1
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Bhatt A, Mishra BP, Gu W, Sorbello M, Xu H, Ve T, Kobe B. Structural characterization of TIR-domain signalosomes through a combination of structural biology approaches. IUCRJ 2024; 11:695-707. [PMID: 39190506 PMCID: PMC11364022 DOI: 10.1107/s2052252524007693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024]
Abstract
The TIR (Toll/interleukin-1 receptor) domain represents a vital structural element shared by proteins with roles in immunity signalling pathways across phyla (from humans and plants to bacteria). Decades of research have finally led to identifying the key features of the molecular basis of signalling by these domains, including the formation of open-ended (filamentous) assemblies (responsible for the signalling by cooperative assembly formation mechanism, SCAF) and enzymatic activities involving the cleavage of nucleotides. We present a historical perspective of the research that led to this understanding, highlighting the roles that different structural methods played in this process: X-ray crystallography (including serial crystallography), microED (micro-crystal electron diffraction), NMR (nuclear magnetic resonance) spectroscopy and cryo-EM (cryogenic electron microscopy) involving helical reconstruction and single-particle analysis. This perspective emphasizes the complementarity of different structural approaches.
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Affiliation(s)
- Akansha Bhatt
- Institute for GlycomicsGriffith UniversitySouthportQLD4222Australia
- School of Pharmacy and Medical SciencesGriffith UniversitySouthportQLD4222Australia
| | - Biswa P. Mishra
- Institute for GlycomicsGriffith UniversitySouthportQLD4222Australia
| | - Weixi Gu
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQLD4072Australia
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
- Australian Infectious Diseases Research CentreThe University of QueenslandBrisbaneQLD4072Australia
| | - Mitchell Sorbello
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQLD4072Australia
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
- Australian Infectious Diseases Research CentreThe University of QueenslandBrisbaneQLD4072Australia
| | - Hongyi Xu
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQLD4072Australia
- Department of Materials and Environmental ChemistryStockholm UniversityStockholmSweden
| | - Thomas Ve
- Institute for GlycomicsGriffith UniversitySouthportQLD4222Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQLD4072Australia
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLD4072Australia
- Australian Infectious Diseases Research CentreThe University of QueenslandBrisbaneQLD4072Australia
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2
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He L, Miguel-Romero L, Patkowski JB, Alqurainy N, Rocha EPC, Costa TRD, Fillol-Salom A, Penadés JR. Tail assembly interference is a common strategy in bacterial antiviral defenses. Nat Commun 2024; 15:7539. [PMID: 39215040 PMCID: PMC11364771 DOI: 10.1038/s41467-024-51915-4] [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: 02/02/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Many bacterial immune systems recognize phage structural components to activate antiviral responses, without inhibiting the function of the phage component. These systems can be encoded in specific chromosomal loci, known as defense islands, and in mobile genetic elements such as prophages and phage-inducible chromosomal islands (PICIs). Here, we identify a family of bacterial immune systems, named Tai (for 'tail assembly inhibition'), that is prevalent in PICIs, prophages and P4-like phage satellites. Tai systems protect their bacterial host population from other phages by blocking the tail assembly step, leading to the release of tailless phages incapable of infecting new hosts. To prevent autoimmunity, some Tai-positive phages have an associated counter-defense mechanism that is expressed during the phage lytic cycle and allows for tail formation. Interestingly, the Tai defense and counter-defense genes are organized in a non-contiguous operon, enabling their coordinated expression.
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Affiliation(s)
- Lingchen He
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Laura Miguel-Romero
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences & King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Alfred Fillol-Salom
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- School of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain.
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3
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Wang S, Kuang S, Song H, Sun E, Li M, Liu Y, Xia Z, Zhang X, Wang X, Han J, Rao VB, Zou T, Tan C, Tao P. The role of TIR domain-containing proteins in bacterial defense against phages. Nat Commun 2024; 15:7384. [PMID: 39191765 DOI: 10.1038/s41467-024-51738-3] [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: 05/02/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
Toll/interleukin-1 receptor (TIR) domain-containing proteins play a critical role in immune responses in diverse organisms, but their function in bacterial systems remains to be fully elucidated. This study, focusing on Escherichia coli, addresses how TIR domain-containing proteins contribute to bacterial immunity against phage attack. Through an exhaustive survey of all E. coli genomes available in the NCBI database and testing of 32 representatives of the 90% of the identified TIR domain-containing proteins, we found that a significant proportion (37.5%) exhibit antiphage activities. These defense systems recognize a variety of phage components, thus providing a sophisticated mechanism for pathogen detection and defense. This study not only highlights the robustness of TIR systems in bacterial immunity, but also draws an intriguing parallel to the diversity seen in mammalian Toll-like receptors (TLRs), enriching our understanding of innate immune mechanisms across life forms and underscoring the evolutionary significance of these defense strategies in prokaryotes.
