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Kim DY, Han JH, Lee SY, Ha HJ, Park HH. Novel structure of the anti-CRISPR protein AcrIE3 and its implication on the CRISPR-Cas inhibition. Biochem Biophys Res Commun 2024; 722:150164. [PMID: 38797150 DOI: 10.1016/j.bbrc.2024.150164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
As a response to viral infections, bacteria have evolved the CRISPR-Cas system as an adaptive immune mechanism, enabling them to target and eliminate viral genetic material introduced during infection. However, viruses have also evolved mechanisms to counteract this bacterial defense, including anti-CRISPR proteins, which can inactivate the CRISPR-Cas adaptive immune system, thus aiding the viruses in their survival and replication within bacterial hosts. In this study, we establish the high-resolution crystal structure of the Type IE anti-CRISPR protein, AcrIE3. Our structural examination showed that AcrIE3 adopts a helical bundle fold comprising four α-helices, with a notably extended loop at the N-terminus. Additionally, surface analysis of AcrIE3 revealed the presence of three acidic regions, which potentially play a crucial role in the inhibitory function of this protein. The structural information we have elucidated for AcrIE3 will provide crucial insights into fully understanding its inhibitory mechanism. Furthermore, this information is anticipated to be important for the application of the AcrIE family in genetic editing, paving the way for advancements in gene editing technologies.
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Affiliation(s)
- Do Yeon Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Ju Hee Han
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - So Yeon Lee
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
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2
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Trost CN, Yang J, Garcia B, Hidalgo-Reyes Y, Fung BCM, Wang J, Lu WT, Maxwell KL, Wang Y, Davidson AR. An anti-CRISPR that pulls apart a CRISPR-Cas complex. Nature 2024:10.1038/s41586-024-07642-3. [PMID: 38961300 DOI: 10.1038/s41586-024-07642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
In biological systems, the activities of macromolecular complexes must sometimes be turned off. Thus, a wide variety of protein inhibitors has evolved for this purpose. These inhibitors function through diverse mechanisms, including steric blocking of crucial interactions, enzymatic modification of key residues or substrates, and perturbation of post-translational modifications1. Anti-CRISPRs-proteins that block the activity of CRISPR-Cas systems-are one of the largest groups of inhibitors described, with more than 90 families that function through diverse mechanisms2-4. Here, we characterize the anti-CRISPR AcrIF25, and we show that it inhibits the type I-F CRISPR-Cas system by pulling apart the fully assembled effector complex. AcrIF25 binds to the predominant CRISPR RNA-binding components of this complex, comprising six Cas7 subunits, and strips them from the RNA. Structural and biochemical studies indicate that AcrIF25 removes one Cas7 subunit at a time, starting at one end of the complex. Notably, this feat is achieved with no apparent enzymatic activity. To our knowledge, AcrIF25 is the first example of a protein that disassembles a large and stable macromolecular complex in the absence of an external energy source. As such, AcrIF25 establishes a paradigm for macromolecular complex inhibitors that may be used for biotechnological applications.
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Affiliation(s)
- Chantel N Trost
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jing Yang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Bianca Garcia
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yurima Hidalgo-Reyes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Beatrice C M Fung
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jiuyu Wang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wang-Ting Lu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yanli Wang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of the Chinese Academy of Sciences, Beijing, China.
| | - Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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3
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Jiang C, Yu C, Sun S, Lin J, Cai M, Wei Z, Feng L, Li J, Zhang Y, Dong K, Guo X, Qin J, Zhang Y. A new anti-CRISPR gene promotes the spread of drug-resistance plasmids in Klebsiella pneumoniae. Nucleic Acids Res 2024:gkae516. [PMID: 38888121 DOI: 10.1093/nar/gkae516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
The Klebsiella pneumoniae (K. pneumoniae, Kp) populations carrying both resistance-encoding and virulence-encoding mobile genetic elements (MGEs) significantly threaten global health. In this study, we identified a new anti-CRISPR gene (acrIE10) on a conjugative plasmid with self-target sequence in K. pneumoniae with type I-E* CRISPR-Cas system. AcrIE10 interacts with the Cas7* subunit of K. pneumoniae I-E* CRISPR-Cas system. The crystal structure of the AcrIE10-KpCas7* complex suggests that AcrIE10 suppresses the I-E* CRISPR-Cas by binding directly to Cas7 to prevent its hexamerization, thereby preventing the surveillance complex assembly and crRNA loading. Bioinformatic and functional analyses revealed that AcrIE10 is functionally widespread across diverse species. Our study reports a novel anti-CRISPR and highlights its potential role in spreading resistance and virulence among pathogens.
