51
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Athukoralage JS, White MF. Cyclic oligoadenylate signalling and regulation by ring nucleases during type III CRISPR defence. RNA (NEW YORK, N.Y.) 2021; 27:rna.078739.121. [PMID: 33986148 PMCID: PMC8284326 DOI: 10.1261/rna.078739.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/08/2021] [Indexed: 06/12/2023]
Abstract
In prokaryotes, CRISPR-Cas immune systems recognise and cleave foreign nucleic acids to defend against Mobile Genetic Elements (MGEs). Type III CRISPR-Cas complexes also synthesise cyclic oligoadenylate (cOA) second messengers, which activate CRISPR ancillary proteins involved in antiviral defence. In particular, cOA-stimulated nucleases degrade RNA and DNA non-specifically, which slows MGE replication but also impedes cell growth, necessitating mechanisms to eliminate cOA in order to mitigate collateral damage. Extant cOA is degraded by a new class of enzyme termed a 'ring nuclease', which cleaves cOA specifically and switches off CRISPR ancillary enzymes. Several ring nuclease families have been characterised to date, including a family used by MGEs to circumvent CRISPR immunity, and encompass diverse protein folds and distinct cOA cleavage mechanisms. In this review we outline cOA signalling, discuss how different ring nucleases regulate the cOA signalling pathway, and reflect on parallels between cyclic nucleotide-based immune systems to reveal new areas for exploration.
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52
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Lu WT, Trost CN, Müller-Esparza H, Randau L, Davidson AR. Anti-CRISPR AcrIF9 functions by inducing the CRISPR-Cas complex to bind DNA non-specifically. Nucleic Acids Res 2021; 49:3381-3393. [PMID: 33660777 PMCID: PMC8034650 DOI: 10.1093/nar/gkab092] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Phages and other mobile genetic elements express anti-CRISPR proteins (Acrs) to protect their genomes from destruction by CRISPR–Cas systems. Acrs usually block the ability of CRISPR–Cas systems to bind or cleave their nucleic acid substrates. Here, we investigate an unusual Acr, AcrIF9, that induces a gain-of-function to a type I-F CRISPR–Cas (Csy) complex, causing it to bind strongly to DNA that lacks both a PAM sequence and sequence complementarity. We show that specific and non-specific dsDNA compete for the same site on the Csy:AcrIF9 complex with rapid exchange, but specific ssDNA appears to still bind through complementarity to the CRISPR RNA. Induction of non-specific DNA-binding is a shared property of diverse AcrIF9 homologues. Substitution of a conserved positively charged surface on AcrIF9 abrogated non-specific dsDNA-binding of the Csy:AcrIF9 complex, but specific dsDNA binding was maintained. AcrIF9 mutants with impaired non-specific dsDNA binding activity in vitro displayed a reduced ability to inhibit CRISPR–Cas activity in vivo. We conclude that misdirecting the CRISPR–Cas complex to bind non-specific DNA is a key component of the inhibitory mechanism of AcrIF9. This inhibitory mechanism is distinct from a previously characterized anti-CRISPR, AcrIF1, that sterically blocks DNA-binding, even though AcrIF1and AcrIF9 bind to the same site on the Csy complex.
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Affiliation(s)
- Wang-Ting Lu
- Department of Biochemistry, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | - Chantel N Trost
- Department of Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
| | - Hanna Müller-Esparza
- Faculty of Biology, University of Marburg, Karl-von-Frisch-Straße 1, 35043 Marburg, Germany
| | - Lennart Randau
- Faculty of Biology, University of Marburg, Karl-von-Frisch-Straße 1, 35043 Marburg, Germany.,Loewe Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada.,Department of Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON, M5G 1M1, Canada
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53
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Philippe C, Moineau S. The endless battle between phages and CRISPR-Cas systems in Streptococcus thermophilus. Biochem Cell Biol 2021; 99:397-402. [PMID: 33534660 DOI: 10.1139/bcb-2020-0593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This review describes the contribution of basic research on phage-bacteria interactions to the understanding of CRISPR-Cas systems and their various applications. It focuses on the natural function of CRISPR-Cas systems as adaptive defense mechanisms against mobile genetic elements such as bacteriophage genomes and plasmids. Some of the advances in the characterization of the type II-A CRISPR-Cas system of Streptococcus thermophilus and Streptococcus pyogenes led to the development of the CRISPR-Cas9 genome-editing technology. We mostly discuss the 3 stages of the CRISPR-Cas system in S. thermophilus, namely the adaptation stage, which is unique to this resistance mechanism; the CRISPR RNA biogenesis; and the DNA-cutting activity in the interference stage to protect bacteria against phages. Finally, we look into applications of CRISPR-Cas in microbiology, including overcoming limitations in genome editing.
