1
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Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature 2024:10.1038/s41586-024-07515-9. [PMID: 38740055 DOI: 10.1038/s41586-024-07515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.
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Affiliation(s)
- Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Institute of Science and Technology Austria (ISTA), Klosterneuberg, Austria.
| | - Delisa A Ramos
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Caiden Ingram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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2
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Huang J, Zhu K, Gao Y, Ye F, Li Z, Ge Y, Liu S, Yang J, Gao A. Molecular basis of bacterial DSR2 anti-phage defense and viral immune evasion. Nat Commun 2024; 15:3954. [PMID: 38729958 PMCID: PMC11087589 DOI: 10.1038/s41467-024-48291-4] [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: 09/23/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Defense-associated sirtuin 2 (DSR2) systems are widely distributed across prokaryotic genomes, providing robust protection against phage infection. DSR2 recognizes phage tail tube proteins and induces abortive infection by depleting intracellular NAD+, a process that is counteracted by another phage-encoded protein, DSR Anti Defense 1 (DSAD1). Here, we present cryo-EM structures of Bacillus subtilis DSR2 in its apo, Tube-bound, and DSAD1-bound states. DSR2 assembles into an elongated tetramer, with four NADase catalytic modules clustered in the center and the regulatory-sensing modules distributed at four distal corners. Interestingly, monomeric Tube protein, rather than its oligomeric states, docks at each corner of the DSR2 tetramer to form a 4:4 DSR2-Tube assembly, which is essential for DSR2 NADase activity. DSAD1 competes with Tube for binding to DSR2 by occupying an overlapping region, thereby inhibiting DSR2 immunity. Thus, our results provide important insights into the assembly, activation and inhibition of the DSR2 anti-phage defense system.
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Affiliation(s)
- Jiafeng Huang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Keli Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yina Gao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feng Ye
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhaolong Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yao Ge
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Songqing Liu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yang
- Department of Neurology, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing, 100049, China.
| | - Ang Gao
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
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3
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Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM. Molecular basis of Gabija anti-phage supramolecular assemblies. Nat Struct Mol Biol 2024:10.1038/s41594-024-01283-w. [PMID: 38627580 DOI: 10.1038/s41594-024-01283-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 03/22/2024] [Indexed: 05/15/2024]
Abstract
As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.
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Affiliation(s)
- Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Program of OSBP, The Ohio State University, Columbus, OH, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jiale Xie
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Program of OSBP, The Ohio State University, Columbus, OH, USA
| | - Jacelyn Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Ila Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Qingpeng Lin
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Wen Jun Xie
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Program of OSBP, The Ohio State University, Columbus, OH, USA.
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4
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Liu S, Liu H, Wang X, Shi L. The immune system of prokaryotes: potential applications and implications for gene editing. Biotechnol J 2024; 19:e2300352. [PMID: 38403433 DOI: 10.1002/biot.202300352] [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: 07/19/2023] [Revised: 11/30/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR-Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR-Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single-base editing is a precise editing tool based on CRISPR-Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti-phage defense, play an important role in complementing the CRISPR-Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.
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Affiliation(s)
- Siyang Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongling Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing, China
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5
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Pozhydaieva N, Wolfram-Schauerte M, Keuthen H, Höfer K. The enigmatic epitranscriptome of bacteriophages: putative RNA modifications in viral infections. Curr Opin Microbiol 2024; 77:102417. [PMID: 38217927 DOI: 10.1016/j.mib.2023.102417] [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: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/15/2024]
Abstract
RNA modifications play essential roles in modulating RNA function, stability, and fate across all kingdoms of life. The entirety of the RNA modifications within a cell is defined as the epitranscriptome. While eukaryotic RNA modifications are intensively studied, understanding bacterial RNA modifications remains limited, and knowledge about bacteriophage RNA modifications is almost nonexistent. In this review, we shed light on known mechanisms of bacterial RNA modifications and propose how this knowledge might be extended to bacteriophages. We build hypotheses on enzymes potentially responsible for regulating the epitranscriptome of bacteriophages and their host. This review highlights the exciting prospects of uncovering the unexplored field of bacteriophage epitranscriptomics and its potential role to shape bacteriophage-host interactions.
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Affiliation(s)
| | | | - Helene Keuthen
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
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6
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Antine SP, Johnson AG, Mooney SE, Leavitt A, Mayer ML, Yirmiya E, Amitai G, Sorek R, Kranzusch PJ. Structural basis of Gabija anti-phage defence and viral immune evasion. Nature 2024; 625:360-365. [PMID: 37992757 PMCID: PMC10781630 DOI: 10.1038/s41586-023-06855-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation1-5. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes1,6,7, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
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Affiliation(s)
- Sadie P Antine
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah E Mooney
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Megan L Mayer
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA, USA
| | - Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
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7
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Shen Z, Lin Q, Yang XY, Fosuah E, Fu TM. Assembly-mediated activation of the SIR2-HerA supramolecular complex for anti-phage defense. Mol Cell 2023; 83:4586-4599.e5. [PMID: 38096827 DOI: 10.1016/j.molcel.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/25/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023]
Abstract
SIR2-HerA, a bacterial two-protein anti-phage defense system, induces bacterial death by depleting NAD+ upon phage infection. Biochemical reconstitution of SIR2, HerA, and the SIR2-HerA complex reveals a dynamic assembly process. Unlike other ATPases, HerA can form various oligomers, ranging from dimers to nonamers. When assembled with SIR2, HerA forms a hexamer and converts SIR2 from a nuclease to an NAD+ hydrolase, representing an unexpected regulatory mechanism mediated by protein assembly. Furthermore, high concentrations of ATP can inhibit NAD+ hydrolysis by the SIR2-HerA complex. Cryo-EM structures of the SIR2-HerA complex reveal a giant supramolecular assembly up to 1 MDa, with SIR2 as a dodecamer and HerA as a hexamer, crucial for anti-phage defense. Unexpectedly, the HerA hexamer resembles a spiral staircase and exhibits helicase activities toward dual-forked DNA. Together, we reveal the supramolecular assembly of SIR2-HerA as a unique mechanism for switching enzymatic activities and bolstering anti-phage defense strategies.