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Affiliation(s)
- Chunyu Jiang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chengzhi Yu
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyi Sun
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Lin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mufeng Cai
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhenquan Wei
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingling Feng
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jianhui Li
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ke Dong
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinhong Qin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- NHC Key Laboratory of Parasite and Vector Biology (National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention), Shanghai 200025, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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4
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Bi M, Su W, Li J, Mo X. Insights into the inhibition of protospacer integration via direct interaction between Cas2 and AcrVA5. Nat Commun 2024; 15:3256. [PMID: 38627399 PMCID: PMC11021501 DOI: 10.1038/s41467-024-47713-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
Spacer acquisition step in CRISPR-Cas system involves the recognition and subsequent integration of protospacer by the Cas1-Cas2 complex in CRISPR-Cas systems. Here we report an anti-CRISPR protein, AcrVA5, and reveal the mechanisms by which it strongly inhibits protospacer integration. Our biochemical data shows that the integration by Cas1-Cas2 was abrogated in the presence of AcrVA5. AcrVA5 exhibits low binding affinity towards Cas2 and acetylates Cas2 at Lys55 on the binding interface of the Cas2 and AcrVA5 N-terminal peptide complex to inhibit the Cas2-mediated endonuclease activity. Moreover, a detailed structural comparison between our crystal structure and homolog structure shows that binding of AcrVA5 to Cas2 causes steric hindrance to the neighboring protospacer resulting in the partial disassembly of the Cas1-Cas2 and protospacer complex, as demonstrated by electrophoretic mobility shift assay. Our study focuses on this mechanism of spacer acquisition inhibition and provides insights into the biology of CRISPR-Cas systems.
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Affiliation(s)
- Mingfang Bi
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China
| | - Wenjing Su
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China
| | - Jiafu Li
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China
| | - Xiaobing Mo
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China.
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, Jilin University, 130062, Changchun, Jilin, China.
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5
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Tao S, Hu C, Fang Y, Zhang H, Xu Y, Zheng L, Chen L, Liang W. Targeted elimination of Vancomycin resistance gene vanA by CRISPR-Cas9 system. BMC Microbiol 2023; 23:380. [PMID: 38049763 PMCID: PMC10694887 DOI: 10.1186/s12866-023-03136-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
OBJECTIVE The purpose of this study is to reduce the spread of the vanA gene by curing the vanA-harboring plasmid of vancomycin-resistant using the CRISPR-Cas9 system. METHODS Two specific spacer sequence (sgRNAs) specific was designed to target the vanA gene and cloned into plasmid CRISPR-Cas9. The role of the CRISPR-Cas system in the plasmid elimination of drug-resistance genes was verified by chemically transformation and conjugation delivery methods. Moreover, the elimination efficiency in strains was evaluated by plate counting, PCR, and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by Etest strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance. RESULTS In the study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the vanA gene. PCR and qPCR results indicated that recombinant pCas9-sgRNA plasmid can efficiently clear vanA-harboring plasmids. There was no significant correlation between sgRNA lengths and curing efficiency. In addition, the drug susceptibility test results showed that the bacterial resistance to vancomycin was significantly reduced after the vanA-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system. The CRISPR-Cas9 system can block the horizontal transfer of the conjugated plasmid pUC19-vanA. CONCLUSION In conclusion, our study demonstrated that CRISPR-Cas9 achieved plasmid clearance and reduced antimicrobial resistance. The CRISPR-Cas9 system could block the horizontal transfer of plasmid carrying vanA. This strategy provided a great potential to counteract the ever-worsening spread of the vanA gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.
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Affiliation(s)
- Shuan Tao
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chunwei Hu
- The Biobank of The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yewei Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China
| | - He Zhang
- Bengbu Medical College, Bengbu, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Lin Zheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China
| | - Luyan Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Wei Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, No 59. Liuting Road, Haishu District, Ningbo, 315010, China.
