enzyme may induce unwanted effects. Bacteriophage- or prophage-region-encoded anti-CRISPR (acr) gene molecules provide the potential to control targeting specificity and potency to allow for optimal RNA editing and nucleic acid detection by spatiotemporally modulating endonuclease activities. Using integrated approaches to screen acrVI candidates and evaluate their effects on Cas13 function, we discovered a series of acrVIA1-7 genes that block the activities of Cas13a. These VI-A CRISPR inhibitors substantially attenuate RNA targeting and editing by Cas13a in human cells. Strikingly, type VI-A anti-CRISPRs (AcrVIAs) also significantly muffle the single-nucleic-acid editing ability of the dCas13a RNA-editing system. Mechanistically, AcrVIA1, -4, -5, and -6 bind LwaCas13a, while AcrVIA2 and -3 can only bind the LwaCas13-crRNA (CRISPR RNA) complex. These identified acr molecules may enable precise RNA editing in Cas13-based application and study of phage-bacterium interaction.
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91
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Multiple Input Sensing and Signal Integration Using a Split Cas12a System. Mol Cell 2020; 78:184-191.e3. [DOI: 10.1016/j.molcel.2020.01.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/19/2019] [Accepted: 01/13/2020] [Indexed: 01/18/2023]
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92
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Watters KE, Shivram H, Fellmann C, Lew RJ, McMahon B, Doudna JA. Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes. Proc Natl Acad Sci U S A 2020; 117:6531-6539. [PMID: 32156733 PMCID: PMC7104187 DOI: 10.1073/pnas.1917668117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Anti-CRISPRs (Acrs) are small proteins that inhibit the RNA-guided DNA targeting activity of CRISPR-Cas enzymes. Encoded by bacteriophage and phage-derived bacterial genes, Acrs prevent CRISPR-mediated inhibition of phage infection and can also block CRISPR-Cas-mediated genome editing in eukaryotic cells. To identify Acrs capable of inhibiting Staphylococcus aureus Cas9 (SauCas9), an alternative to the most commonly used genome editing protein Streptococcus pyogenes Cas9 (SpyCas9), we used both self-targeting CRISPR screening and guilt-by-association genomic search strategies. Here we describe three potent inhibitors of SauCas9 that we name AcrIIA13, AcrIIA14, and AcrIIA15. These inhibitors share a conserved N-terminal sequence that is dispensable for DNA cleavage inhibition and have divergent C termini that are required in each case for inhibition of SauCas9-catalyzed DNA cleavage. In human cells, we observe robust inhibition of SauCas9-induced genome editing by AcrIIA13 and moderate inhibition by AcrIIA14 and AcrIIA15. We also find that the conserved N-terminal domain of AcrIIA13-AcrIIA15 binds to an inverted repeat sequence in the promoter of these Acr genes, consistent with its predicted helix-turn-helix DNA binding structure. These data demonstrate an effective strategy for Acr discovery and establish AcrIIA13-AcrIIA15 as unique bifunctional inhibitors of SauCas9.
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Affiliation(s)
- Kyle E Watters
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Haridha Shivram
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, School of Medicine, University of California, San Francisco, CA 94158
| | - Rachel J Lew
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158
| | - Blake McMahon
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720;
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158
- Department of Chemistry, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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93
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Cui YR, Wang SJ, Chen J, Li J, Chen W, Wang S, Meng B, Zhu W, Zhang Z, Yang B, Jiang B, Yang G, Ma P, Liu J. Allosteric inhibition of CRISPR-Cas9 by bacteriophage-derived peptides. Genome Biol 2020; 21:51. [PMID: 32102684 PMCID: PMC7045643 DOI: 10.1186/s13059-020-01956-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/10/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells without a temporal control system. Excessive and prolonged expression of CRISPR-Cas9 can lead to elevated off-target cleavage. The need for modulating CRISPR-Cas9 activity over time and dose has created the demand of developing CRISPR-Cas off switches. Protein and small molecule-based CRISPR-Cas inhibitors have been reported in previous studies. RESULTS We report the discovery of Cas9-inhibiting peptides from inoviridae bacteriophages. These peptides, derived from the periplasmic domain of phage major coat protein G8P (G8PPD), can inhibit the in vitro activity of Streptococcus pyogenes Cas9 (SpCas9) proteins in an allosteric manner. Importantly, the inhibitory activity of G8PPD on SpCas9 is dependent on the order of guide RNA addition. Ectopic expression of full-length G8P (G8PFL) or G8PPD in human cells can inactivate the genome-editing activity of SpyCas9 with minimum alterations of the mutation patterns. Furthermore, unlike the anti-CRISPR protein AcrII4A that completely abolishes the cellular activity of CRISPR-Cas9, G8P co-transfection can reduce the off-target activity of co-transfected SpCas9 while retaining its on-target activity. CONCLUSION G8Ps discovered in the current study represent the first anti-CRISPR peptides that can allosterically inactivate CRISPR-Cas9. This finding may provide insights into developing next-generation CRISPR-Cas inhibitors for precision genome engineering.
