1
|
Katz MA, Sawyer EM, Oriolt L, Kozlova A, Williams MC, Margolis SR, Johnson M, Bondy-Denomy J, Meeske AJ. Diverse viral cas genes antagonize CRISPR immunity. Nature 2024:10.1038/s41586-024-07923-x. [PMID: 39232173 DOI: 10.1038/s41586-024-07923-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/07/2024] [Indexed: 09/06/2024]
Abstract
Prokaryotic CRISPR-Cas immunity is subverted by anti-CRISPRs (Acrs), which inhibit Cas protein activities when expressed during the phage lytic cycle or from resident prophages or plasmids1. Acrs often bind to specific cognate Cas proteins, and hence inhibition is typically limited to a single CRISPR-Cas subtype2. Furthermore, although acr genes are frequently organized together in phage-associated gene clusters3, how such inhibitors initially evolve has remained unclear. Here we investigated the Acr content and inhibition specificity of diverse Listeria isolates, which naturally harbour four CRISPR-Cas systems (types I-B, II-A, II-C and VI-A). We observed widespread antagonism of CRISPR, which we traced to 11 previously unknown and 4 known acr gene families encoded by endogenous mobile elements. Among these were two Acrs that possess sequence homology to type I-B Cas proteins, one of which assembles into a defective interference complex. Surprisingly, an additional type I-B Cas homologue did not affect type I immunity, but instead inhibited the RNA-targeting type VI CRISPR system by means of CRISPR RNA (crRNA) degradation. By probing viral sequence databases, we detected abundant orphan cas genes located within putative anti-defence gene clusters. Among them, we verified the activity of a particularly broad-spectrum cas3 homologue that inhibits type I-B, II-A and VI-A CRISPR immunity. Our observations provide direct evidence of Acr evolution by cas gene co-option, and new genes with potential for broad-spectrum control of genome editing technologies.
Collapse
Affiliation(s)
- Mark A Katz
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Edith M Sawyer
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Luke Oriolt
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Albina Kozlova
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Shally R Margolis
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Matthew Johnson
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | | |
Collapse
|
2
|
He Y, Liu S, Chen L, Pu D, Zhong Z, Xu T, Ren Q, Dong C, Wang Y, Wang D, Zheng X, Guo F, Zhang T, Qi Y, Zhang Y. Versatile plant genome engineering using anti-CRISPR-Cas12a systems. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2704-7. [PMID: 39158766 DOI: 10.1007/s11427-024-2704-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
CRISPR-Cas12a genome engineering systems have been widely used in plant research and crop breeding. To date, the performance and use of anti-CRISPR-Cas12a systems have not been fully established in plants. Here, we conduct in silico analysis to identify putative anti-CRISPR systems for Cas12a. These putative anti-CRISPR proteins, along with known anti-CRISPR proteins, are assessed for their ability to inhibit Cas12a cleavage activity in vivo and in planta. Among all anti-CRISPR proteins tested, AcrVA1 shows robust inhibition of Mb2Cas12a and LbCas12a in E. coli. Further tests show that AcrVA1 inhibits LbCas12a mediated genome editing in rice protoplasts and stable transgenic lines. Impressively, co-expression of AcrVA1 mitigates off-target effects by CRISPR-LbCas12a, as revealed by whole genome sequencing. In addition, transgenic plants expressing AcrVA1 exhibit different levels of inhibition to LbCas12a mediated genome editing, representing a novel way of fine-tuning genome editing efficiency. By controlling temporal and spatial expression of AcrVA1, we show that inducible and tissue specific genome editing can be achieved in plants. Furthermore, we demonstrate that AcrVA1 also inhibits LbCas12a-based CRISPR activation (CRISPRa) and based on this principle we build logic gates to turn on and off target genes in plant cells. Together, we have established an efficient anti-CRISPR-Cas12a system in plants and demonstrate its versatile applications in mitigating off-target effects, fine-tuning genome editing efficiency, achieving spatial-temporal control of genome editing, and generating synthetic logic gates for controlling target gene expression in plant cells.
Collapse
Affiliation(s)
- Yao He
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Long Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Dongkai Pu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Tang Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Yawei Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Danning Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xuelian Zheng
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Fengbiao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430017, China.
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, 20850, USA.
| | - Yong Zhang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Chongqing Key Laboratory of Tree Germplasm Innovation and Utilization, School of Life Sciences, Southwest University, Chongqing, 400715, China.
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| |
Collapse
|
3
|
Sun M, Gao J, Tang H, Wu T, Ma Q, Zhang S, Zuo Y, Li Q. Increasing CRISPR/Cas9-mediated gene editing efficiency in T7 phage by reducing the escape rate based on insight into the survival mechanism. Acta Biochim Biophys Sin (Shanghai) 2024; 56:937-944. [PMID: 38761011 PMCID: PMC11294054 DOI: 10.3724/abbs.2024030] [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: 12/13/2023] [Accepted: 02/18/2024] [Indexed: 05/20/2024] Open
Abstract
Bacteriophages have been used across various fields, and the utilization of CRISPR/Cas-based genome editing technology can accelerate the research and applications of bacteriophages. However, some bacteriophages can escape from the cleavage of Cas protein, such as Cas9, and decrease the efficiency of genome editing. This study focuses on the bacteriophage T7, which is widely utilized but whose mechanism of evading the cleavage of CRISPR/Cas9 has not been elucidated. First, we test the escape rates of T7 phage at different cleavage sites, ranging from 10 -2 to 10 -5. The sequencing results show that DNA point mutations and microhomology-mediated end joining (MMEJ) at the target sites are the main causes. Next, we indicate the existence of the hotspot DNA region of MMEJ and successfully reduce MMEJ events by designing targeted sites that bypass the hotspot DNA region. Moreover, we also knock out the ATP-dependent DNA ligase 1. 3 gene, which may be involved in the MMEJ event, and the frequency of MMEJ at 4. 3 is reduced from 83% to 18%. Finally, the genome editing efficiency in T7 Δ 1. 3 increases from 20% to 100%. This study reveals the mechanism of T7 phage evasion from the cleavage of CRISPR/Cas9 and demonstrates that the special design of editing sites or the deletion of key gene 1. 3 can reduce MMEJ events and enhance gene editing efficiency. These findings will contribute to advancing CRISPR/Cas-based tools for efficient genome editing in phages and provide a theoretical foundation for the broader application of phages.
Collapse
Affiliation(s)
- Mingjun Sun
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| | - Jie Gao
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| | - Hongjie Tang
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| | - Ting Wu
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| | - Qinqin Ma
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| | - Suyi Zhang
- Luzhou Laojiao CoLtdLuzhou646000China
- National Engineering Research Center of Solid-State BrewingLuzhou646000China
| | - Yong Zuo
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityChengdu610101China
| |
Collapse
|
4
|
Wang X, Li D, Qin Z, Chen J, Zhou J. CRISPR/Cpf1-FOKI-induced gene editing in Gluconobacter oxydans. Synth Syst Biotechnol 2024; 9:369-379. [PMID: 38559425 PMCID: PMC10980938 DOI: 10.1016/j.synbio.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Gluconobacter oxydans is an important Gram-negative industrial microorganism that produces vitamin C and other products due to its efficient membrane-bound dehydrogenase system. Its incomplete oxidation system has many crucial industrial applications. However, it also leads to slow growth and low biomass, requiring further metabolic modification for balancing the cell growth and incomplete oxidation process. As a non-model strain, G. oxydans lacks efficient genome editing tools and cannot perform rapid multi-gene editing and complex metabolic network regulation. In the last 15 years, our laboratory attempted to deploy multiple CRISPR/Cas systems in different G. oxydans strains and found none of them as functional. In this study, Cpf1-based or dCpf1-based CRISPRi was constructed to explore the targeted binding ability of Cpf1, while Cpf1-FokI was deployed to study its nuclease activity. A study on Cpf1 found that the CRISPR/Cpf1 system could locate the target genes in G. oxydans but lacked the nuclease cleavage activity. Therefore, the CRISPR/Cpf1-FokI system based on FokI nuclease was constructed. Single-gene knockout with efficiency up to 100% and double-gene iterative editing were achieved in G. oxydans. Using this system, AcrVA6, the anti-CRISPR protein of G. oxydans was discovered for the first time, and efficient genome editing was realized.