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6
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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7
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Tao S, Chen H, Li N, Fang Y, Zhang H, Xu Y, Chen L, Liang W. Elimination of bla KPC-2-mediated carbapenem resistance in Escherichia coli by CRISPR-Cas9 system. BMC Microbiol 2023; 23:310. [PMID: 37884864 PMCID: PMC10601263 DOI: 10.1186/s12866-023-03058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
OBJECTIVE The purpose of this study is to re-sensitive bacteria to carbapenemases and reduce the transmission of the blaKPC-2 gene by curing the blaKPC-2-harboring plasmid of carbapenem-resistant using the CRISPR-Cas9 system. METHODS The single guide RNA (sgRNA) specifically targeted to the blaKPC-2 gene was designed and cloned into plasmid pCas9. The recombinant plasmid pCas9-sgRNA(blaKPC-2) was transformed into Escherichia coli (E.coli) carrying pET24-blaKPC-2. The elimination efficiency in strains was evaluated by polymerase chain reaction (PCR) and quantitative real-time PCR (qPCR). Susceptibility testing was performed by broth microdilution assay and by E-test strips (bioMérieux, France) to detect changes in bacterial drug resistance phenotype after drug resistance plasmid clearance. RESULTS In the present study, we constructed a specific prokaryotic CRISPR-Cas9 system plasmid targeting cleavage of the blaKPC-2 gene. PCR and qPCR results indicated that prokaryotic CRISPR-Cas9 plasmid transforming drug-resistant bacteria can efficiently clear blaKPC-2-harboring plasmids. In addition, the drug susceptibility test results showed that the bacterial resistance to imipenem was significantly reduced and allowed the resistant model bacteria to restore susceptibility to antibiotics after the blaKPC-2-containing drug-resistant plasmid was specifically cleaved by the CRISPR-Cas system. CONCLUSION In conclusion, our study demonstrated that the one plasmid-mediated CRISPR-Cas9 system can be used as a novel tool to remove resistance plasmids and re-sensitize the recipient bacteria to antibiotics. This strategy provided a great potential to counteract the ever-worsening spread of the blaKPC-2 gene among bacterial pathogens and laid the foundation for subsequent research using the CRISPR-Cas9 system as adjuvant antibiotic therapy.
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Affiliation(s)
- Shuan Tao
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Huimin Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Na Li
- Bengbu Medical College, Bengbu, China
| | - Yewei Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - He Zhang
- Bengbu Medical College, Bengbu, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Luyan Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Wei Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China.
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8
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Kang YJ, Kim JH, Lee GH, Ha HJ, Park YH, Hong E, Park HH. The structure of AcrIC9 revealing the putative inhibitory mechanism of AcrIC9 against the type IC CRISPR-Cas system. IUCRJ 2023; 10:624-634. [PMID: 37668219 PMCID: PMC10478522 DOI: 10.1107/s2052252523007236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
CRISPR-Cas systems are known to be part of the bacterial adaptive immune system that provides resistance against intruders such as viruses, phages and other mobile genetic elements. To combat this bacterial defense mechanism, phages encode inhibitors called Acrs (anti-CRISPR proteins) that can suppress them. AcrIC9 is the most recently identified member of the AcrIC family that inhibits the type IC CRISPR-Cas system. Here, the crystal structure of AcrIC9 from Rhodobacter capsulatus is reported, which comprises a novel fold made of three central antiparallel β-strands surrounded by three α-helixes, a structure that has not been detected before. It is also shown that AcrIC9 can form a dimer via disulfide bonds generated by the Cys69 residue. Finally, it is revealed that AcrIC9 directly binds to the type IC cascade. Analysis and comparison of its structure with structural homologs indicate that AcrIC9 belongs to DNA-mimic Acrs that directly bind to the cascade complex and hinder the target DNA from binding to the cascade.
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Affiliation(s)
- Yong Jun Kang
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hyeong Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Gwan Hee Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Young-Hoon Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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9
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Figueroa W, Cazares A, Cazares D, Wu Y, de la Cruz A, Welch M, Kameyama L, Nobrega FL, Guarneros G. Distribution and molecular evolution of the anti-CRISPR family AcrIF7. PLoS Biol 2023; 21:e3002072. [PMID: 37083687 PMCID: PMC10155984 DOI: 10.1371/journal.pbio.3002072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/03/2023] [Accepted: 03/10/2023] [Indexed: 04/22/2023] Open
Abstract
Anti-clustered regularly interspaced short palindromic repeats (CRISPRs) are proteins capable of blocking CRISPR-Cas systems and typically their genes are located on mobile genetic elements. Since their discovery, numerous anti-CRISPR families have been identified. However, little is known about the distribution and sequence diversity of members within a family, nor how these traits influence the anti-CRISPR's function and evolution. Here, we use AcrIF7 to explore the dissemination and molecular evolution of an anti-CRISPR family. We uncovered 5 subclusters and prevalent anti-CRISPR variants within the group. Remarkably, AcrIF7 homologs display high similarity despite their broad geographical, ecological, and temporal distribution. Although mainly associated with Pseudomonas aeruginosa, AcrIF7 was identified in distinct genetic backgrounds indicating horizontal dissemination, primarily by phages. Using mutagenesis, we recreated variation observed in databases but also extended the sequence diversity of the group. Characterisation of the variants identified residues key for the anti-CRISPR function and other contributing to its mutational tolerance. Moreover, molecular docking revealed that variants with affected function lose key interactions with its CRISPR-Cas target. Analysis of publicly available data and the generated variants suggests that the dominant AcrIF7 variant corresponds to the minimal and optimal anti-CRISPR selected in the family. Our study provides a blueprint to investigate the molecular evolution of anti-CRISPR families.