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Affiliation(s)
- Shuangshuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Sirong Kuang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Haiguang Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Erchao Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mengling Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuepeng Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ziwei Xia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xueqi Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xialin Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiumin Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Tingting Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- Hubei Hongshan Lab, Wuhan, Hubei, 430070, China.
- Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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4
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Went SC, Picton DM, Morgan RD, Nelson A, Brady A, Mariano G, Dryden DTF, Smith DL, Wenner N, Hinton JCD, Blower TR. Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence. Nat Commun 2024; 15:7236. [PMID: 39174540 PMCID: PMC11341690 DOI: 10.1038/s41467-024-51629-7] [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: 12/20/2023] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.
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Affiliation(s)
- Sam C Went
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - David M Picton
- Department of Biosciences, Durham University, South Road, Durham, UK
| | | | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Aisling Brady
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Giuseppina Mariano
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - David T F Dryden
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham, UK.
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5
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Boyd CM, Seed KD. A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread. Nucleic Acids Res 2024:gkae675. [PMID: 39149900 DOI: 10.1093/nar/gkae675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024] Open
Abstract
ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery and virion components results in inhibition of ICP1's lifecycle. PLEs are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
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Affiliation(s)
- Caroline M Boyd
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
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6
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Kever L, Zhang Q, Hardy A, Westhoff P, Yu Y, Frunzke J. Resistance against aminoglycoside antibiotics via drug or target modification enables community-wide antiphage defense. MICROLIFE 2024; 5:uqae015. [PMID: 39205678 PMCID: PMC11350373 DOI: 10.1093/femsml/uqae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/02/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
The ongoing arms race between bacteria and phages has forced bacteria to evolve a sophisticated set of antiphage defense mechanisms that constitute the bacterial immune system. In our previous study, we highlighted the antiphage properties of aminoglycoside antibiotics, which are naturally secreted by Streptomyces. Successful inhibition of phage infection was achieved by addition of pure compounds and supernatants from a natural producer strain emphasizing the potential for community-wide antiphage defense. However, given the dual functionality of these compounds, neighboring bacterial cells require resistance to the antibacterial activity of aminoglycosides to benefit from the protection they confer against phages. In this study, we tested a variety of different aminoglycoside resistance mechanisms acting via drug or target (16S rRNA) modification and demonstrated that they do not interfere with the antiphage properties of the molecules. Furthermore, we confirmed the antiphage impact of aminoglycosides in a community context by coculturing phage-susceptible, apramycin-resistant Streptomyces venezuelae with the apramycin-producing strain Streptoalloteichus tenebrarius. Given the prevalence of aminoglycoside resistance among natural bacterial isolates, this study highlights the ecological relevance of chemical defense via aminoglycosides at the community level.
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Affiliation(s)
- Larissa Kever
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Qian Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Aël Hardy
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Philipp Westhoff
- Institute of Plant Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Yi Yu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Julia Frunzke
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich 52425, Germany
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7
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van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe 2024; 32:1427-1443.e8. [PMID: 39094584 DOI: 10.1016/j.chom.2024.07.007] [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: 12/04/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Prokaryotes have evolved a multitude of defense systems to protect against phage predation. Some of these resemble eukaryotic genes involved in antiviral responses. Here, we set out to systematically project the current knowledge of eukaryotic-like antiviral defense systems onto prokaryotic genomes, using Pseudomonas aeruginosa as a model organism. Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates. We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling. Collectively, these defense systems support the concept of deep evolutionary links and shared antiviral mechanisms between prokaryotes and eukaryotes.