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Affiliation(s)
- Cécile Philippe
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, QC G1V 0A6, Canada
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54
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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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55
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Wang J, Dai W, Li J, Li Q, Xie R, Zhang Y, Stubenrauch C, Lithgow T. AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins. Nucleic Acids Res 2021; 49:D630-D638. [PMID: 33137193 PMCID: PMC7779044 DOI: 10.1093/nar/gkaa951] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Anti-CRISPR (Acr) proteins naturally inhibit CRISPR-Cas adaptive immune systems across bacterial and archaeal domains of life. This emerging field has caused a paradigm shift in the way we think about the CRISPR-Cas system, and promises a number of useful applications from gene editing to phage therapy. As the number of verified and predicted Acrs rapidly expands, few online resources have been developed to deal with this wealth of information. To overcome this shortcoming, we developed AcrHub, an integrative database to provide an all-in-one solution for investigating, predicting and mapping Acr proteins. AcrHub catalogs 339 non-redundant experimentally validated Acrs and over 70 000 predicted Acrs extracted from genome sequence data from a diverse range of prokaryotic organisms and their viruses. It integrates state-of-the-art predictors to predict potential Acrs, and incorporates three analytical modules: similarity analysis, phylogenetic analysis and homology network analysis, to analyze their relationships with known Acrs. By interconnecting all modules as a platform, AcrHub presents enriched and in-depth analysis of known and potential Acrs and therefore provides new and exciting insights into the future of Acr discovery and validation. AcrHub is freely available at http://pacrispr.erc.monash.edu/AcrHub/.
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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
| | - Qi 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
| | - Yanju Zhang
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Christopher Stubenrauch
- 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
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56
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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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57
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Shivram H, Cress BF, Knott GJ, Doudna JA. Controlling and enhancing CRISPR systems. Nat Chem Biol 2021; 17:10-19. [PMID: 33328654 PMCID: PMC8101458 DOI: 10.1038/s41589-020-00700-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022]
Abstract
Many bacterial and archaeal organisms use clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) systems to defend themselves from mobile genetic elements. These CRISPR-Cas systems are classified into six types based on their composition and mechanism. CRISPR-Cas enzymes are widely used for genome editing and offer immense therapeutic opportunity to treat genetic diseases. To realize their full potential, it is important to control the timing, duration, efficiency and specificity of CRISPR-Cas enzyme activities. In this Review we discuss the mechanisms of natural CRISPR-Cas regulatory biomolecules and engineering strategies that enhance or inhibit CRISPR-Cas immunity by altering enzyme function. We also discuss the potential applications of these CRISPR regulators and highlight unanswered questions about their evolution and purpose in nature.