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Affiliation(s)
- Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Yi Wu
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ana de la Cruz
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Luis Kameyama
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Franklin L Nobrega
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Gabriel Guarneros
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
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10
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Unveil the Secret of the Bacteria and Phage Arms Race. Int J Mol Sci 2023; 24:ijms24054363. [PMID: 36901793 PMCID: PMC10002423 DOI: 10.3390/ijms24054363] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage's nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and other defense systems to interfere with the replication of phage genes in the host; through the quorum sensing (QS) enhancement of phage's resistant effect. At the same time, phages have also evolved a variety of counter-defense strategies, such as degrading extracellular polymeric substances (EPS) that mask receptors or recognize new receptors, thereby regaining the ability to adsorb host cells; modifying its own genes to prevent the R-M systems from recognizing phage genes or evolving proteins that can inhibit the R-M complex; through the gene mutation itself, building nucleus-like compartments or evolving anti-CRISPR (Acr) proteins to resist CRISPR-Cas systems; and by producing antirepressors or blocking the combination of autoinducers (AIs) and its receptors to suppress the QS. The arms race between bacteria and phages is conducive to the coevolution between bacteria and phages. This review details bacterial anti-phage strategies and anti-defense strategies of phages and will provide basic theoretical support for phage therapy while deeply understanding the interaction mechanism between bacteria and phages.
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11
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Yin P, Zhang Y, Yang L, Feng Y. Non-canonical inhibition strategies and structural basis of anti-CRISPR proteins targeting type I CRISPR-Cas systems. J Mol Biol 2023; 435:167996. [PMID: 36754343 DOI: 10.1016/j.jmb.2023.167996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023]
Abstract
Mobile genetic elements (MGEs) such as bacteriophages and their host prokaryotes are trapped in an eternal battle against each other. To cope with foreign infection, bacteria and archaea have evolved multiple immune strategies, out of which CRISPR-Cas system is up to now the only discovered adaptive system in prokaryotes. Despite the fact that CRISPR-Cas system provides powerful and delicate protection against MGEs, MGEs have also evolved anti-CRISPR proteins (Acrs) to counteract the CRISPR-Cas immune defenses. To date, 46 families of Acrs targeting type I CRISPR-Cas system have been characterized, out of which structure information of 21 families have provided insights on their inhibition strategies. Here, we review the non-canonical inhibition strategies adopted by Acrs targeting type I CRISPR-Cas systems based on their structure information by incorporating the most recent advances in this field, and discuss our current understanding and future perspectives. The delicate interplay between type I CRISPR-Cas systems and their Acrs provides us with important insights into the ongoing fierce arms race between prokaryotic hosts and their predators.
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Affiliation(s)
- Peipei Yin
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, College of Chemical and Biological Engineering, Yichun University, Yichun 336000, 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
| | - Lingguang Yang
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, College of Chemical and Biological Engineering, Yichun University, Yichun 336000, 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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12
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Kim GE, Lee SY, Birkholz N, Kamata K, Jeong JH, Kim YG, Fineran PC, Park HH. Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24. Nucleic Acids Res 2022; 50:11344-11358. [PMID: 36243977 DOI: 10.1093/nar/gkac880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/24/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas systems are adaptive immune systems in bacteria and archaea that provide resistance against phages and other mobile genetic elements. To fight against CRISPR-Cas systems, phages and archaeal viruses encode anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas systems. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins encoded within acr-aca operons. AcrIF24 is a recently identified Acr that inhibits the type I-F CRISPR-Cas system. Interestingly, AcrIF24 was predicted to be a dual-function Acr and Aca. Here, we elucidated the crystal structure of AcrIF24 from Pseudomonas aeruginosa and identified its operator sequence within the regulated acr-aca operon promoter. The structure of AcrIF24 has a novel domain composition, with wing, head and body domains. The body domain is responsible for recognition of promoter DNA for Aca regulatory activity. We also revealed that AcrIF24 directly bound to type I-F Cascade, specifically to Cas7 via its head domain as part of its Acr mechanism. Our results provide new molecular insights into the mechanism of a dual functional Acr-Aca protein.