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Affiliation(s)
- Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Jelger Q Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Ilinka Stanciu
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Jasper Q Geissler
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | | | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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8
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Maestri A, Pons BJ, Pursey E, Chong CE, Gandon S, Custodio R, Olina A, Agapov A, Chisnall MAW, Grasso A, Paterson S, Szczelkun MD, Baker KS, van Houte S, Chevallereau A, Westra ER. The bacterial defense system MADS interacts with CRISPR-Cas to limit phage infection and escape. Cell Host Microbe 2024; 32:1412-1426.e11. [PMID: 39094583 DOI: 10.1016/j.chom.2024.07.005] [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: 08/09/2023] [Revised: 04/23/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024]
Abstract
The constant arms race between bacteria and their parasites has resulted in a large diversity of bacterial defenses, with many bacteria carrying multiple systems. Here, we report the discovery of a phylogenetically widespread defense system, coined methylation-associated defense system (MADS), which is distributed across gram-positive and gram-negative bacteria. MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages. While phages can acquire epigenetic-mediated resistance against MADS, co-existence of MADS and a CRISPR-Cas system limits escape emergence. MADS comprises eight genes with predicted nuclease, ATPase, kinase, and methyltransferase domains, most of which are essential for either self/non-self discrimination, DNA restriction, or both. The complex genetic architecture of MADS and MADS-like systems, relative to other prokaryotic defenses, points toward highly elaborate mechanisms of sensing infections, defense activation, and/or interference.
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Affiliation(s)
- Alice Maestri
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Benoit J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Charlotte E Chong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; Department of Genetics, University of Cambridge, Downing Place, Cambridge CB2 3EH, UK
| | - Sylvain Gandon
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Montpellier 34293, France
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anna Olina
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Aleksei Agapov
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Matthew A W Chisnall
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anita Grasso
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Kate S Baker
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; Department of Genetics, University of Cambridge, Downing Place, Cambridge CB2 3EH, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anne Chevallereau
- Université Paris Cité, CNRS, INSERM, Institut Cochin, Paris 75014, France.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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9
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Zhang H, Li Y, Li L, Chen L, Zhu C, Sun L, Dong P, Jing D, Yang J, Fu L, Xiao F, Xia N, Li S, Zheng Q, Wu Y. Structural insights into activation mechanisms on NADase of the bacterial DSR2 anti-phage defense system. SCIENCE ADVANCES 2024; 10:eadn5691. [PMID: 39083599 PMCID: PMC11290490 DOI: 10.1126/sciadv.adn5691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD+) of infected cells, which can be activated by tail tube protein (TTP) and inhibited by DSR anti-defense 1 (DSAD1) of diverse phages. However, the regulating mechanism remains elusive. Here, we determined the cryo-electron microscopy structure of apo DSR2, as well as the respective complex structures with TTP and DSAD1. Structural analyses and biochemical studies reveal that DSR2 forms a tetramer with a SIR2 central core and two distinct conformations. Monomeric TTP preferentially binds to the closed conformation of DSR2, inducing conformational distortions on SIR2 tetramer assembly to activate its NADase activity. DSAD1 combines with the open conformation of DSR2, directly or allosterically inhibiting TTP activation on DSR2 NAD+ hydrolysis. Our findings decipher the detailed molecule mechanisms for DSR2 NADase activity regulation and lay a foundation for in-depth understanding of the DSR2 anti-phage defense system.
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Affiliation(s)
- Hong Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Yu Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Lanlan Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Lifei Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Chunhua Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Panpan Dong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Dingding Jing
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Jinbo Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Lei Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Fangnan Xiao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Qingbing Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
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10
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Kwiatkowski M, Zhang J, Zhou W, Gehring C, Wong A. Cyclic nucleotides - the rise of a family. TRENDS IN PLANT SCIENCE 2024; 29:915-924. [PMID: 38480090 DOI: 10.1016/j.tplants.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 08/10/2024]
Abstract
Cyclic nucleotides 3',5'-cAMP and 3',5'-cGMP are now established signaling components of the plant cell while their 2',3' positional isomers are increasingly recognized as such. 3',5'-cAMP/cGMP is generated by adenylate cyclases (ACs) or guanylate cyclases (GCs) from ATP or GTP, respectively, whereas 2',3'-cAMP/cGMP is produced through the hydrolysis of double-stranded DNA or RNA by synthetases. Recent evidence suggests that the cyclic nucleotide generating and inactivating enzymes moonlight in proteins with diverse domain architecture operating as molecular tuners to enable dynamic and compartmentalized regulation of cellular signals. Further characterization of such moonlighting enzymes and extending the studies to noncanonical cyclic nucleotides promises new insights into the complex regulatory networks that underlie plant development and responses, thus offering exciting opportunities for crop improvement.
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Affiliation(s)
- Mateusz Kwiatkowski
- Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Toruń, Lwowska St. 1, 87-100 Toruń, Poland
| | - Jinwen Zhang
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Wei Zhou
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China
| | - Chris Gehring
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia 06121, Italy.
| | - Aloysius Wong
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou 325060, Zhejiang Province, China.