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Affiliation(s)
- Yan-Ru Cui
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Jie Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhang Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Zhuhong Zhang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 264005, Yantai, Shandong, People's Republic of China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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94
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Liu Q, Zhang H, Huang X. Anti-CRISPR proteins targeting the CRISPR-Cas system enrich the toolkit for genetic engineering. FEBS J 2020; 287:626-644. [PMID: 31730297 DOI: 10.1111/febs.15139] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/08/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas adaptive immune defense systems, which are widely distributed in bacteria and Archaea, can provide sequence-specific protection against foreign DNA or RNA in some cases. However, the evolution of defense systems in bacterial hosts did not lead to the elimination of phages, and some phages carry anti-CRISPR genes that encode products that bind to the components mediating the defense mechanism and thus antagonize CRISPR-Cas immune systems of bacteria. Given the extensive application of CRISPR-Cas9 technologies in gene editing, in this review, we focus on the anti-CRISPR proteins (Acrs) that inhibit CRISPR-Cas systems for gene editing. We describe the discovery of Acrs in immune systems involving type I, II, and V CRISPR-Cas immunity, discuss the potential function of Acrs in inactivating type II and V CRISPR-Cas systems for gene editing and gene modulation, and provide an outlook on the development of important biotechnology tools for genetic engineering using Acrs.
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Affiliation(s)
- Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, China
| | - Hongxia Zhang
- Department of Medical Microbiology, School of Medicine, Nanchang University, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, China
- Key Laboratory of Tumor Pathogenesis and Molecular Pathology, School of Medicine, Nanchang University, China
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95
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Broeders M, Herrero-Hernandez P, Ernst MPT, van der Ploeg AT, Pijnappel WWMP. Sharpening the Molecular Scissors: Advances in Gene-Editing Technology. iScience 2020; 23:100789. [PMID: 31901636 PMCID: PMC6941877 DOI: 10.1016/j.isci.2019.100789] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/26/2019] [Accepted: 12/13/2019] [Indexed: 12/20/2022] Open
Abstract
The ability to precisely modify human genes has been made possible by the development of tools such as meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas. These now make it possible to generate targeted deletions, insertions, gene knock outs, and point variants; to modulate gene expression by targeting transcription factors or epigenetic machineries to DNA; or to target and modify RNA. Endogenous repair mechanisms are used to make the modifications required in DNA; they include non-homologous end joining, homology-directed repair, homology-independent targeted integration, microhomology-mediated end joining, base-excision repair, and mismatch repair. Off-target effects can be monitored using in silico prediction and sequencing and minimized using Cas proteins with higher accuracy, such as high-fidelity Cas9, enhanced-specificity Cas9, and hyperaccurate Cas9. Alternatives to Cas9 have been identified, including Cpf1, Cas12a, Cas12b, and smaller Cas9 orthologs such as CjCas9. Delivery of gene-editing components is performed ex vivo using standard techniques or in vivo using AAV, lipid nanoparticles, or cell-penetrating peptides. Clinical development of gene-editing technology is progressing in several fields, including immunotherapy in cancer treatment, antiviral therapy for HIV infection, and treatment of genetic disorders such as β-thalassemia, sickle cell disease, lysosomal storage disorders, and retinal dystrophy. Here we review these technological advances and the challenges to their clinical implementation.
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Affiliation(s)
- Mike Broeders
- Department of Pediatrics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, Netherlands
| | - Pablo Herrero-Hernandez
- Department of Pediatrics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, Netherlands
| | - Martijn P T Ernst
- Department of Pediatrics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, Netherlands
| | - W W M Pim Pijnappel
- Department of Pediatrics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Department of Clinical Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, Netherlands; Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, Netherlands.