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Affiliation(s)
- Gi Eob Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - So Yeon Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Kotaro Kamata
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.,Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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13
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Gao Z, Zhang L, Ge Z, Wang H, Yue Y, Jiang Z, Wang X, Xu C, Zhang Y, Yang M, Feng Y. Anti-CRISPR protein AcrIF4 inhibits the type I-F CRISPR-Cas surveillance complex by blocking nuclease recruitment and DNA cleavage. J Biol Chem 2022; 298:102575. [PMID: 36209819 PMCID: PMC9637919 DOI: 10.1016/j.jbc.2022.102575] [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: 08/30/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides prokaryotes with protection against mobile genetic elements such as phages. In turn, phages deploy anti-CRISPR (Acr) proteins to evade this immunity. AcrIF4, an Acr targeting the type I-F CRISPR-Cas system, has been reported to bind the crRNA-guided surveillance (Csy) complex. However, it remains controversial whether AcrIF4 inhibits target DNA binding to the Csy complex. Here, we present structural and mechanistic studies into AcrIF4, exploring its unique anti-CRISPR mechanism. While the Csy-AcrIF4 complex displays decreased affinity for target DNA, it is still able to bind the DNA. Our structural and functional analyses of the Csy-AcrIF4-dsDNA complex revealed that AcrIF4 binding prevents rotation of the helical bundle of the Cas8f subunit induced by dsDNA binding, therefore resulting in failure of nuclease Cas2/3 recruitment and DNA cleavage. Overall, our study provides an interesting example of attack on the nuclease recruitment event by an Acr, but not conventional mechanisms of blocking binding of target DNA.
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Affiliation(s)
- Zhengyu 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, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zihao Ge
- 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, China
| | - Hao Wang
- 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, China
| | - Yourun Yue
- 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, China
| | - Zhuobing Jiang
- 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, China
| | - Xin Wang
- 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, China
| | - Chenying Xu
- 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, 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, China,For correspondence: Yue Feng; Maojun Yang; Yi Zhang
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China,For correspondence: Yue Feng; Maojun Yang; Yi Zhang
| | - 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, China,For correspondence: Yue Feng; Maojun Yang; Yi Zhang
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14
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Mukherjee IA, Gabel C, Noinaj N, Bondy-Denomy J, Chang L. Structural basis of AcrIF24 as an anti-CRISPR protein and transcriptional suppressor. Nat Chem Biol 2022; 18:1417-1424. [PMID: 36163386 PMCID: PMC9691602 DOI: 10.1038/s41589-022-01137-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Anti-CRISPR (Acr) proteins are encoded by phages to inactivate CRISPR-Cas systems of bacteria and archaea and are used to enhance the CRISPR toolbox for genome editing. Here we report the structure and mechanism of AcrIF24, an Acr protein that inhibits the type I-F CRISPR-Cas system from Pseudomonas aeruginosa. AcrIF24 is a homodimer that associates with two copies of the surveillance complex (Csy) and prevents the hybridization between CRISPR RNA and target DNA. Furthermore, AcrIF24 functions as an anti-CRISPR-associated (Aca) protein to repress the transcription of the acrIF23-acrIF24 operon. Alone or in complex with Csy, AcrIF24 is capable of binding to the acrIF23-acrIF24 promoter DNA with nanomolar affinity. The structure of a Csy-AcrIF24-promoter DNA complex at 2.7 Å reveals the mechanism for transcriptional suppression. Our results reveal that AcrIF24 functions as an Acr-Aca fusion protein, and they extend understanding of the diverse mechanisms used by Acr proteins.
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Affiliation(s)
| | - Clinton Gabel
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.,Innovative Genomics Institute, Berkeley, CA, USA
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA. .,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA.
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15
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Disarming of type I-F CRISPR-Cas surveillance complex by anti-CRISPR proteins AcrIF6 and AcrIF9. Sci Rep 2022; 12:15548. [PMID: 36109551 PMCID: PMC9478129 DOI: 10.1038/s41598-022-19797-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems that protect against phages and other invading nucleic acids. The evolutionary arms race between prokaryotes and phages gave rise to phage anti-CRISPR (Acr) proteins that act as a counter defence against CRISPR-Cas systems by inhibiting the effector complex. Here, we used a combination of bulk biochemical experiments, X-ray crystallography and single-molecule techniques to explore the inhibitory activity of AcrIF6 and AcrIF9 proteins against the type I-F CRISPR-Cas system from Aggregatibacter actinomycetemcomitans (Aa). We showed that AcrIF6 and AcrIF9 proteins hinder Aa-Cascade complex binding to target DNA. We solved a crystal structure of Aa1-AcrIF9 protein, which differ from other known AcrIF9 proteins by an additional structurally important loop presumably involved in the interaction with Cascade. We revealed that AcrIF9 association with Aa-Cascade promotes its binding to off-target DNA sites, which facilitates inhibition of CRISPR-Cas protection.