Collapse
Affiliation(s)
- Xuyang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Dong Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Zhijie Qin
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jian Chen
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Kang W, Xiao F, Zhu X, Ling X, Xie S, Li R, Yu P, Cao L, Lei C, Qiu Y, Liu T, Nie Z. Engineering Anti-CRISPR Proteins to Create CRISPR-Cas Protein Switches for Activatable Genome Editing and Viral Protease Detection. Angew Chem Int Ed Engl 2024; 63:e202400599. [PMID: 38407550 DOI: 10.1002/anie.202400599] [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: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 02/27/2024]
Abstract
Proteins capable of switching between distinct active states in response to biochemical cues are ideal for sensing and controlling biological processes. Activatable CRISPR-Cas systems are significant in precise genetic manipulation and sensitive molecular diagnostics, yet directly controlling Cas protein function remains challenging. Herein, we explore anti-CRISPR (Acr) proteins as modules to create synthetic Cas protein switches (CasPSs) based on computational chemistry-directed rational protein interface engineering. Guided by molecular fingerprint analysis, electrostatic potential mapping, and binding free energy calculations, we rationally engineer the molecular interaction interface between Cas12a and its cognate Acr proteins (AcrVA4 and AcrVA5) to generate a series of orthogonal protease-responsive CasPSs. These CasPSs enable the conversion of specific proteolytic events into activation of Cas12a function with high switching ratios (up to 34.3-fold). These advancements enable specific proteolysis-inducible genome editing in mammalian cells and sensitive detection of viral protease activities during virus infection. This work provides a promising strategy for developing CRISPR-Cas tools for controllable gene manipulation and regulation and clinical diagnostics.
Collapse
Affiliation(s)
- Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
- Key Laboratory of Tropical Medicinal Resource Chemistry of Ministry of Education & Key Laboratory of Tropical Medicinal Plant Chemistry of Hainan Province, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, 571158, P. R. China
| | - Fei Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Xi Zhu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ruimiao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Peihang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Linxin Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| |
Collapse
|
7
|
Mayo-Muñoz D, Pinilla-Redondo R, Camara-Wilpert S, Birkholz N, Fineran PC. Inhibitors of bacterial immune systems: discovery, mechanisms and applications. Nat Rev Genet 2024; 25:237-254. [PMID: 38291236 DOI: 10.1038/s41576-023-00676-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 02/01/2024]
Abstract
To contend with the diversity and ubiquity of bacteriophages and other mobile genetic elements, bacteria have developed an arsenal of immune defence mechanisms. Bacterial defences include CRISPR-Cas, restriction-modification and a growing list of mechanistically diverse systems, which constitute the bacterial 'immune system'. As a response, bacteriophages and mobile genetic elements have evolved direct and indirect mechanisms to circumvent or block bacterial defence pathways and ensure successful infection. Recent advances in methodological and computational approaches, as well as the increasing availability of genome sequences, have boosted the discovery of direct inhibitors of bacterial defence systems. In this Review, we discuss methods for the discovery of direct inhibitors, their diverse mechanisms of action and perspectives on their emerging applications in biotechnology and beyond.
Collapse
Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
8
|
Ruta GV, Ciciani M, Kheir E, Gentile MD, Amistadi S, Casini A, Cereseto A. Eukaryotic-driven directed evolution of Cas9 nucleases. Genome Biol 2024; 25:79. [PMID: 38528620 PMCID: PMC10962177 DOI: 10.1186/s13059-024-03215-9] [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: 09/26/2023] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Further advancement of genome editing highly depends on the development of tools with higher compatibility with eukaryotes. A multitude of described Cas9s have great potential but require optimization for genome editing purposes. Among these, the Cas9 from Campylobacter jejuni, CjCas9, has a favorable small size, facilitating delivery in mammalian cells. Nonetheless, its full exploitation is limited by its poor editing activity. RESULTS Here, we develop a Eukaryotic Platform to Improve Cas Activity (EPICA) to steer weakly active Cas9 nucleases into highly active enzymes by directed evolution. The EPICA platform is obtained by coupling Cas nuclease activity with yeast auxotrophic selection followed by mammalian cell selection through a sensitive reporter system. EPICA is validated with CjCas9, generating an enhanced variant, UltraCjCas9, following directed evolution rounds. UltraCjCas9 is up to 12-fold more active in mammalian endogenous genomic loci, while preserving high genome-wide specificity. CONCLUSIONS We report a eukaryotic pipeline allowing enhancement of Cas9 systems, setting the ground to unlock the multitude of RNA-guided nucleases existing in nature.
Collapse
Affiliation(s)
- Giulia Vittoria Ruta
- Laboratory of Molecular Virology, Department CIBIO, University of Trento, Trento, Italy.
| | - Matteo Ciciani
- Laboratory of Molecular Virology, Department CIBIO, University of Trento, Trento, Italy
- Laboratory of Computational Metagenomics, Department CIBIO, University of Trento, Trento, Italy
| | - Eyemen Kheir
- Laboratory of Molecular Virology, Department CIBIO, University of Trento, Trento, Italy
| | | | - Simone Amistadi
- Laboratory of Molecular Virology, Department CIBIO, University of Trento, Trento, Italy
- Present address: Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | | | - Anna Cereseto
- Laboratory of Molecular Virology, Department CIBIO, University of Trento, Trento, Italy.
| |
Collapse
|
9
|
Zhuang S, Hu T, Zhou H, He S, Li J, Zhang Y, Gu D, Xu Y, Chen Y, Wang J. CRISPR-HOLMES-based NAD + detection. Front Bioeng Biotechnol 2024; 12:1355640. [PMID: 38590607 PMCID: PMC10999544 DOI: 10.3389/fbioe.2024.1355640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 04/10/2024] Open
Abstract
Studies have indicated that the intracellular nicotinamide adenine dinucleotide (NAD+) level is associated with the occurrence and development of many diseases. However, traditional nicotinamide adenine dinucleotide (NAD+) detection techniques are time-consuming and may require large and expensive instruments. We recently found that the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a protein can be inactivated by AcrVA5-mediated acetylation and reactivated by CobB, using NAD+ as the co-factor. Therefore, in this study, we created a CRISPR-Cas12a-based one-step HOLMES(NAD+) system for rapid and convenient NAD+ detection with the employment of both acetylated Cas12a and CobB. In HOLMES(NAD+), acetylated Cas12a loses its trans-cleavage activities and can be reactivated by CobB in the presence of NAD+, cutting ssDNA reporters to generate fluorescence signals. HOLMES(NAD+) shows both sensitivity and specificity in NAD+ detection and can be used for quantitative determination of intracellular NAD+ concentrations. Therefore, HOLMES(NAD+) not only provides a convenient and rapid approach for target NAD+ quantitation but also expands the application scenarios of HOLMES to non-nucleic acid detection.