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11
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Roberts CG, Fishman CB, Banh DV, Marraffini LA. A bacterial TIR-based immune system senses viral capsids to initiate defense. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605636. [PMID: 39131286 PMCID: PMC11312562 DOI: 10.1101/2024.07.29.605636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Toll/interleukin-1 receptor (TIR) domains are present in immune systems that protect prokaryotes from viral (phage) attack. In response to infection, TIRs can produce a cyclic adenosine diphosphate-ribose (ADPR) signaling molecule, which activates an effector that depletes the host of the essential metabolite NAD+ to limit phage propagation. How bacterial TIRs recognize phage infection is not known. Here we describe the sensing mechanism for the staphylococcal Thoeris defense system, which consists of two TIR domain sensors, ThsB1 and ThsB2, and the effector ThsA. We show that the major capsid protein of phage Φ80α forms a complex with ThsB1 and ThsB2, which is sufficient for the synthesis of 1"-3' glycocyclic ADPR (gcADPR) and subsequent activation of NAD+ cleavage by ThsA. Consistent with this, phages that escape Thoeris immunity harbor mutations in the capsid that prevent complex formation. We show that capsid proteins from staphylococcal Siphoviridae belonging to the capsid serogroup B, but not A, are recognized by ThsB1/B2, a result that suggests that capsid recognition by Sau-Thoeris and other anti-phage defense systems may be an important evolutionary force behind the structural diversity of prokaryotic viruses. More broadly, since mammalian toll-like receptors harboring TIR domains can also recognize viral structural components to produce an inflammatory response against infection, our findings reveal a conserved mechanism for the activation of innate antiviral defense pathways.
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Affiliation(s)
- Cameron G. Roberts
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Chloe B. Fishman
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | | | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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12
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Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S. Nucleic acid-induced NADase activation of a short Sir2-associated prokaryotic Argonaute system. Cell Rep 2024; 43:114391. [PMID: 38923459 DOI: 10.1016/j.celrep.2024.114391] [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: 09/06/2023] [Revised: 04/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Inhibition of nucleic acid targets is mediated by Argonaute (Ago) proteins guided by RNA or DNA. Although the mechanisms underpinning the functions of eukaryotic and "long" prokaryotic Ago proteins (pAgos) are well understood, those for short pAgos remain enigmatic. Here, we determine two cryoelectron microscopy structures of short pAgos in association with the NADase-domain-containing protein Sir2-APAZ from Geobacter sulfurreducens (GsSir2/Ago): the guide RNA-target DNA-loaded GsSir2/Ago quaternary complex (2.58 Å) and the dimer of the quaternary complex (2.93Å). These structures show that the nucleic acid binding causes profound conformational changes that result in disorder or partial dissociation of the Sir2 domain, suggesting that it adopts a NADase-active conformation. Subsequently, two RNA-/DNA-loaded GsSir2/Ago complexes form a dimer through their MID domains, further enhancing NADase activity through synergistic effects. The findings provide a structural basis for short-pAgo-mediated defense against invading nucleic acids.
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Affiliation(s)
- Dapeng Sun
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Zhixia Mu
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Kang Wu
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Lei Hua
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Medical School, Yan'an University, Yan'an, Shaanxi 716000, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
| | - Yumei Wang
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
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13
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Kronborg K, Zhang YE. Unresolved mystery of cyclic nucleotide second messengers, periplasmic acid phosphatases and bacterial natural competence. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:235-241. [PMID: 39040525 PMCID: PMC11261661 DOI: 10.15698/mic2024.07.828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024]
Abstract
We recently characterized the competitive inhibition of cyclic AMP (cAMP) on three periplasmic acid phosphatases, AphAHi, NadNHi, and eP4 (HelHi), in Haemophilus influenzae Rd KW20. This inhibitory effect is vital for orchestrating the nutritional growth and competence development in KW20. Initially discovered in Escherichia coli, the function of AphA remains however obscure. This study investigates the regulation of E. coli aphA expression under nutrient starvation conditions. Using transcriptional reporters with truncated aphA promoter sequences, we found that starvations of carbon and phosphate, but not amino acid, stimulated aphA expression through distinct promoter regions. Deletions of crp or cyaA abolished aphA expression, confirming their crucial roles. Conversely, CytR deletion increased aphA expression, suggesting CytR's role as a repressor of aphA expression. Additionally, we extended the study of three other second messengers, i.e., cyclic GMP, cyclic UMP, and cyclic CMP, each sharing structural similarities with cAMP. Notably, cGMP competitively inhibits AphAHi's acid phosphatase activity akin to cAMP. In contrast, both cUMP and cCMP stimulate AphAHi's phosphatase activity in a concentration dependent manner. Collectively, these data imply a complicated connection between nucleotide metabolism, AphA, cyclic purine and pyrimidine nucleotides in bacterial nutrient uptake and natural competence.