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16
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Kang YJ, Park HH. High-resolution crystal structure of the anti-CRISPR protein AcrIC5. Biochem Biophys Res Commun 2022; 625:102-108. [DOI: 10.1016/j.bbrc.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
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17
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Ren J, Wang H, Yang L, Li F, Wu Y, Luo Z, Chen Z, Zhang Y, Feng Y. Structural and mechanistic insights into the inhibition of type I-F CRISPR-Cas system by anti-CRISPR protein AcrIF23. J Biol Chem 2022; 298:102124. [PMID: 35697070 PMCID: PMC9270243 DOI: 10.1016/j.jbc.2022.102124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Prokaryotes evolved CRISPR and CRISPR-associated (Cas) proteins as a kind of adaptive immune defense against mobile genetic elements (MGEs) including harmful phages. To counteract this defense, many MGEs in turn encode anti-CRISPR proteins (Acrs) to inactivate the CRISPR-Cas system. While multiple mechanisms of Acrs have been uncovered, it remains unknown whether other mechanisms are also utilized by uncharacterized Acrs. Here, we report a novel mechanism adopted by recently identified AcrIF23. We show that AcrIF23 interacts with the Cas2/3 helicase-nuclease in the type I-F CRISPR-Cas system, similar to AcrIF3. The structure of AcrIF23 demonstrated a novel fold and structure-based mutagenesis identified a surface region of AcrIF23 involved in both Cas2/3-binding and its inhibition capacity. Unlike AcrIF3, however, we found AcrIF23 only potently inhibits the DNA cleavage activity of Cas2/3, but does not hinder the recruitment of Cas2/3 to the CRISPR RNA (crRNA)-guided surveillance complex (the Csy complex). Also in contrast to AcrIF3 which hinders substrate DNA recognition by Cas2/3, we show AcrIF23 promotes DNA binding to Cas2/3. Taken together, our study identifies a novel anti-CRISPR mechanism used by AcrIF23 and highlights the diverse mechanisms adopted by Acrs.
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Affiliation(s)
- Junhui Ren
- 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
| | - Hao Wang
- 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; Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun 336000, China
| | - Feixue Li
- 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
| | - Yao Wu
- State Key Laboratory of Plant Genomic, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, Jiangsu, China
| | - 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.
| | - 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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18
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Yang L, Zhang L, Yin P, Ding H, Xiao Y, Zeng J, Wang W, Zhou H, Wang Q, Zhang Y, Chen Z, Yang M, Feng Y. Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24. Nat Commun 2022; 13:1931. [PMID: 35411005 PMCID: PMC9001735 DOI: 10.1038/s41467-022-29581-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 03/16/2022] [Indexed: 11/18/2022] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding. Phages use anti-CRISPR proteins (Acrs) to counteract the bacterial CRISPR-Cas systems. Here, the authors characterize AcrIF24, which functions as an Aca (Acr-associated) to repress and regulate its own transcription, dimerizes the Csy complex, blocks the hybridization of target DNA, and tethers non-sequence-specific DNA to the Csy complex.
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19
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AcrIF5 specifically targets DNA-bound CRISPR-Cas surveillance complex for inhibition. Nat Chem Biol 2022; 18:670-677. [PMID: 35301482 DOI: 10.1038/s41589-022-00995-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 02/10/2022] [Indexed: 01/04/2023]
Abstract
CRISPR-Cas systems are prokaryotic antiviral systems, and phages use anti-CRISPR proteins (Acrs) to inactivate these systems. Here we present structural and functional analyses of AcrIF5, exploring its unique anti-CRISPR mechanism. AcrIF5 shows binding specificity only for the target DNA-bound form of the crRNA-guided surveillance (Csy) complex, but not the apo Csy complex from the type I-F CRISPR-Cas system. We solved the structure of the Csy-dsDNA-AcrIF5 complex, revealing that the conformational changes of the Csy complex caused by dsDNA binding dictate the binding specificity for the Csy-dsDNA complex by AcrIF5. Mechanistically, five AcrIF5 molecules bind one Csy-dsDNA complex, which destabilizes the helical bundle domain of Cas8f, thus preventing subsequent Cas2/3 recruitment. AcrIF5 exists in symbiosis with AcrIF3, which blocks Cas2/3 recruitment. This attack on the recruitment event stands in contrast to the conventional mechanisms of blocking binding of target DNA. Overall, our study reveals an unprecedented mechanism of CRISPR-Cas inhibition by AcrIF5.