Collapse
Affiliation(s)
- Songkuan Zhuang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Tianshuai Hu
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Hongzhong Zhou
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Shiping He
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Jie Li
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Yuehui Zhang
- Shenzhen Bao An Peoples Hospital, Shenzhen, China
| | - Dayong Gu
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Yong Xu
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Yijian Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University & Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission, Shanghai, China
| | - Jin Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
- Shanghai Tolo Biotechnology Co Ltd, Shanghai, China
| |
Collapse
|
10
|
Wang H, Zheng K, Wang M, Ma K, Ren L, Guo R, Ma L, Zhang H, Liu Y, Xiong Y, Wu M, Shao H, Sung YY, Mok WJ, Wong LL, McMinn A, Liang Y. Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family. Microbiol Spectr 2024; 12:e0336723. [PMID: 38214523 PMCID: PMC10846135 DOI: 10.1128/spectrum.03367-23] [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: 09/17/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024] Open
Abstract
Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.
Collapse
Affiliation(s)
- Hongmin Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Kaiyang Zheng
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Keran Ma
- Haide College, Ocean University of China, Qingdao, China
| | - Linyi Ren
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Ruizhe Guo
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Lina Ma
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yundan Liu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Yao Xiong
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Miaolan Wu
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Li Lian Wong
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Andrew McMinn
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Yantao Liang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Center for Ocean Carbon Neutrality, Ocean University of China, Qingdao, China
- Universiti Malaysia Terengganu-Ocean Unversity of China Joint Centre for Marine Studies, Qingdao, China
| |
Collapse
|
11
|
Longin H, Broeckaert N, van Noort V, Lavigne R, Hendrix H. Posttranslational modifications in bacteria during phage infection. Curr Opin Microbiol 2024; 77:102425. [PMID: 38262273 DOI: 10.1016/j.mib.2024.102425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/08/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
During phage infection, both virus and bacteria attempt to gain and/or maintain control over critical bacterial functions, through a plethora of strategies. These strategies include posttranslational modifications (PTMs, including phosphorylation, ribosylation, and acetylation), as rapid and dynamic regulators of protein behavior. However, to date, knowledge on the topic remains scarce and fragmented, while a more systematic investigation lies within reach. The release of AlphaFold, which advances PTM enzyme discovery and functional elucidation, and the increasing inclusivity and scale of mass spectrometry applications to new PTM types, could significantly accelerate research in the field. In this review, we highlight the current knowledge on PTMs during phage infection, and conceive a possible pipeline for future research, following an enzyme-target-function scheme.
Collapse
Affiliation(s)
- Hannelore Longin
- Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 box 2460, 3001 Heverlee, Belgium; Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium
| | - Nand Broeckaert
- Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 box 2460, 3001 Heverlee, Belgium; Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium
| | - Vera van Noort
- Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 box 2460, 3001 Heverlee, Belgium; Institute of Biology, Leiden University, Sylviusweg 72, 2333 Leiden, the Netherlands
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001 Heverlee, Belgium.
| |
Collapse
|
12
|
Wimmer F, Englert F, Wandera KG, Alkhnbashi O, Collins S, Backofen R, Beisel C. Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation. Nucleic Acids Res 2024; 52:769-783. [PMID: 38015466 PMCID: PMC10810201 DOI: 10.1093/nar/gkad1097] [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: 04/15/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host's genomic DNA, leading to lethal self-targeting. While self-targeting can be circumvented through different mechanisms, natural examples remain poorly explored. Here, we investigate extensive self-targeting by two CRISPR-Cas systems encoding 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans. We show that the native I-C and I-F1 systems are actively expressed and that CRISPR RNAs are properly processed. When expressed in Escherichia coli, each Cascade complex binds its PAM-flanked DNA target to block transcription, while the addition of Cas3 paired with genome targeting induces cell killing. While exploring how X. albilineans survives self-targeting, we predicted putative anti-CRISPR proteins (Acrs) encoded within the bacterium's genome. Screening of identified candidates with cell-free transcription-translation systems and in E. coli revealed two Acrs, which we named AcrIC11 and AcrIF12Xal, that inhibit the activity of Cas3 but not Cascade of the respective system. While AcrF12Xal is homologous to AcrIF12, AcrIC11 shares sequence and structural homology with the anti-restriction protein KlcA. These findings help explain tolerance of self-targeting through two CRISPR-Cas systems and expand the known suite of DNA degradation-inhibiting Acrs.
Collapse
Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Omer S Alkhnbashi
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
- Interdisciplinary Research Center for Intelligent Secure Systems (IRC-ISS), King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
| | - Scott P Collins
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| |
Collapse
|
13
|
Duan N, Hand E, Pheko M, Sharma S, Emiola A. Structure-guided discovery of anti-CRISPR and anti-phage defense proteins. Nat Commun 2024; 15:649. [PMID: 38245560 PMCID: PMC10799925 DOI: 10.1038/s41467-024-45068-7] [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: 11/24/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Bacteria use a variety of defense systems to protect themselves from phage infection. In turn, phages have evolved diverse counter-defense measures to overcome host defenses. Here, we use protein structural similarity and gene co-occurrence analyses to screen >66 million viral protein sequences and >330,000 metagenome-assembled genomes for the identification of anti-phage and counter-defense systems. We predict structures for ~300,000 proteins and perform large-scale, pairwise comparison to known anti-CRISPR (Acr) and anti-phage proteins to identify structural homologs that otherwise may not be uncovered using primary sequence search. This way, we identify a Bacteroidota phage Acr protein that inhibits Cas12a, and an Akkermansia muciniphila anti-phage defense protein, termed BxaP. Gene bxaP is found in loci encoding Bacteriophage Exclusion (BREX) and restriction-modification defense systems, but confers immunity independently. Our work highlights the advantage of combining protein structural features and gene co-localization information in studying host-phage interactions.
Collapse
Affiliation(s)
- Ning Duan
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Emily Hand
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Mannuku Pheko
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Shikha Sharma
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Akintunde Emiola
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
14
|
Lin J, Alfastsen L, Bhoobalan-Chitty Y, Peng X. Molecular basis for inhibition of type III-B CRISPR-Cas by an archaeal viral anti-CRISPR protein. Cell Host Microbe 2023; 31:1837-1849.e5. [PMID: 37909049 DOI: 10.1016/j.chom.2023.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
Despite a wide presence of type III clustered regularly interspaced short palindromic repeats, CRISPR-associated (CRISPR-Cas) in archaea and bacteria, very few anti-CRISPR (Acr) proteins inhibiting type III immunity have been identified, and even less is known about their inhibition mechanism. Here, we present the discovery of a type III CRISPR-Cas inhibitor, AcrIIIB2, encoded by Sulfolobus virus S. islandicus rod-shaped virus 3 (SIRV3). AcrIIIB2 inhibits type III-B CRISPR-Cas immune response to protospacers encoded in middle/late-expressed viral genes. Investigation of the interactions between S. islandicus type III-B CRISPR-Cas Cmr-α-related proteins and AcrIIIB2 reveals that the Acr does not bind to Csx1 but rather interacts with the Cmr-α effector complex. Furthermore, in vitro assays demonstrate that AcrIIIB2 can block the dissociation of cleaved target RNA from the Cmr-α complex, thereby inhibiting the Cmr-α turnover, thus preventing host cellular dormancy and further viral genome degradation by the type III-B CRISPR-Cas immunity.