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Affiliation(s)
- Kristina Kronborg
- Department of Biology, University of CopenhagenCopenhagen, DK2200Denmark
| | - Yong Everett Zhang
- Department of Biology, University of CopenhagenCopenhagen, DK2200Denmark
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14
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Richmond-Buccola D, Hobbs SJ, Garcia JM, Toyoda H, Gao J, Shao S, Lee ASY, Kranzusch PJ. A large-scale type I CBASS antiphage screen identifies the phage prohead protease as a key determinant of immune activation and evasion. Cell Host Microbe 2024; 32:1074-1088.e5. [PMID: 38917809 PMCID: PMC11239291 DOI: 10.1016/j.chom.2024.05.021] [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: 05/31/2023] [Revised: 02/27/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Cyclic oligonucleotide-based signaling system (CBASS) is an antiviral system that protects bacteria from phage infection and is evolutionarily related to human cGAS-STING immunity. cGAS-STING signaling is initiated by the recognition of viral DNA, but the molecular cues activating CBASS are incompletely understood. Using a screen of 975 type I CBASS operon-phage challenges, we show that operons with distinct cGAS/DncV-like nucleotidyltransferases (CD-NTases) and CD-NTase-associated protein (Cap) effectors exhibit marked patterns of phage restriction. We find that some type I CD-NTase enzymes require a C-terminal AGS-C immunoglobulin (Ig)-like fold domain for defense against select phages. Escaper phages evade CBASS via protein-coding mutations in virion assembly proteins, and acquired resistance is largely operon specific. We demonstrate that the phage Bas13 prohead protease interacts with the CD-NTase EcCdnD12 and can induce CBASS-dependent growth arrest in cells. Our results define phage virion assembly as a determinant of type I CBASS immune evasion and support viral protein recognition as a putative mechanism of cGAS-like enzyme activation.
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Affiliation(s)
- Desmond Richmond-Buccola
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Samuel J Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jasmine M Garcia
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hunter Toyoda
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Gao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy S Y Lee
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana, Farber Cancer Institute, Boston, MA 02115, USA.
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15
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Hou MH, Chen CJ, Yang CS, Wang YC, Chen Y. Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system. Nat Commun 2024; 15:5634. [PMID: 38965224 PMCID: PMC11224242 DOI: 10.1038/s41467-024-49861-2] [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: 07/09/2023] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
3',5'-cyclic uridine monophosphate (cUMP) and 3',5'-cyclic cytidine monophosphate (cCMP) have been established as bacterial second messengers in the phage defense system, named pyrimidine cyclase system for anti-phage resistance (Pycsar). This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein. However, the molecular mechanism underlying cyclic pyrimidine synthesis and recognition remains unclear. Herein, we determine the crystal structures of a uridylate cyclase and a cytidylate cyclase, revealing the conserved residues for cUMP and cCMP production, respectively. In addition, a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections. Furthermore, structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation. Overall, our results contribute to the understanding of cyclic pyrimidine-mediated bacterial defense.
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Affiliation(s)
- Mei-Hui Hou
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, 40447, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Chia-Shin Yang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yu-Chuan Wang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan.
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16
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Hör J, Wolf SG, Sorek R. Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly. Nature 2024; 631:850-856. [PMID: 39020165 DOI: 10.1038/s41586-024-07616-5] [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: 08/24/2023] [Accepted: 05/28/2024] [Indexed: 07/19/2024]
Abstract
Several immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defence1-5. Here we studied an antiphage defence system in bacteria, comprising a ubiquitin-like protein, ubiquitin-conjugating enzymes E1 and E2, and a deubiquitinase. We show that during phage infection, this system specifically conjugates the ubiquitin-like protein to the phage central tail fibre, a protein at the tip of the tail that is essential for tail assembly as well as for recognition of the target host receptor. Following infection, cells encoding this defence system release a mixture of partially assembled, tailless phage particles and fully assembled phages in which the central tail fibre is obstructed by the covalently attached ubiquitin-like protein. These phages show severely impaired infectivity, explaining how the defence system protects the bacterial population from the spread of phage infection. Our findings demonstrate that conjugation of ubiquitin-like proteins is an antiviral strategy conserved across the tree of life.