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20
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Wang H, Gao T, Zhou Y, Ren J, Guo J, Zeng J, Xiao Y, Zhang Y, Feng Y. Mechanistic insights into the inhibition of the CRISPR-Cas Surveillance Complex by anti-CRISPR protein AcrIF13. J Biol Chem 2022; 298:101636. [PMID: 35085557 PMCID: PMC8857482 DOI: 10.1016/j.jbc.2022.101636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide prokaryotes with nucleic acid–based adaptive immunity against infections of mobile genetic elements, including phages. To counteract this immune process, phages have evolved various anti-CRISPR (Acr) proteins which deactivate CRISPR-Cas–based immunity. However, the mechanisms of many of these Acr-mediated inhibitions are not clear. Here, we report the crystal structure of AcrIF13 and explore its inhibition mechanism. The structure of AcrIF13 is unique and displays a negatively charged surface. Additionally, biochemical studies identified that AcrIF13 interacts with the type I-F CRISPR-Cas surveillance complex (Csy complex) to block target DNA recognition and that the Cas5f-8f tail and Cas7.6f subunit of the Csy complex are specific binding targets of AcrIF13. Further mutational studies demonstrated that several negatively charged residues of AcrIF13 and positively charged residues of Cas8f and Cas7f of the Csy complex are involved in AcrIF13–Csy binding. Together, our findings provide mechanistic insights into the inhibition mechanism of AcrIF13 and further suggest the prevalence of the function of Acr proteins as DNA mimics.
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Affiliation(s)
- Hao Wang
- 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, 100029 Beijing, 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, 100029 Beijing, China
| | - Yu Zhou
- National Institute of Biological Sciences, 102206 Beijing, China
| | - Junhui Ren
- 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, 100029 Beijing, China
| | - Junhua Guo
- 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, 100029 Beijing, China
| | - Jianwei Zeng
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Yu Xiao
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, 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, 100029 Beijing, 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, 100029 Beijing, China.
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21
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Vyas P, Harish. Anti-CRISPR proteins as a therapeutic agent against drug-resistant bacteria. Microbiol Res 2022; 257:126963. [PMID: 35033831 DOI: 10.1016/j.micres.2022.126963] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 02/08/2023]
Abstract
The continuous deployment of various antibiotics to treat multiple serious bacterial infections leads to multidrug resistance among the bacterial population. It has failed the standard treatment strategies through different antibacterial agents and serves as a significant threat to public health worldwide at devastating levels. The discovery of anti-CRISPR proteins catches the interest of researchers around the world as a promising therapeutic agent against drug-resistant bacteria. Anti-CRISPR proteins are known to inhibit bacterial CRISPR-Cas defense systems in multiple possible ways. The CRISPR-Cas nucleoprotein assembly provides adaptive immunity in bacteria against diverse categories of phage infections. Parallelly, phages also try to break the CRISPR-Cas barrier by producing anti-CRISPR proteins, leading to growth inhibition and bacterial lysis. This review begins with a brief description of the bacterial CRISPR-Cas system, followed by a detailed portrayal of anti-CRISPR proteins, including their discovery and evolution, mechanism of action, regulation of expression, and potential applications in the healthcare sector as an alternative therapeutic strategy to combat severe bacterial infections.
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Affiliation(s)
- Pallavi Vyas
- Plant Biotechnology Laboratory, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313 001, Rajasthan, India
| | - Harish
- Plant Biotechnology Laboratory, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313 001, Rajasthan, India.