Collapse
Affiliation(s)
- Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Lauge Alfastsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | | | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| |
Collapse
|
15
|
Gao Z, Feng Y. Bacteriophage strategies for overcoming host antiviral immunity. Front Microbiol 2023; 14:1211793. [PMID: 37362940 PMCID: PMC10286901 DOI: 10.3389/fmicb.2023.1211793] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
Phages and their bacterial hosts together constitute a vast and diverse ecosystem. Facing the infection of phages, prokaryotes have evolved a wide range of antiviral mechanisms, and phages in turn have adopted multiple tactics to circumvent or subvert these mechanisms to survive. An in-depth investigation into the interaction between phages and bacteria not only provides new insight into the ancient coevolutionary conflict between them but also produces precision biotechnological tools based on anti-phage systems. Moreover, a more complete understanding of their interaction is also critical for the phage-based antibacterial measures. Compared to the bacterial antiviral mechanisms, studies into counter-defense strategies adopted by phages have been a little slow, but have also achieved important advances in recent years. In this review, we highlight the numerous intracellular immune systems of bacteria as well as the countermeasures employed by phages, with an emphasis on the bacteriophage strategies in response to host antiviral immunity.
Collapse
|
16
|
Makarova KS, Wolf YI, Koonin EV. In Silico Approaches for Prediction of Anti-CRISPR Proteins. J Mol Biol 2023; 435:168036. [PMID: 36868398 PMCID: PMC10073340 DOI: 10.1016/j.jmb.2023.168036] [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: 10/26/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
Abstract
Numerous viruses infecting bacteria and archaea encode CRISPR-Cas system inhibitors, known as anti-CRISPR proteins (Acr). The Acrs typically are highly specific for particular CRISPR variants, resulting in remarkable sequence and structural diversity and complicating accurate prediction and identification of Acrs. In addition to their intrinsic interest for understanding the coevolution of defense and counter-defense systems in prokaryotes, Acrs could be natural, potent on-off switches for CRISPR-based biotechnological tools, so their discovery, characterization and application are of major importance. Here we discuss the computational approaches for Acr prediction. Due to the enormous diversity and likely multiple origins of the Acrs, sequence similarity searches are of limited use. However, multiple features of protein and gene organization have been successfully harnessed to this end including small protein size and distinct amino acid compositions of the Acrs, association of acr genes in virus genomes with genes encoding helix-turn-helix proteins that regulate Acr expression (Acr-associated proteins, Aca), and presence of self-targeting CRISPR spacers in bacterial and archaeal genomes containing Acr-encoding proviruses. Productive approaches for Acr prediction also involve genome comparison of closely related viruses, of which one is resistant and the other one is sensitive to a particular CRISPR variant, and "guilt by association" whereby genes adjacent to a homolog of a known Aca are identified as candidate Acrs. The distinctive features of Acrs are employed for Acr prediction both by developing dedicated search algorithms and through machine learning. New approaches will be needed to identify novel types of Acrs that are likely to exist.
Collapse
Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
| |
Collapse
|
17
|
Forsberg KJ. Anti-CRISPR Discovery: Using Magnets to Find Needles in Haystacks. J Mol Biol 2023; 435:167952. [PMID: 36638909 PMCID: PMC10073268 DOI: 10.1016/j.jmb.2023.167952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
CRISPR-Cas immune systems in bacteria and archaea protect against viral infection, which has spurred viruses to develop dedicated inhibitors of these systems called anti-CRISPRs (Acrs). Like most host-virus arms races, many diverse examples of these immune and counter-immune proteins are encoded by the genomes of bacteria, archaea, and their viruses. For the case of Acrs, it is almost certain that just a small minority of nature's true diversity has been described. In this review, I discuss the various approaches used to identify these Acrs and speculate on the future for Acr discovery. Because Acrs can determine infection outcomes in nature and regulate CRISPR-Cas activities in applied settings, they have a dual importance to both host-virus conflicts and emerging biotechnologies. Thus, revealing the largely hidden world of Acrs should provide important lessons in microbiology that have the potential to ripple far beyond the field.
Collapse
Affiliation(s)
- Kevin J Forsberg
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
18
|
Marino ND. Phage Against the Machine: Discovery and Mechanism of Type V Anti-CRISPRs. J Mol Biol 2023; 435:168054. [PMID: 36934807 DOI: 10.1016/j.jmb.2023.168054] [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: 12/14/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
The discovery of diverse bacterial CRISPR-Cas systems has reignited interest in understanding bacterial defense pathways while yielding exciting new tools for genome editing. CRISPR-Cas systems are widely distributed in prokaryotes, found in 40% of bacteria and 90% of archaea, where they function as adaptive immune systems against bacterial viruses (phage) and other mobile genetic elements. In turn, phage have evolved inhibitors, called anti-CRISPR proteins, to prevent targeting. Type V CRISPR-Cas12 systems have emerged as a particularly exciting arena in this co-evolutionary arms race. Type V anti-CRISPRs have highly diverse and novel mechanisms of action, some of which appear to be unusually potent or widespread. In this review, we discuss the discovery and mechanism of these anti-CRISPRs as well as future areas for exploration.
Collapse
Affiliation(s)
- Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Hwang S, Shah M, Garcia B, Hashem N, Davidson AR, Moraes TF, Maxwell KL. Anti-CRISPR Protein AcrIIC5 Inhibits CRISPR-Cas9 by Occupying the Target DNA Binding Pocket. J Mol Biol 2023; 435:167991. [PMID: 36736884 DOI: 10.1016/j.jmb.2023.167991] [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: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Anti-CRISPR proteins inhibit CRISPR-Cas immune systems through diverse mechanisms. Previously, the anti-CRISPR protein AcrIIC5Smu was shown to potently inhibit a type II-C Cas9 from Neisseria meningitidis (Nme1Cas9). In this work, we explore the mechanism of activity of the AcrIIC5 homologue from Neisseria chenwenguii (AcrIIC5Nch) and show that it prevents Cas9 binding to target DNA. We show that AcrIIC5Nch targets the PAM-interacting domain (PID) of Nme1Cas9 for inhibition, agreeing with previous findings for AcrIIC5Smu, and newly establish that strong binding of the anti-CRISPR requires guide RNA be pre-loaded on Cas9. We determined the crystal structure of AcrIIC5Nch using X-ray crystallography and identified amino acid residues that are critical for its function. Using a protein docking algorithm we show that AcrIIC5Nch likely occupies the Cas9 DNA binding pocket, thereby inhibiting target DNA binding through a mechanism similar to that previously described for AcrIIA2 and AcrIIA4.
Collapse
Affiliation(s)
- Sungwon Hwang
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada. https://twitter.com/s1hwang_21
| | - Megha Shah
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada
| | - Bianca Garcia
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada
| | - Noor Hashem
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada; Department of Molecular Genetics, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada. https://twitter.com/ARDavidson_UofT
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada. https://twitter.com/MoraesTrevor
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario M5G 1M1, Canada.
| |
Collapse
|
21
|
Belato HB, Lisi GP. The Many (Inter)faces of Anti-CRISPRs: Modulation of CRISPR-Cas Structure and Dynamics by Mechanistically Diverse Inhibitors. Biomolecules 2023; 13:biom13020264. [PMID: 36830633 PMCID: PMC9953297 DOI: 10.3390/biom13020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs), has enabled the development of highly controllable and precise CRISPR-Cas tools. Anti-CRISPRs share very little structural or sequential resemblance to each other or to other proteins, which raises intriguing questions regarding their modes of action. Many structure-function studies have shed light on the mechanism(s) of Acrs, which can act as orthosteric or allosteric inhibitors of CRISPR-Cas machinery, as well as enzymes that irreversibly modify CRISPR-Cas components. Only recently has the breadth of diversity of Acr structures and functions come to light, and this remains a rapidly evolving field. Here, we draw attention to a plethora of Acr mechanisms, with particular focus on how their action toward Cas proteins modulates conformation, dynamic (allosteric) signaling, nucleic acid binding, and cleavage ability.