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Affiliation(s)
- Haridha Shivram
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Brady F Cress
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria, Australia
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
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58
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Mejdani M, Pawluk A, Maxwell KL, Davidson AR. Anti-CRISPR AcrIE2 Binds the Type I-E CRISPR-Cas Complex But Does Not Block DNA Binding. J Mol Biol 2020; 433:166759. [PMID: 33338493 DOI: 10.1016/j.jmb.2020.166759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
Anti-CRISPRs are protein inhibitors of CRISPR-Cas systems. They are produced by phages and other mobile genetic elements to evade CRISPR-Cas-mediated destruction. Anti-CRISPRs are remarkably diverse in sequence, structure, and functional mechanism; thus, structural and mechanistic investigations of anti-CRISPRs continue to yield exciting new insights. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AcrIE2, an anti-CRISPR that inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. Guided by the structure, we used site-directed mutagenesis to identify key residues that are required for AcrIE2 function. Using affinity purification experiments, we found that AcrIE2 binds the type I-E CRISPR-Cas complex (Cascade). In vivo transcriptional assays, in which Cascade was targeted to promoter regions, demonstrated that Cascade still binds to DNA in the presence of AcrIE2. This is the first instance of a type I anti-CRISPR that binds to a CRISPR-Cas complex but does not prevent DNA-binding. Another unusual property of AcrIE2 is that the effect of Cascade:AcrIE2 complex binding to promoter regions varied depending on the position of the binding site. Most surprisingly, Cascade:AcrIE2 binding led to transcriptional activation in some cases rather than repression, which did not occur when Cascade alone bound to the same sites. We conclude that AcrIE2 operates through a distinct mechanism compared to other type I anti-CRISPRs. While AcrIE2 does not prevent Cascade from binding DNA, it likely blocks subsequent recruitment of the Cas3 nuclease to Cascade thereby preventing DNA cleavage.
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Affiliation(s)
- Marios Mejdani
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - April Pawluk
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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59
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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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60
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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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61
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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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62
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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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63
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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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64
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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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65
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Abstract
CRISPR research began over 30 years ago with the incidental discovery of an unusual nucleotide arrangement in the Escherichia coli genome. It took 20 years to find the main function of CRISPR-Cas systems as an adaptive defence mechanism against invading nucleic acids, and our knowledge of their biology has steadily increased ever since. In parallel, the number of applications derived from CRISPR-Cas systems has risen spectacularly. The CRISPR-based genome editing tool is arguably the most exciting application in both basic and applied research. Lately, CRISPR-Cas research has partially shifted to the least understood aspect of its biology: the ability of CRISPR-Cas systems to acquire new immunities during the so-called adaptation step. To date, the most efficient natural system to readily acquire new spacers is the type II-A system of the gram-positive dairy bacterium Streptococcus thermophilus. The discovery of additional systems able to acquire new spacers will hopefully draw more attention to this step of CRISPR-Cas biology. This review focuses on the breakthroughs that have helped to unravel the adaptation phase and on questions that remain to be answered.
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Affiliation(s)
- Cas Mosterd
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
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66
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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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67
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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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68
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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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69
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Marino ND, Pinilla-Redondo R, Csörgő B, Bondy-Denomy J. Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies. Nat Methods 2020; 17:471-479. [DOI: 10.1038/s41592-020-0771-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/05/2020] [Indexed: 12/20/2022]
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70
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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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71
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An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 2020; 577:572-575. [PMID: 31942067 PMCID: PMC6986909 DOI: 10.1038/s41586-019-1909-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
Abstract
The CRISPR system in bacteria and archaea provides adaptive immunity against mobile genetic elements. Type III CRISPR systems detect viral RNA, resulting in the activation of two regions of the Cas10 protein: an HD nuclease domain (which degrades viral DNA)1,2 and a cyclase domain (which synthesizes cyclic oligoadenylates from ATP)3-5. Cyclic oligoadenylates in turn activate defence enzymes with a CRISPR-associated Rossmann fold domain6, sculpting a powerful antiviral response7-10 that can drive viruses to extinction7,8. Cyclic nucleotides are increasingly implicated in host-pathogen interactions11-13. Here we identify a new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA4). The viral ring nuclease AcrIII-1 is widely distributed in archaeal and bacterial viruses and in proviruses. The enzyme uses a previously unknown fold to bind cA4 specifically, and a conserved active site to rapidly cleave this signalling molecule, allowing viruses to neutralize the type III CRISPR defence system. The AcrIII-1 family has a broad host range, as it targets cA4 signalling molecules rather than specific CRISPR effector proteins. Our findings highlight the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts.