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22
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Hong SH, Lee G, Park C, Koo J, Kim EH, Bae E, Suh JY. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2363-2376. [PMID: 35166843 PMCID: PMC8887544 DOI: 10.1093/nar/gkac096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteria and archaea use the CRISPR-Cas system to fend off invasions of bacteriophages and foreign plasmids. In response, bacteriophages encode anti-CRISPR (Acr) proteins that potently inhibit host Cas proteins to suppress CRISPR-mediated immunity. AcrIE4-F7, which was isolated from Pseudomonas citronellolis, is a fused form of AcrIE4 and AcrIF7 that inhibits both type I-E and type I-F CRISPR-Cas systems. Here, we determined the structure of AcrIE4-F7 and identified its Cas target proteins. The N-terminal AcrIE4 domain adopts a novel α-helical fold that targets the PAM interaction site of the type I-E Cas8e subunit. The C-terminal AcrIF7 domain exhibits an αβ fold like native AcrIF7, which disables target DNA recognition by the PAM interaction site in the type I-F Cas8f subunit. The two Acr domains are connected by a flexible linker that allows prompt docking onto their cognate Cas8 targets. Conserved negative charges in each Acr domain are required for interaction with their Cas8 targets. Our results illustrate a common mechanism by which AcrIE4-F7 inhibits divergent CRISPR-Cas types.
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Affiliation(s)
| | | | - Changkon Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Eun-Hee Kim
- Bio-Chemical Analysis Team, Korea Basic Science Institute, Ochang 28119, Korea
| | - Euiyoung Bae
- Correspondence may also be addressed to Euiyoung Bae. Tel: +82 2 880 4648; Fax: +82 2 873 3112;
| | - Jeong-Yong Suh
- To whom correspondence should be addressed. Tel: +82 2 880 4879; Fax: +82 2 877 4906;
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23
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Yang L, Zhang Y, Yin P, Feng Y. Structural insights into the inactivation of the type I-F CRISPR-Cas system by anti-CRISPR proteins. RNA Biol 2021; 18:562-573. [PMID: 34606423 DOI: 10.1080/15476286.2021.1985347] [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: 10/20/2022] Open
Abstract
Phage infection is one of the major threats to prokaryotic survival, and prokaryotes in turn have evolved multiple protection approaches to fight against this challenge. Various delicate mechanisms have been discovered from this eternal arms race, among which the CRISPR-Cas systems are the prokaryotic adaptive immune systems and phages evolve diverse anti-CRISPR (Acr) proteins to evade this immunity. Until now, about 90 families of Acr proteins have been identified, out of which 24 families were verified to fight against subtype I-F CRISPR-Cas systems. Here, we review the structural and biochemical mechanisms of the characterized type I-F Acr proteins, classify their inhibition mechanisms into two major groups and provide insights for future studies of other Acr proteins. Understanding Acr proteins in this context will lead to a variety of practical applications in genome editing and also provide exciting insights into the molecular arms race between prokaryotes and phages.
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Affiliation(s)
- 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, China.,Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun, 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, 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, China.,Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, Department of Chemistry and Bioengineering, Yichun University, Yichun, 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, China
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24
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Liu X, Zhang L, Xiu Y, Gao T, Huang L, Xie Y, Yang L, Wang W, Wang P, Zhang Y, Yang M, Feng Y. Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR-Cas surveillance complex. Nucleic Acids Res 2021; 49:10178-10191. [PMID: 34432044 PMCID: PMC8464039 DOI: 10.1093/nar/gkab738] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/20/2021] [Accepted: 08/17/2021] [Indexed: 11/21/2022] Open
Abstract
CRISPR–Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of both AcrIF14 and its complex with the crRNA-guided surveillance (Csy) complex. Our study demonstrates that apart from interacting with the Csy complex to block the hybridization of target DNA to the crRNA, AcrIF14 also endows the Csy complex with the ability to interact with non-sequence-specific dsDNA as AcrIF9 does. Further structural studies of the Csy–AcrIF14–dsDNA complex and biochemical studies uncover that the PAM recognition loop of the Cas8f subunit of the Csy complex and electropositive patches within the N-terminal domain of AcrIF14 are essential for the non-sequence-specific dsDNA binding to the Csy–AcrIF14 complex, which is different from the mechanism of AcrIF9. Our findings highlight the prevalence of Acr-induced non-specific DNA binding and shed light on future studies into the mechanisms of such Acr proteins.
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Affiliation(s)
- 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, 100029 Beijing, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, 100084 Beijing, China
| | - Yu Xiu
- 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, 100029 Beijing, 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, 100029 Beijing, China
| | - Ling Huang
- 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, 100029 Beijing, 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, 100029 Beijing, 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, 100029 Beijing, China
| | - Wenhe Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, 100084 Beijing, China
| | - Peiyi Wang
- Cryo-EM Centre, Department of Biology, Southern University of Science and Technology, 515055 Shenzhen, 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, 100029 Beijing, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, 100084 Beijing, 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, 100029 Beijing, China
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25
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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: 53] [Impact Index Per Article: 17.7] [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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26
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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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