Collapse
Affiliation(s)
- Helen B. Belato
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, USA
- Graduate Program in Therapeutic Sciences, Brown University, Providence, RI 02903, USA
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, USA
- Correspondence:
| |
Collapse
|
22
|
Ecology and evolution of phages encoding anti-CRISPR proteins. J Mol Biol 2023; 435:167974. [PMID: 36690071 DOI: 10.1016/j.jmb.2023.167974] [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: 10/27/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
CRISPR-Cas are prokaryotic defence systems that provide protection against invasion by mobile genetic elements (MGE), including bacteriophages. MGE can overcome CRISPR-Cas defences by encoding anti-CRISPR (Acr) proteins. These proteins are produced in the early stages of the infection and inhibit the CRISPR-Cas machinery to allow phage replication. While research on Acr has mainly focused on their discovery, structure and mode of action, and their applications in biotechnology, the impact of Acr on the ecology of MGE as well as on the coevolution with their bacterial hosts only begins to be unravelled. In this review, we summarise our current understanding on the distribution of anti-CRISPR genes in MGE, the ecology of phages encoding Acr, and their coevolution with bacterial defence mechanisms. We highlight the need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in MGE-host interactions.
Collapse
|
23
|
Shim H. Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity. Antibiotics (Basel) 2023; 12:antibiotics12020204. [PMID: 36830114 PMCID: PMC9952447 DOI: 10.3390/antibiotics12020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as the emergence and spread of antimicrobial resistance against these antibacterial compounds are outpacing the discovery and development of new antibiotics. The current antibiotic market suffers from various shortcomings, including the absence of profitability and investment. The most important underlying issue of traditional antibiotics arises from the inherent properties of these small molecules being mostly broad-spectrum and non-programmable. As the scientific knowledge of microbes progresses, the scientific community is starting to explore entirely novel approaches to tackling antimicrobial resistance. One of the most prominent approaches is to develop next-generation antibiotics. In this review, we discuss three innovations of next-generation antibiotics compared to traditional antibiotics as specificity, evolvability, and non-immunogenicity. We present a number of potential antimicrobial agents, including bacteriophage-based therapy, CRISPR-Cas-based antimicrobials, and microbiome-derived antimicrobial agents. These alternative antimicrobial agents possess innovative properties that may overcome the inherent shortcomings of traditional antibiotics, and some of these next-generation antibiotics are not merely far-fetched ideas but are currently in clinical development. We further discuss some related issues and challenges such as infection diagnostics and regulatory frameworks that still need to be addressed to bring these next-generation antibiotics to the antibiotic market as viable products to combat antimicrobial resistance using a diversified set of strategies.
Collapse
Affiliation(s)
- Hyunjin Shim
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea
| |
Collapse
|
24
|
Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA. Nature 2023; 613:588-594. [PMID: 36599979 PMCID: PMC9811890 DOI: 10.1038/s41586-022-05559-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/11/2022] [Indexed: 01/05/2023]
Abstract
Bacterial abortive-infection systems limit the spread of foreign invaders by shutting down or killing infected cells before the invaders can replicate1,2. Several RNA-targeting CRISPR-Cas systems (that is, types III and VI) cause abortive-infection phenotypes by activating indiscriminate nucleases3-5. However, a CRISPR-mediated abortive mechanism that leverages indiscriminate DNase activity of an RNA-guided single-effector nuclease has yet to be observed. Here we report that RNA targeting by the type V single-effector nuclease Cas12a2 drives abortive infection through non-specific cleavage of double-stranded DNA (dsDNA). After recognizing an RNA target with an activating protospacer-flanking sequence, Cas12a2 efficiently degrades single-stranded RNA (ssRNA), single-stranded DNA (ssDNA) and dsDNA. Within cells, the activation of Cas12a2 induces an SOS DNA-damage response and impairs growth, preventing the dissemination of the invader. Finally, we harnessed the collateral activity of Cas12a2 for direct RNA detection, demonstrating that Cas12a2 can be repurposed as an RNA-guided RNA-targeting tool. These findings expand the known defensive abilities of CRISPR-Cas systems and create additional opportunities for CRISPR technologies.
Collapse
|
25
|
Zakrzewska M, Burmistrz M. Mechanisms regulating the CRISPR-Cas systems. Front Microbiol 2023; 14:1060337. [PMID: 36925473 PMCID: PMC10013973 DOI: 10.3389/fmicb.2023.1060337] [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: 10/07/2022] [Accepted: 02/10/2023] [Indexed: 03/08/2023] Open
Abstract
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR associated proteins) is a prokaryotic system that enables sequence specific recognition and cleavage of nucleic acids. This is possible due to cooperation between CRISPR array which contains short fragments of DNA called spacers that are complimentary to the targeted nucleic acid and Cas proteins, which take part in processes of: acquisition of new spacers, processing them into their functional form as well as recognition and cleavage of targeted nucleic acids. The primary role of CRISPR-Cas systems is to provide their host with an adaptive and hereditary immunity against exogenous nucleic acids. This system is present in many variants in both Bacteria and Archea. Due to its modular structure, and programmability CRISPR-Cas system become attractive tool for modern molecular biology. Since their discovery and implementation, the CRISPR-Cas systems revolutionized areas of gene editing and regulation of gene expression. Although our knowledge on how CRISPR-Cas systems work has increased rapidly in recent years, there is still little information on how these systems are controlled and how they interact with other cellular mechanisms. Such regulation can be the result of both auto-regulatory mechanisms as well as exogenous proteins of phage origin. Better understanding of these interaction networks would be beneficial for optimization of current and development of new CRISPR-Cas-based tools. In this review we summarize current knowledge on the various molecular mechanisms that affect activity of CRISPR-Cas systems.
Collapse
Affiliation(s)
- Marta Zakrzewska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland.,Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michal Burmistrz
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| |
Collapse
|
26
|
Zhao L, You D, Wang T, Zou ZP, Yin BC, Zhou Y, Ye BC. Acylation driven by intracellular metabolites in host cells inhibits Cas9 activity used for genome editing. PNAS NEXUS 2022; 1:pgac277. [PMID: 36712324 PMCID: PMC9802096 DOI: 10.1093/pnasnexus/pgac277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas, the immune system of bacteria and archaea, has been widely harnessed for genome editing, including gene knockouts and knockins, single-base editing, gene activation, and silencing. However, the molecular mechanisms underlying fluctuations in the genome editing efficiency of crispr in various cells under different conditions remain poorly understood. In this work, we found that Cas9 can be ac(et)ylated by acetyl-phosphate or acyl-CoA metabolites both in vitro and in vivo. Several modifications are associated with the DNA or sgRNA binding sites. Notably, ac(et)ylation of Cas9 driven by these metabolites in host cells potently inhibited its binding and cleavage activity with the target DNA, thereby decreasing Crispr genome editing efficiency. This study provides more insights into understanding the effect of the intracellular environment on genome editing application of crispr with varying efficiency in hosts.