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Affiliation(s)
- Jens Hör
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Sharon G Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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17
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Ledvina HE, Whiteley AT. Conservation and similarity of bacterial and eukaryotic innate immunity. Nat Rev Microbiol 2024; 22:420-434. [PMID: 38418927 DOI: 10.1038/s41579-024-01017-1] [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: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Pathogens are ubiquitous and a constant threat to their hosts, which has led to the evolution of sophisticated immune systems in bacteria, archaea and eukaryotes. Bacterial immune systems encode an astoundingly large array of antiviral (antiphage) systems, and recent investigations have identified unexpected similarities between the immune systems of bacteria and animals. In this Review, we discuss advances in our understanding of the bacterial innate immune system and highlight the components, strategies and pathogen restriction mechanisms conserved between bacteria and eukaryotes. We summarize evidence for the hypothesis that components of the human immune system originated in bacteria, where they first evolved to defend against phages. Further, we discuss shared mechanisms that pathogens use to overcome host immune pathways and unexpected similarities between bacterial immune systems and interbacterial antagonism. Understanding the shared evolutionary path of immune components across domains of life and the successful strategies that organisms have arrived at to restrict their pathogens will enable future development of therapeutics that activate the human immune system for the precise treatment of disease.
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Affiliation(s)
- Hannah E Ledvina
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Aaron T Whiteley
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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18
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Shi Y, Masic V, Mosaiab T, Rajaratman P, Hartley-Tassell L, Sorbello M, Goulart CC, Vasquez E, Mishra BP, Holt S, Gu W, Kobe B, Ve T. Structural characterization of macro domain-containing Thoeris antiphage defense systems. SCIENCE ADVANCES 2024; 10:eadn3310. [PMID: 38924412 PMCID: PMC11204291 DOI: 10.1126/sciadv.adn3310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD+) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Premraj Rajaratman
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Mitchell Sorbello
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cassia C. Goulart
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Biswa P. Mishra
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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19
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Watanabe S, Nsofor CA, Thitiananpakorn K, Tan XE, Aiba Y, Takenouchi R, Kiga K, Sasahara T, Miyanaga K, Veeranarayanan S, Shimamori Y, Lian AYS, Nguyen TM, Nguyen HM, Alessa O, Kumwenda GP, Jayathilake S, Revilleza JEC, Baranwal P, Nishikawa Y, Li FY, Kawaguchi T, Sankaranarayanan S, Arbaah M, Zhang Y, Maniruzzaman, Liu Y, Sarah H, Li J, Sugano T, Ho TMD, Batbold A, Nayanjin T, Cui L. Metabolic remodeling by RNA polymerase gene mutations is associated with reduced β-lactam susceptibility in oxacillin-susceptible MRSA. mBio 2024; 15:e0033924. [PMID: 38988221 PMCID: PMC11237739 DOI: 10.1128/mbio.00339-24] [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: 02/01/2024] [Accepted: 03/27/2024] [Indexed: 07/12/2024] Open
Abstract
The emergence of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) has imposed further challenges to the clinical management of MRSA infections. When exposed to β-lactam antibiotics, these strains can easily acquire reduced β-lactam susceptibility through chromosomal mutations, including those in RNA polymerase (RNAP) genes such as rpoBC, which may then lead to treatment failure. Despite the increasing prevalence of such strains and the apparent challenges they pose for diagnosis and treatment, there is limited information available on the actual mechanisms underlying such chromosomal mutation-related transitions to reduced β-lactam susceptibility, as it does not directly associate with the expression of mecA. This study investigated the cellular physiology and metabolism of six missense mutants with reduced oxacillin susceptibility, each carrying respective mutations on RpoBH929P, RpoBQ645H, RpoCG950R, RpoCG498D, RpiAA64E, and FruBA211E, using capillary electrophoresis-mass spectrometry-based metabolomics analysis. Our results showed that rpoBC mutations caused RNAP transcription dysfunction, leading to an intracellular accumulation of ribonucleotides. These mutations also led to the accumulation of UDP-Glc/Gal and UDP-GlcNAc, which are precursors of UTP-associated peptidoglycan and wall teichoic acid. Excessive amounts of building blocks then contributed to the cell wall thickening of mutant strains, as observed in transmission electron microscopy, and ultimately resulted in decreased susceptibility to β-lactam in OS-MRSA. IMPORTANCE The emergence of oxacillin-susceptible methicillin-resistant Staphylococcus aureus (OS-MRSA) strains has created new challenges for treating MRSA infections. These strains can become resistant to β-lactam antibiotics through chromosomal mutations, including those in the RNA polymerase (RNAP) genes such as rpoBC, leading to treatment failure. This study investigated the mechanisms underlying reduced β-lactam susceptibility in four rpoBC mutants of OS-MRSA. The results showed that rpoBC mutations caused RNAP transcription dysfunction, leading to an intracellular accumulation of ribonucleotides and precursors of peptidoglycan as well as wall teichoic acid. This, in turn, caused thickening of the cell wall and ultimately resulted in decreased susceptibility to β-lactam in OS-MRSA. These findings provide insights into the mechanisms of antibiotic resistance in OS-MRSA and highlight the importance of continued research in developing effective treatments to combat antibiotic resistance.