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72
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Sahoo N, Cuello V, Udawant S, Litif C, Mustard JA, Keniry M. CRISPR-Cas9 Genome Editing in Human Cell Lines with Donor Vector Made by Gibson Assembly. Methods Mol Biol 2020; 2115:365-383. [PMID: 32006411 PMCID: PMC7391466 DOI: 10.1007/978-1-0716-0290-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CRISPR Cas9 genome editing allows researchers to modify genes in a multitude of ways including to obtain deletions, epitope-tagged loci, and knock-in mutations. Within 6 years of its initial application, CRISPR-Cas9 genome editing has been widely employed, but disadvantages to this method, such as low modification efficiencies and off-target effects, need careful consideration. Obtaining custom donor vectors can also be expensive and time-consuming. This chapter details strategies to overcome barriers to CRISPR-Cas9 genome editing as well as recent developments in employing this technique.
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Affiliation(s)
- Nirakar Sahoo
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Victoria Cuello
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Shreya Udawant
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Carl Litif
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Julie A Mustard
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA
| | - Megan Keniry
- Department of Biology, University of Texas - Rio Grande Valley, Edinburg, TX, USA.
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73
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Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6. Mol Cell 2019; 76:922-937.e7. [PMID: 31604602 DOI: 10.1016/j.molcel.2019.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/02/2019] [Accepted: 09/06/2019] [Indexed: 12/26/2022]
Abstract
In the arms race against bacteria, bacteriophages have evolved diverse anti-CRISPR proteins (Acrs) that block CRISPR-Cas immunity. Acrs play key roles in the molecular coevolution of bacteria with their predators, use a variety of mechanisms of action, and provide tools to regulate Cas-based genome manipulation. Here, we present structural and functional analyses of AcrIIA6, an Acr from virulent phages, exploring its unique anti-CRISPR action. Our cryo-EM structures and functional data of AcrIIA6 binding to Streptococcus thermophilus Cas9 (St1Cas9) show that AcrIIA6 acts as an allosteric inhibitor and induces St1Cas9 dimerization. AcrIIA6 reduces St1Cas9 binding affinity for DNA and prevents DNA binding within cells. The PAM and AcrIIA6 recognition sites are structurally close and allosterically linked. Mechanistically, AcrIIA6 affects the St1Cas9 conformational dynamics associated with PAM binding. Finally, we identify a natural St1Cas9 variant resistant to AcrIIA6 illustrating Acr-driven mutational escape and molecular diversification of Cas9 proteins.
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74
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Forsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik HS. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. eLife 2019; 8:e46540. [PMID: 31502535 PMCID: PMC6739867 DOI: 10.7554/elife.46540] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 08/09/2019] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas systems protect bacteria and archaea from phages and other mobile genetic elements, which use small anti-CRISPR (Acr) proteins to overcome CRISPR-Cas immunity. Because Acrs are challenging to identify, their natural diversity and impact on microbial ecosystems are underappreciated. To overcome this discovery bottleneck, we developed a high-throughput functional selection to isolate ten DNA fragments from human oral and fecal metagenomes that inhibit Streptococcus pyogenes Cas9 (SpyCas9) in Escherichia coli. The most potent Acr from this set, AcrIIA11, was recovered from a Lachnospiraceae phage. We found that AcrIIA11 inhibits SpyCas9 in bacteria and in human cells. AcrIIA11 homologs are distributed across diverse bacteria; many distantly-related homologs inhibit both SpyCas9 and a divergent Cas9 from Treponema denticola. We find that AcrIIA11 antagonizes SpyCas9 using a different mechanism than other previously characterized Type II-A Acrs. Our study highlights the power of functional selection to uncover widespread Cas9 inhibitors within diverse microbiomes.