Collapse
Affiliation(s)
| | | | - Ting Wang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bin-Cheng Yin
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China,Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- To whom correspondence should be addressed:
| |
Collapse
|
27
|
Patterson A, White A, Waymire E, Fleck S, Golden S, Wilkinson RA, Wiedenheft B, Bothner B. Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex. Nucleic Acids Res 2022; 50:11243-11254. [PMID: 36215034 DOI: 10.1093/nar/gkac841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR RNA-guided detection and degradation of foreign DNA is a dynamic process. Viruses can interfere with this cellular defense by expressing small proteins called anti-CRISPRs. While structural models of anti-CRISPRs bound to their target complex provide static snapshots that inform mechanism, the dynamics and thermodynamics of these interactions are often overlooked. Here, we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) and differential scanning fluorimetry (DSF) experiments to determine how anti-CRISPR binding impacts the conformational landscape of the type IF CRISPR RNA guided surveillance complex (Csy) upon binding of two different anti-CRISPR proteins (AcrIF9 and AcrIF2). The results demonstrate that AcrIF2 binding relies on enthalpic stabilization, whereas AcrIF9 uses an entropy driven reaction to bind the CRISPR RNA-guided surveillance complex. Collectively, this work reveals the thermodynamic basis and mechanistic versatility of anti-CRISPR-mediated immune suppression. More broadly, this work presents a striking example of how allosteric effectors are employed to regulate nucleoprotein complexes.
Collapse
Affiliation(s)
- Angela Patterson
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Aidan White
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Elizabeth Waymire
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Sophie Fleck
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Sarah Golden
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Royce A Wilkinson
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Brian Bothner
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| |
Collapse
|
28
|
Wirth J, Young M. Viruses in Subsurface Environments. Annu Rev Virol 2022; 9:99-119. [PMID: 36173700 DOI: 10.1146/annurev-virology-093020-015957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.
Collapse
Affiliation(s)
- Jennifer Wirth
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| | - Mark Young
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| |
Collapse
|
29
|
Kang W, Liu L, Yu P, Zhang T, Lei C, Nie Z. A switchable Cas12a enabling CRISPR-based direct histone deacetylase activity detection. Biosens Bioelectron 2022; 213:114468. [PMID: 35700604 DOI: 10.1016/j.bios.2022.114468] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/02/2022]
Abstract
The efficient and robust signal reporting ability of CRISPR-Cas system exhibits huge value in biosensing, but its applicability for non-nucleic acid analyte detection relies on the coupling of additional recognition modules. To address this limitation, we described a switchable Cas12a and exploited it for CRISPR-based direct analysis of histone deacetylase (HDAC) activity. Starting from the acetylation-mediated inactivation of Cas12a by anti-CRISPR protein AcrVA5, we demonstrated that the acetyl-inactivated Cas12a could be reversibly activated by HDAC-mediated deacetylation based on computational simulations (e.g., deep learning and protein-protein docking analysis) and experimental verifications. By leveraging this switchable Cas12a for both target sensing and signal amplification, we established a sensitive one-pot assay capable of detecting deacetylase sirtuin-1 with sub-nanomolar sensitivity, which is 50 times lower than the standard two-step peptide-based assay. The versability of this assay was validated by the sensitive assessment of cellular HDAC activities in different cell lines with good accuracy, making it a valuable tool for biochemical studies and clinical diagnostics.
Collapse
Affiliation(s)
- Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Lin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Peihang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Tianyi Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, PR China.
| |
Collapse
|
30
|
Kang X, Yin L, Zhuang S, Hu T, Wu Z, Zhao G, Chen Y, Xu Y, Wang J. Reversible regulation of Cas12a activities by AcrVA5-mediated acetylation and CobB-mediated deacetylation. Cell Discov 2022; 8:45. [PMID: 35581175 PMCID: PMC9114340 DOI: 10.1038/s41421-022-00396-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/10/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Xiaoman Kang
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lei Yin
- Tolo Biotechnology Company Limited, Shanghai, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Second People's Hospital & Institute of Translational Medicine/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Tianshuai Hu
- Department of Clinical Laboratory, Shenzhen Second People's Hospital & Institute of Translational Medicine/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Zhile Wu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guoping Zhao
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yijian Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China. .,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission, Shanghai, China.
| | - Yong Xu
- Department of Clinical Laboratory, Shenzhen Second People's Hospital & Institute of Translational Medicine/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Second People's Hospital & Institute of Translational Medicine/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China. .,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University, Shenzhen, China.
| |
Collapse
|
31
|
Rethinking Protein Drug Design with Highly Accurate Structure Prediction of Anti-CRISPR Proteins. Pharmaceuticals (Basel) 2022; 15:ph15030310. [PMID: 35337108 PMCID: PMC8949011 DOI: 10.3390/ph15030310] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/22/2022] Open
Abstract
Protein therapeutics play an important role in controlling the functions and activities of disease-causing proteins in modern medicine. Despite protein therapeutics having several advantages over traditional small-molecule therapeutics, further development has been hindered by drug complexity and delivery issues. However, recent progress in deep learning-based protein structure prediction approaches, such as AlphaFold2, opens new opportunities to exploit the complexity of these macro-biomolecules for highly specialised design to inhibit, regulate or even manipulate specific disease-causing proteins. Anti-CRISPR proteins are small proteins from bacteriophages that counter-defend against the prokaryotic adaptive immunity of CRISPR-Cas systems. They are unique examples of natural protein therapeutics that have been optimized by the host-parasite evolutionary arms race to inhibit a wide variety of host proteins. Here, we show that these anti-CRISPR proteins display diverse inhibition mechanisms through accurate structural prediction and functional analysis. We find that these phage-derived proteins are extremely distinct in structure, some of which have no homologues in the current protein structure domain. Furthermore, we find a novel family of anti-CRISPR proteins which are structurally similar to the recently discovered mechanism of manipulating host proteins through enzymatic activity, rather than through direct inference. Using highly accurate structure prediction, we present a wide variety of protein-manipulating strategies of anti-CRISPR proteins for future protein drug design.
Collapse
|
32
|
Hwang S, Pan C, Garcia B, Davidson AR, Moraes TF, Maxwell KL. Structural and mechanistic insight into CRISPR-Cas9 inhibition by anti-CRISPR protein AcrIIC4 Hpa. J Mol Biol 2021; 434:167420. [PMID: 34954237 DOI: 10.1016/j.jmb.2021.167420] [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: 07/07/2021] [Revised: 11/16/2021] [Accepted: 12/18/2021] [Indexed: 11/25/2022]
Abstract
Phages, plasmids, and other mobile genetic elements express inhibitors of CRISPR-Cas immune systems, known as anti-CRISPR proteins, to protect themselves from targeted destruction. These anti-CRISPR proteins have been shown to function through very diverse mechanisms. In this work we investigate the activity of an anti-CRISPR isolated from a prophage in Haemophilus parainfluenzae that blocks CRISPR-Cas9 DNA cleavage activity. We determine the three-dimensional crystal structure of AcrIIC4Hpa and show that it binds to the Cas9 Recognition Domain. This binding does not prevent the Cas9-anti-CRISPR complex from interacting with target DNA but does inhibit DNA cleavage. AcrIIC4Hpa likely acts by blocking the conformational changes that allow the HNH and RuvC endonuclease domains to contact the DNA sites to be nicked.