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Affiliation(s)
- Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Chijioke A Nsofor
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
- Department of Biotechnology, School of Biological Sciences, Federal University of Technology Owerri Nigeria, Owerri, Nigeria
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Remi Takenouchi
- School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Kazuhiko Miyanaga
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Srivani Veeranarayanan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yuzuki Shimamori
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Adeline Yeo Syin Lian
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Thuy Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Ola Alessa
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | | | - Sarangi Jayathilake
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | | | - Priyanka Baranwal
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yutaro Nishikawa
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Feng-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Sowmiya Sankaranarayanan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Mahmoud Arbaah
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yuancheng Zhang
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Maniruzzaman
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Yi Liu
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Hossain Sarah
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Junjie Li
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Takashi Sugano
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Thi My Duyen Ho
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Anujin Batbold
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Tergel Nayanjin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
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20
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Carabias A, Camara-Wilpert S, Mestre MR, Lopéz-Méndez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SHC, Nielsen ML, Pinilla-Redondo R, Montoya G. Retron-Eco1 assembles NAD +-hydrolyzing filaments that provide immunity against bacteriophages. Mol Cell 2024; 84:2185-2202.e12. [PMID: 38788717 DOI: 10.1016/j.molcel.2024.05.001] [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: 09/26/2023] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD+ during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD+ hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity.
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Affiliation(s)
- Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Sarah Camara-Wilpert
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mario Rodríguez Mestre
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Blanca Lopéz-Méndez
- Protein Purification and Characterization Facility, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruiliang Zhao
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Tillmann Pape
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders Fuglsang
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sean Hoi-Ching Luk
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rafael Pinilla-Redondo
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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21
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Olszak T, Augustyniak D, García-Romero I, Markwitz P, Gula G, Molinaro A, Valvano MA, Drulis-Kawa Z. Phage treatment of Pseudomonas aeruginosa yields a phage-resistant population with different susceptibility to innate immune responses and mild effects on metabolic profiles. Microbiol Res 2024; 282:127609. [PMID: 38428337 DOI: 10.1016/j.micres.2024.127609] [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: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
In this study, we have investigated innate immune activation capacity and metabolic features of a population of P. aeruginosa PAO1 phage-resistant mutants with diverse genetic modification (large genomic deletions and point mutations) arising after exposure to phages targetting lipopolysaccharide (LPS) or Type-4 pili (T4P). Deletions led to the loss of genes involved in LPS synthesis, cell envelope permeability, efflux systems, biofilm production, oxidative stress tolerance, and DNA repair. Loss of LPS O antigen resulted in bacterial sensitivity to serum complement and stimulation of inflammatory cascades but did not cause increased phagocytosis, while T4P phage-resistant mutants were more effectively phagocytized than LPS-defective mutants. Changes in the utilization of different carbon, nitrogen, sulphur, and phosphorus sources were identified, especially in mutants where the two phage DNA persisted in the bacterial population (pseudolysogeny). However, the metabolic changes did not directly correlate with single-gene mutations or the large gene deletions, suggesting they reflect adaptive changes to the gene modifications that arise during the selection of resistant mutants. In contrast, phage-resistant mutants were susceptible to humoral innate immune responses, suggesting that phage resistance may be a beneficial outcome of phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Daria Augustyniak
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Inmaculada García-Romero
- Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Pawel Markwitz
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Naples, Italy
| | - Miguel A Valvano
- Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland.