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Affiliation(s)
- Kevin J Forsberg
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ishan V Bhatt
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Danica T Schmidtke
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute of Cellular and Molecular BiologyUniversity of Texas at AustinAustinUnited States
| | - Kaylee E Dillard
- Department of Molecular Biosciences and Institute of Cellular and Molecular BiologyUniversity of Texas at AustinAustinUnited States
| | - Barry L Stoddard
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Cellular and Molecular BiologyUniversity of Texas at AustinAustinUnited States
- Center for Systems Biology and Synthetic BiologyUniversity of Texas at AustinAustinUnited States
| | - Brett K Kaiser
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of BiologySeattle UniversitySeattleUnited States
| | - Harmit S Malik
- Division of Basic SciencesFred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research CenterSeattleUnited States
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75
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Bioinformatics Identification of Anti-CRISPR Loci by Using Homology, Guilt-by-Association, and CRISPR Self-Targeting Spacer Approaches. mSystems 2019; 4:4/5/e00455-19. [PMID: 31506266 PMCID: PMC6739104 DOI: 10.1128/msystems.00455-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
As a naturally occurring adaptive immune system, CRISPR-Cas (clustered regularly interspersed short palindromic repeats–CRISPR-associated genes) systems are widely found in bacteria and archaea to defend against viruses. Since 2013, the application of various bacterial CRISPR-Cas systems has become very popular due to their development into targeted and programmable genome engineering tools with the ability to edit almost any genome. As the natural off-switch of CRISPR-Cas systems, anti-CRISPRs have a great potential to serve as regulators of CRISPR-Cas tools and enable safer and more controllable genome editing. This study will help understand the relative usefulness of the three bioinformatics approaches for new Acr discovery, as well as guide the future development of new bioinformatics tools to facilitate anti-CRISPR research. The thousands of Acr homologs and hundreds of new anti-CRISPR loci identified in this study will be a valuable data resource for genome engineers to search for new CRISPR-Cas regulators. Anti-CRISPR (Acr) loci/operons encode Acr proteins and Acr-associated (Aca) proteins. Forty-five Acr families have been experimentally characterized inhibiting seven subtypes of CRISPR-Cas systems. We have developed a bioinformatics pipeline to identify genomic loci containing Acr homologs and/or Aca homologs by combining three computational approaches: homology, guilt-by-association, and self-targeting spacers. Homology search found thousands of Acr homologs in bacterial and viral genomes, but most are homologous to AcrIIA7 and AcrIIA9. Investigating the gene neighborhood of these Acr homologs revealed that only a small percentage (23.0% in bacteria and 8.2% in viruses) of them have neighboring Aca homologs and thus form Acr-Aca operons. Surprisingly, although a self-targeting spacer is a strong indicator of the presence of Acr genes in a genome, a large percentage of Acr-Aca loci are found in bacterial genomes without self-targeting spacers or even without complete CRISPR-Cas systems. Additionally, for Acr homologs from genomes with self-targeting spacers, homology-based Acr family assignments do not always agree with the self-targeting CRISPR-Cas subtypes. Last, by investigating Acr genomic loci coexisting with self-targeting spacers in the same genomes, five known subtypes (I-C, I-E, I-F, II-A, and II-C) and five new subtypes (I-B, III-A, III-B, IV-A, and V-U4) of Acrs were inferred. Based on these findings, we conclude that the discovery of new anti-CRISPRs should not be restricted to genomes with self-targeting spacers and loci with Acr homologs. The evolutionary arms race of CRISPR-Cas systems and anti-CRISPR systems may have driven the adaptive and rapid gain and loss of these elements in closely related genomes. IMPORTANCE As a naturally occurring adaptive immune system, CRISPR-Cas (clustered regularly interspersed short palindromic repeats–CRISPR-associated genes) systems are widely found in bacteria and archaea to defend against viruses. Since 2013, the application of various bacterial CRISPR-Cas systems has become very popular due to their development into targeted and programmable genome engineering tools with the ability to edit almost any genome. As the natural off-switch of CRISPR-Cas systems, anti-CRISPRs have a great potential to serve as regulators of CRISPR-Cas tools and enable safer and more controllable genome editing. This study will help understand the relative usefulness of the three bioinformatics approaches for new Acr discovery, as well as guide the future development of new bioinformatics tools to facilitate anti-CRISPR research. The thousands of Acr homologs and hundreds of new anti-CRISPR loci identified in this study will be a valuable data resource for genome engineers to search for new CRISPR-Cas regulators.