Collapse
Affiliation(s)
| | | | - Bianca Garcia
- Department of Molecular Genetics. University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario, M5G 1M1, Canada
| | - Alan R Davidson
- Department of Biochemistry; Department of Molecular Genetics. University of Toronto, 661 University Avenue, Suite 1600, Toronto, Ontario, M5G 1M1, Canada
| | | | | |
Collapse
|
33
|
Wang X, Dong K, Kong D, Zhou Y, Yin J, Cai F, Wang M, Ye H. A far-red light-inducible CRISPR-Cas12a platform for remote-controlled genome editing and gene activation. SCIENCE ADVANCES 2021; 7:eabh2358. [PMID: 34890237 PMCID: PMC8664267 DOI: 10.1126/sciadv.abh2358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The CRISPR-Cas12a has been harnessed as a powerful tool for manipulating targeted gene expression. The possibility to manipulate the activity of CRISPR-Cas12a with a more precise spatiotemporal resolution and deep tissue permeability will enable targeted genome engineering and deepen our understanding of the gene functions underlying complex cellular behaviors. However, currently available inducible CRISPR-Cas12a systems are limited by diffusion, cytotoxicity, and poor tissue permeability. Here, we developed a far-red light (FRL)–inducible CRISPR-Cas12a (FICA) system that can robustly induce gene editing in mammalian cells, and an FRL-inducible CRISPR-dCas12a (FIdCA) system based on the protein-tagging system SUperNova (SunTag) that can be used for gene activation under light-emitting diode–based FRL. Moreover, we show that the FIdCA system can be deployed to activate target genes in mouse livers. These results demonstrate that these systems developed here provide robust and efficient platforms for programmable genome manipulation in a noninvasive and spatiotemporal fashion.
Collapse
Affiliation(s)
- Xinyi Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Kaili Dong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Deqiang Kong
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Jianli Yin
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Fengfeng Cai
- Department of Breast Surgery, Yangpu Hospital, School of Medicine, Tongji University, 450 Tengyue Road, Shanghai 200090, China
| | - Meiyan Wang
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author. (M.W.); (H.Y.)
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering Laboratory, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
- Corresponding author. (M.W.); (H.Y.)
| |
Collapse
|
34
|
Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
Collapse
Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
- Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Zhang Y, Marchisio MA. Type II anti-CRISPR proteins as a new tool for synthetic biology. RNA Biol 2021; 18:1085-1098. [PMID: 32991234 PMCID: PMC8244766 DOI: 10.1080/15476286.2020.1827803] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/03/2020] [Accepted: 09/20/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) system represents, in prokaryotes, an adaptive and inheritable immune response against invading DNA. The discovery of anti-CRISPR proteins (Acrs), which are inhibitors of CRISPR-Cas, mainly encoded by phages and prophages, showed a co-evolution history between prokaryotes and phages. In the past decade, the CRISPR-Cas systems together with the corresponding Acrs have been turned into a genetic-engineering tool. Among the six types of CRISPR-Cas characterized so far, type II CRISPR-Cas system is the most popular in biotechnology. Here, we discuss about the discovery, the reported inhibitory mechanisms, and the applications in both gene editing and gene transcriptional regulation of type II Acrs. Moreover, we provide insights into future potential research and feasible applications.
Collapse
Affiliation(s)
- Yadan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | | |
Collapse
|
38
|
Jia N, Patel DJ. Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins. Nat Rev Mol Cell Biol 2021; 22:563-579. [PMID: 34089013 DOI: 10.1038/s41580-021-00371-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
CRISPR loci and Cas proteins provide adaptive immunity in prokaryotes against invading bacteriophages and plasmids. In response, bacteriophages have evolved a broad spectrum of anti-CRISPR proteins (anti-CRISPRs) to counteract and overcome this immunity pathway. Numerous anti-CRISPRs have been identified to date, which suppress single-subunit Cas effectors (in CRISPR class 2, type II, V and VI systems) and multisubunit Cascade effectors (in CRISPR class 1, type I and III systems). Crystallography and cryo-electron microscopy structural studies of anti-CRISPRs bound to effector complexes, complemented by functional experiments in vitro and in vivo, have identified four major CRISPR-Cas suppression mechanisms: inhibition of CRISPR-Cas complex assembly, blocking of target binding, prevention of target cleavage, and degradation of cyclic oligonucleotide signalling molecules. In this Review, we discuss novel mechanistic insights into anti-CRISPR function that have emerged from X-ray crystallography and cryo-electron microscopy studies, and how these structures in combination with function studies provide valuable tools for the ever-growing CRISPR-Cas biotechnology toolbox, to be used for precise and robust genome editing and other applications.
Collapse
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.
| |
Collapse
|
39
|
Barkau CL, O'Reilly D, Eddington SB, Damha MJ, Gagnon KT. Small nucleic acids and the path to the clinic for anti-CRISPR. Biochem Pharmacol 2021; 189:114492. [PMID: 33647260 PMCID: PMC8725204 DOI: 10.1016/j.bcp.2021.114492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-based therapeutics have entered clinical trials but no methods to inhibit Cas enzymes have been demonstrated in a clinical setting. The ability to inhibit CRISPR-based gene editing or gene targeting drugs should be considered a critical step in establishing safety standards for many CRISPR-Cas therapeutics. Inhibitors can act as a failsafe or as an adjuvant to reduce off-target effects in patients. In this review we discuss the need for clinical inhibition of CRISPR-Cas systems and three existing inhibitor technologies: anti-CRISPR (Acr) proteins, small molecule Cas inhibitors, and small nucleic acid-based CRISPR inhibitors, CRISPR SNuBs. Due to their unique properties and the recent successes of other nucleic acid-based therapeutics, CRISPR SNuBs appear poised for clinical application in the near-term.
Collapse
Affiliation(s)
- Christopher L Barkau
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Daniel O'Reilly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Seth B Eddington
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA.
| |
Collapse
|
40
|
Liu H, Zhu Y, Lu Z, Huang Z. Structural basis of Staphylococcus aureus Cas9 inhibition by AcrIIA14. Nucleic Acids Res 2021; 49:6587-6595. [PMID: 34107040 PMCID: PMC8216286 DOI: 10.1093/nar/gkab487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 12/27/2022] Open
Abstract
Bacteriophages have evolved a range of anti-CRISPR proteins (Acrs) to escape the adaptive immune system of prokaryotes, therefore Acrs can be used as switches to regulate gene editing. Herein, we report the crystal structure of a quaternary complex of AcrIIA14 bound SauCas9-sgRNA-dsDNA at 2.22 Å resolution, revealing the molecular basis for AcrIIA14 recognition and inhibition. Our structural and biochemical data analysis suggest that AcrIIA14 binds to a non-conserved region of SauCas9 HNH domain that is distinctly different from AcrIIC1 and AcrIIC3, with no significant effect on sgRNA or dsDNA binding. Further, our structural data shows that the allostery of the HNH domain close to the substrate DNA is sterically prevented by AcrIIA14 binding. In addition, the binding of AcrIIA14 triggers the conformational allostery of the HNH domain and the L1 linker within the SauCas9, driving them to make new interactions with the target-guide heteroduplex, enhancing the inhibitory ability of AcrIIA14. Our research both expands the current understanding of anti-CRISPRs and provides additional culues for the rational use of the CRISPR-Cas system in genome editing and gene regulation.