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96
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Wimmer F, Beisel CL. CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers. Front Microbiol 2020; 10:3078. [PMID: 32038537 PMCID: PMC6990116 DOI: 10.3389/fmicb.2019.03078] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas immune systems in bacteria and archaea record prior infections as spacers within each system’s CRISPR arrays. Spacers are normally derived from invasive genetic material and direct the immune system to complementary targets as part of future infections. However, not all spacers appear to be derived from foreign genetic material and instead can originate from the host genome. Their presence poses a paradox, as self-targeting spacers would be expected to induce an autoimmune response and cell death. In this review, we discuss the known frequency of self-targeting spacers in natural CRISPR-Cas systems, how these spacers can be incorporated into CRISPR arrays, and how the host can evade lethal attack. We also discuss how self-targeting spacers can become the basis for alternative functions performed by CRISPR-Cas systems that extend beyond adaptive immunity. Overall, the acquisition of genome-targeting spacers poses a substantial risk but can aid in the host’s evolution and potentially lead to or support new functionalities.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.,Medical Faculty, University of Würzburg, Würzburg, Germany
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97
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Heffel MG, Finnigan GC. Mathematical modeling of self-contained CRISPR gene drive reversal systems. Sci Rep 2019; 9:20050. [PMID: 31882576 PMCID: PMC6934693 DOI: 10.1038/s41598-019-54805-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022] Open
Abstract
There is a critical need for further research into methods to control biological populations. Numerous challenges to agriculture, ecological systems, and human health could be mitigated by the targeted reduction and management of key species (e.g. pests, parasites, and vectors for pathogens). The discovery and adaptation of the CRISPR/Cas editing platform co-opted from bacteria has provided a mechanism for a means to alter an entire population. A CRISPR-based gene drive system can allow for the forced propagation of a genetic element that bypasses Mendelian inheritance which can be used to bias sex determination, install exogenous information, or remove endogenous DNA within an entire species. Laboratory studies have demonstrated the potency by which gene drives can operate within insects and other organisms. However, continued research and eventual application face serious opposition regarding issues of policy, biosafety, effectiveness, and reversal. Previous mathematical work has suggested the use of modified gene drive designs that are limited in spread such as daisy chain or underdominance drives. However, no system has yet been proposed that allows for an inducible reversal mechanism without requiring the introduction of additional individuals. Here, we study gene drive effectiveness, fitness, and inducible drive systems that could respond to external stimuli expanding from a previous frequency-based population model. We find that programmed modification during gene drive propagation could serve as a potent safeguard to either slow or completely reverse drive systems and allow for a return to the original wild-type population.
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Affiliation(s)
- Matthew G Heffel
- Division of Biology, 116 Ackert Hall, Kansas State University, Manhattan, KS 66506, USA
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, 141 Chalmers Hall, Kansas State University, Manhattan, KS 66506, USA.
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98
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Li B, Zeng C, Li W, Zhang X, Luo X, Zhao W, Zhang C, Dong Y. Synthetic Oligonucleotides Inhibit CRISPR-Cpf1-Mediated Genome Editing. Cell Rep 2019; 25:3262-3272.e3. [PMID: 30566855 PMCID: PMC6326575 DOI: 10.1016/j.celrep.2018.11.079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/12/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Previously, researchers discovered a series of anti-CRISPR proteins that inhibit CRISPR-Cas activity, such as Cas9 and Cpf1 (Cas12a). Herein, we constructed crRNA variants consisting of chemically modified DNA-crRNA and RNA-crRNA duplexes and identified that phosphorothioate (PS)-modified DNA-crRNA duplex completely blocked the function of Cpf1. More important, without prehybridization, these PS-modified DNA oligonucleotides showed the ability to suppress DNA double-strand breaks induced by two Cpf1 orthologs, AsCpf1 and LbCpf1. Time-dependent inhibitory effects were validated in multiple loci of different human cells. Further studies demonstrated that PS-modified DNA oligo-nucleotides were able to serve as Cpf1 inhibitors in a sequence-independent manner. Mechanistic studies indicate that PS-modified DNA oligonucleotides hinder target DNA binding and recognition by Cpf1. Consequently, these synthetic DNA molecules expand the sources of CRISPR inhibitors, providing a platform to inactivate Cpf1-mediated genome editing. Li et al. show that phosphorothioate-modified DNA (psDNA) oligonucleotides inhibit Cpf1-mediated genome-editing activity in a sequence-independent manner in human cells. These psDNA oligonucleotides interact with Cpf1 protein and block the formation of Cpf1-crRNA-target DNA complex. They also display inhibitory effects on the CRISPR-Cas9 system.
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Affiliation(s)
- Bin Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chunxi Zeng
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Wenqing Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Xinfu Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Xiao Luo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Weiyu Zhao
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Chengxiang Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Yizhou Dong
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA; The Center for Clinical and Translational Science, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA.
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Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
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