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Dong C, Zeng Z, Pu DK, Wen QF, Liu S, Du MZ, Sun Y, Gao YZ, Rao N, Huang J, Guo FB. CasLocusAnno: a web-based server for annotating cas loci and their corresponding (sub)types. FEBS Lett 2019; 593:2646-2654. [PMID: 31260103 DOI: 10.1002/1873-3468.13519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 02/05/2023]
Abstract
In prokaryotes, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems constitute adaptive immune systems against mobile genetic elements (MGEs). Here, we introduce the Markov cluster algorithm (MCL) to Makarova et al.'s method in order to select a more reasonable profile. Additionally, our new Maximum Continuous Cas Subcluster (MCCS) method helps identification of tightly clustered loci. The comparison with two other commonly used programs shows that the method could identify Cas proteins with higher accuracy and lower Additional Prediction Rate (APR). Moreover, we developed a web-based server, CasLocusAnno (http://cefg.uestc.cn/CasLocusAnno), capable of annotating Cas proteins, cas loci and their (sub)types less than ~ 28 s following the whole proteome sequence submission. Its standalone version can be downloaded at https://github.com/RiversDong/CasLocusAnno.
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Affiliation(s)
- Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhi Zeng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong-Kai Pu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing-Feng Wen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Meng-Ze Du
- School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Yan Sun
- Institutes for Systems Genetics, West China Hospital, Chengdu, China
| | - Yi-Zhou Gao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Nini Rao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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77
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Zhang F, Song G, Tian Y. Anti-CRISPRs: The natural inhibitors for CRISPR-Cas systems. Animal Model Exp Med 2019; 2:69-75. [PMID: 31392299 PMCID: PMC6600654 DOI: 10.1002/ame2.12069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated protein) systems serve as the adaptive immune system by which prokaryotes defend themselves against phages. It has also been developed into a series of powerful gene-editing tools. As the natural inhibitors of CRISPR-Cas systems, anti-CRISPRs (Acrs) can be used as the "off-switch" for CRISPR-Cas systems to limit the off-target effects caused by Cas9. Since the discovery of CRISPR-Cas systems, much research has focused on the identification, mechanisms and applications of Acrs. In light of the rapid development and scientific significance of this field, this review summarizes the history and research status of Acrs, and considers future applications.
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Affiliation(s)
- Fei Zhang
- CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guoxu Song
- CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Yong Tian
- CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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78
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Fineran PC. Resistance is not futile: bacterial 'innate' and CRISPR-Cas 'adaptive' immune systems. MICROBIOLOGY-SGM 2019; 165:834-841. [PMID: 30958259 DOI: 10.1099/mic.0.000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria are under a constant pressure from their viruses (phages) and other mobile genetic elements. They protect themselves through a range of defence strategies, which can be broadly classified as 'innate' and 'adaptive'. The bacterial innate immune systems include defences provided by restriction modification and abortive infection, among others. Bacterial adaptive immunity is elicited by a diverse range of CRISPR-Cas systems. Here, I discuss our research on both innate and adaptive phage resistance mechanisms and some of the evasion strategies employed by phages.
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Affiliation(s)
- Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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79
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Hwang S, Maxwell KL. Meet the Anti-CRISPRs: Widespread Protein Inhibitors of CRISPR-Cas Systems. CRISPR J 2019; 2:23-30. [DOI: 10.1089/crispr.2018.0052] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Sungwon Hwang
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Karen L. Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Canada
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80
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Wilkinson RA, Martin C, Nemudryi AA, Wiedenheft B. CRISPR RNA-guided autonomous delivery of Cas9. Nat Struct Mol Biol 2019; 26:14-24. [PMID: 30598555 PMCID: PMC7703833 DOI: 10.1038/s41594-018-0173-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/13/2018] [Indexed: 02/06/2023]
Abstract
Cas9 is an endonuclease that can be programed to autonomously deliver diverse effectors to specified genetic addresses. High-resolution structures of this protein and its associated CRISPR RNA guide explain the molecular mechanisms of CRISPR-RNA-guided DNA recognition and provide a molecular blueprint that has facilitated structure-guided functional remodeling. Here we retrace events that led from early efforts to understand the central role of Cas9 in CRISPR-mediated adaptive immunity to contemporary efforts aimed at developing and deploying this enzyme for programmable genetic editing.
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Affiliation(s)
- Royce A Wilkinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Coleman Martin
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Artem A Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA.
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