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Affiliation(s)
- Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Qingpeng Lin
- Department of Biological Chemistry and Pharmacology, The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; Program of OSBP, The Ohio State University, Columbus, OH 43210, USA
| | - Elizabeth Fosuah
- Department of Biological Chemistry and Pharmacology, The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; Program of OSBP, The Ohio State University, Columbus, OH 43210, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA; Program of OSBP, The Ohio State University, Columbus, OH 43210, USA.
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8
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Tang D, Chen Y, Chen H, Jia T, Chen Q, Yu Y. Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense. Mol Cell 2023; 83:4600-4613.e6. [PMID: 38096825 DOI: 10.1016/j.molcel.2023.11.010] [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: 06/08/2023] [Revised: 09/14/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023]
Abstract
In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of a Sir2 NADase and a HerA helicase. Cryo-electron microscopy reveals that Sir2 and HerA assemble into a ∼1 MDa supramolecular octadecamer. Unexpectedly, this complex exhibits various enzymatic activities, including ATPase, NADase, helicase, and nuclease, which work together in a sophisticated manner to fulfill the antiphage function. Therefore, we name this defense system "Nezha" after a divine warrior in Chinese mythology who employs multiple weapons to defeat enemies. Our findings demonstrate that Nezha could sense phage infections, self-activate to arrest cell growth, eliminate phage genomes, and subsequently deactivate to allow for cell recovery. Collectively, Nezha represents a paradigm of sophisticated and multifaceted strategies bacteria use to defend against viral infections.
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Affiliation(s)
- Dongmei Tang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yijun Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tingting Jia
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yamei Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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9
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Oh H, Koo J, An SY, Hong SH, Suh JY, Bae E. Structural and functional investigation of GajB protein in Gabija anti-phage defense. Nucleic Acids Res 2023; 51:11941-11951. [PMID: 37897358 PMCID: PMC10681800 DOI: 10.1093/nar/gkad951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/13/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.
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Affiliation(s)
- Hyejin Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jasung Koo
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - So Young An
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Hyun Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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10
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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11
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Huiting E, Bondy-Denomy J. Defining the expanding mechanisms of phage-mediated activation of bacterial immunity. Curr Opin Microbiol 2023; 74:102325. [PMID: 37178480 PMCID: PMC11080646 DOI: 10.1016/j.mib.2023.102325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/07/2023] [Accepted: 04/08/2023] [Indexed: 05/15/2023]
Abstract
Due to recent discovery efforts, over 100 immune systems encoded by bacteria that antagonize bacteriophage (phage) replication have been uncovered. These systems employ direct and indirect mechanisms to detect phage infection and activate bacterial immunity. The most well-studied mechanisms are direct detection and activation by phage-associated molecular patterns (PhAMPs), such as phage DNA and RNA sequences, and expressed phage proteins that directly activate abortive infection systems. Phage effectors may also inhibit host processes and, therefore, indirectly activate immunity. Here, we discuss our current understanding of these protein PhAMPs and effectors expressed during various stages of the phage life cycle that activate immunity. Immune activators are predominantly identified from genetic approaches that isolate phage mutants that escape a bacterial immune system, coupled with biochemical validation. Although the mechanism of phage-mediated activation remains uncertain for most systems, it has become clear that each stage of the phage life cycle has the potential to induce a bacterial immune response.
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Affiliation(s)
- Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA, USA.
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12
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Mayo-Muñoz D, Pinilla-Redondo R, Birkholz N, Fineran PC. A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Rep 2023; 42:112672. [PMID: 37347666 DOI: 10.1016/j.celrep.2023.112672] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and plasmids. However, MGEs can also impose a fitness cost due to their often parasitic nature and differing evolutionary trajectories. In response, prokaryotes have evolved diverse immune mechanisms against MGEs. Recently, our understanding of the abundance and diversity of prokaryotic immune systems has greatly expanded. These defense systems can degrade the invading genetic material, inhibit genome replication, or trigger abortive infection, leading to population protection. In this review, we highlight these strategies, focusing on the most recent discoveries. The study of prokaryotic defenses not only sheds light on microbial evolution but also uncovers novel enzymatic activities with promising biotechnological applications.
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Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
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Wiryaman T, MacRae IJ. Structural studies put phage defense mystery on the RADAR. Cell 2023; 186:903-905. [PMID: 36868213 PMCID: PMC10846546 DOI: 10.1016/j.cell.2023.02.003] [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: 01/24/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/05/2023]
Abstract
Phage restriction by adenosine deaminase acting on RNA (RADAR) is a process by which bacteria may alter their own transcriptome to resist bacteriophage. In this issue of Cell, Duncan-Lowey and Tal et al. and Gao et al. both show RADAR proteins assemble into massive molecular complexes but present distinct views about how these assemblies obstruct phage.
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Affiliation(s)
- Timothy Wiryaman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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