Collapse
Affiliation(s)
- Hongnan Liu
- Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
| | - Yuwei Zhu
- Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
| | - Zebin Lu
- Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
| | - Zhiwei Huang
- Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, 150080 Harbin, China
| |
Collapse
|
41
|
Wörle E, Jakob L, Schmidbauer A, Zinner G, Grohmann D. Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions. Nucleic Acids Res 2021; 49:5278-5293. [PMID: 34009379 PMCID: PMC8136826 DOI: 10.1093/nar/gkab286] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/26/2022] Open
Abstract
The widespread and versatile prokaryotic CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR-Cas system was added to the Cas enzymes repertoire employed for gene editing purposes. Cas12a is a bilobal enzyme composed of the REC and Nuc lobe connected by the wedge, REC1 domain and bridge helix (BH). We generated BH variants and integrated biochemical and single-molecule FRET (smFRET) studies to elucidate the role of the BH for the enzymatic activity and conformational flexibility of Francisella novicida Cas12a. We demonstrate that the BH impacts the trimming activity and mismatch sensitivity of Cas12a resulting in Cas12a variants with improved cleavage accuracy. smFRET measurements reveal the hitherto unknown open and closed state of apo Cas12a. BH variants preferentially adopt the open state. Transition to the closed state of the Cas12a-crRNA complex is inefficient in BH variants but the semi-closed state of the ternary complex can be adopted even if the BH is deleted in its entirety. Taken together, these insights reveal that the BH is a structural element that influences the catalytic activity and impacts conformational transitions of FnCas12a.
Collapse
Affiliation(s)
- Elisabeth Wörle
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Gabriel Zinner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| |
Collapse
|
42
|
Yu L, Marchisio MA. Saccharomyces cerevisiae Synthetic Transcriptional Networks Harnessing dCas12a and Type V-A anti-CRISPR Proteins. ACS Synth Biol 2021; 10:870-883. [PMID: 33819020 DOI: 10.1021/acssynbio.1c00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Type V-A anti-CRISPR proteins (AcrVAs) represent the response from phages to the CRISPR-Cas12a prokaryotic immune system. CRISPR-Cas12a was repurposed, in high eukaryotes, to carry out gene editing and transcription regulation, the latter via a nuclease-dead Cas12a (dCas12a). Consequently, AcrVAs were adopted to regulate (d)Cas12a activity. However, the usage of both dCas12a-based transcription factors and AcrVAs in the yeast Saccharomyces cerevisiae has not been explored. In this work, we show that, in the baker's yeast, two dCas12a proteins (denAsCas12a and dLbCas12a) work both as activators (upon fusion to a strong activation domain) and repressors, whereas dMbCa12a is nonfunctional. The activation efficiency of dCas12a-ADs manifests a dependence on the number of crRNA binding sites, whereas it is not directly correlated to the amount of crRNA in the cells. Moreover, AcrVA1, AcrVA4, and AcrVA5 are able to inhibit dLbCa12a in yeast, and denAsCas12a is only inhibited by AcrVA1. However, AcrVA1 performs well at high concentration only. Coexpression of two or three AcrVAs does not enhance inhibition of dCas12a(-AD), suggesting a competition between different AcrVAs. Further, AcrVA4 significantly limits gene editing by LbCas12a. Overall, our results indicate that dCas12a:crRNA and AcrVA proteins are highly performant components in S. cerevisiae synthetic transcriptional networks.
Collapse
Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
| |
Collapse
|
43
|
Diversity of molecular mechanisms used by anti-CRISPR proteins: the tip of an iceberg? Biochem Soc Trans 2021; 48:507-516. [PMID: 32196554 DOI: 10.1042/bst20190638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/14/2022]
Abstract
Bacteriophages (phages) and their preys are engaged in an evolutionary arms race driving the co-adaptation of their attack and defense mechanisms. In this context, phages have evolved diverse anti-CRISPR proteins to evade the bacterial CRISPR-Cas immune system, and propagate. Anti-CRISPR proteins do not share much resemblance with each other and with proteins of known function, which raises intriguing questions particularly relating to their modes of action. In recent years, there have been many structure-function studies shedding light on different CRISPR-Cas inhibition strategies. As the anti-CRISPR field of research is rapidly growing, it is opportune to review the current knowledge on these proteins, with particular emphasis on the molecular strategies deployed to inactivate distinct steps of CRISPR-Cas immunity. Anti-CRISPR proteins can be orthosteric or allosteric inhibitors of CRISPR-Cas machineries, as well as enzymes that irreversibly modify CRISPR-Cas components. This repertoire of CRISPR-Cas inhibition mechanisms will likely expand in the future, providing fundamental knowledge on phage-bacteria interactions and offering great perspectives for the development of biotechnological tools to fine-tune CRISPR-Cas-based gene edition.
Collapse
|
44
|
Gabel C, Li Z, Zhang H, Chang L. Structural basis for inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14. Nucleic Acids Res 2021; 49:584-594. [PMID: 33332569 PMCID: PMC7797054 DOI: 10.1093/nar/gkaa1199] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas systems are adaptive immune systems in bacteria and archaea to defend against mobile genetic elements (MGEs) and have been repurposed as genome editing tools. Anti-CRISPR (Acr) proteins are produced by MGEs to counteract CRISPR-Cas systems and can be used to regulate genome editing by CRISPR techniques. Here, we report the cryo-EM structures of three type I-F Acr proteins, AcrIF4, AcrIF7 and AcrIF14, bound to the type I-F CRISPR-Cas surveillance complex (the Csy complex) from Pseudomonas aeruginosa. AcrIF4 binds to an unprecedented site on the C-terminal helical bundle of Cas8f subunit, precluding conformational changes required for activation of the Csy complex. AcrIF7 mimics the PAM duplex of target DNA and is bound to the N-terminal DNA vise of Cas8f. Two copies of AcrIF14 bind to the thumb domains of Cas7.4f and Cas7.6f, preventing hybridization between target DNA and the crRNA. Our results reveal structural detail of three AcrIF proteins, each binding to a different site on the Csy complex for inhibiting degradation of MGEs.
Collapse
Affiliation(s)
- Clinton Gabel
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Heng Zhang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| |
Collapse
|
45
|
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.
Collapse
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.
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
Abstract
Prokaryotes have developed numerous defense strategies to combat the constant threat posed by the diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts with an immunization phase, in which short pieces of the invader's genome, known as spacers, are captured and integrated into the CRISPR locus after infection. Next, during the targeting phase, spacers are transcribed into CRISPR RNAs (crRNAs) that guide CRISPR-associated (Cas) nucleases to destroy the invader's DNA or RNA. Here we describe the many different molecular mechanisms of CRISPR targeting and how they are interconnected with the immunization phase through a third phase of the CRISPR-Cas immune response: primed spacer acquisition. In this phase, Cas proteins direct the crRNA-guided acquisition of additional spacers to achieve a more rapid and robust immunization of the population.
Collapse
Affiliation(s)
- Philip M. Nussenzweig
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| |
Collapse
|
48
|
Conquering CRISPR: how phages overcome bacterial adaptive immunity. Curr Opin Biotechnol 2020; 68:30-36. [PMID: 33113496 DOI: 10.1016/j.copbio.2020.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022]
Abstract
The rise of antibiotic-resistant bacteria has led to renewed interest in the use of their natural enemies, phages, for the prevention and treatment of infections. However, phage therapy requires detailed knowledge of the interactions between these entities. Bacteria defend themselves against phage predation with a large repertoire of defences. Among these, CRISPR-Cas systems stand out due to their adaptive character, mechanistic complexity and diversity, and present a significant hurdle for phage infection. Here, we provide an overview of how phages can circumvent CRISPR-Cas defence, ranging from target sequence mutations and DNA modifications to anti-CRISPR proteins and nucleus-like protective structures. An in-depth understanding of these phage evasion strategies is crucial for the successful development of phage therapy applications.
Collapse
|
49
|
Lammens EM, Nikel PI, Lavigne R. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
Collapse
Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, DK, Denmark
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium.
| |
Collapse
|
50
|
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.
Collapse
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.
| |
Collapse
|