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22
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Boyd CM, Seed KD. A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590561. [PMID: 38712175 PMCID: PMC11071384 DOI: 10.1101/2024.04.22.590561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery, and virion components results in inhibition of ICP1's lifecycle. PLEs' are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
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Affiliation(s)
- Caroline M. Boyd
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Kimberley D. Seed
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
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23
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Garb J, Amitai G, Lu A, Ofir G, Brandis A, Mehlman T, Kranzusch PJ, Sorek R. The SARM1 TIR domain produces glycocyclic ADPR molecules as minor products. PLoS One 2024; 19:e0302251. [PMID: 38635746 PMCID: PMC11025887 DOI: 10.1371/journal.pone.0302251] [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: 10/04/2023] [Accepted: 03/31/2024] [Indexed: 04/20/2024] Open
Abstract
Sterile alpha and TIR motif-containing 1 (SARM1) is a protein involved in programmed death of injured axons. Following axon injury or a drug-induced insult, the TIR domain of SARM1 degrades the essential molecule nicotinamide adenine dinucleotide (NAD+), leading to a form of axonal death called Wallerian degeneration. Degradation of NAD+ by SARM1 is essential for the Wallerian degeneration process, but accumulating evidence suggest that other activities of SARM1, beyond the mere degradation of NAD+, may be necessary for programmed axonal death. In this study we show that the TIR domains of both human and fruit fly SARM1 produce 1''-2' and 1''-3' glycocyclic ADP-ribose (gcADPR) molecules as minor products. As previously reported, we observed that SARM1 TIR domains mostly convert NAD+ to ADPR (for human SARM1) or cADPR (in the case of SARM1 from Drosophila melanogaster). However, we now show that human and Drosophila SARM1 additionally convert ~0.1-0.5% of NAD+ into gcADPR molecules. We find that SARM1 TIR domains produce gcADPR molecules both when purified in vitro and when expressed in bacterial cells. Given that gcADPR is a second messenger involved in programmed cell death in bacteria and likely in plants, we propose that gcADPR may play a role in SARM1-induced programmed axonal death in animals.
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Affiliation(s)
- Jeremy Garb
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Allen Lu
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tevie Mehlman
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, United States of America
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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24
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Grüschow S, McQuarrie S, Ackermann K, McMahon S, Bode B, Gloster T, White M. CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23. Nucleic Acids Res 2024; 52:2761-2775. [PMID: 38471818 PMCID: PMC11014256 DOI: 10.1093/nar/gkae167] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae. Csx23 provides immunity against plasmids and phage when expressed in Escherichia coli along with its cognate type III CRISPR system. The Csx23 protein localises in the membrane using an N-terminal transmembrane α-helical domain and has a cytoplasmic C-terminal domain that binds cyclic tetra-adenylate (cA4), activating its defence function. Structural studies reveal a tetrameric structure with a novel fold that binds cA4 specifically. Using pulse EPR, we demonstrate that cA4 binding to the cytoplasmic domain of Csx23 results in a major perturbation of the transmembrane domain, consistent with the opening of a pore and/or disruption of membrane integrity. This work reveals a new class of cyclic nucleotide binding protein and provides key mechanistic detail on a membrane-associated CRISPR effector.
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Affiliation(s)
- Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Stephen McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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25
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Wenzl SJ, de Oliveira Mann CC. How enzyme-centered approaches are advancing research on cyclic oligo-nucleotides. FEBS Lett 2024; 598:839-863. [PMID: 38453162 DOI: 10.1002/1873-3468.14838] [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: 12/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
Cyclic nucleotides are the most diversified category of second messengers and are found in all organisms modulating diverse pathways. While cAMP and cGMP have been studied over 50 years, cyclic di-nucleotide signaling in eukaryotes emerged only recently with the anti-viral molecule 2´3´cGAMP. Recent breakthrough discoveries have revealed not only the astonishing chemical diversity of cyclic nucleotides but also surprisingly deep-rooted evolutionary origins of cyclic oligo-nucleotide signaling pathways and structural conservation of the proteins involved in their synthesis and signaling. Here we discuss how enzyme-centered approaches have paved the way for the identification of several cyclic nucleotide signals, focusing on the advantages and challenges associated with deciphering the activation mechanisms of such enzymes.
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Affiliation(s)
- Simon J Wenzl
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Carina C de Oliveira Mann
- Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany
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26
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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.
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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.
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27
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Zhang JT, Wei XY, Cui N, Tian R, Jia N. Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system. Nat Chem Biol 2024; 20:503-511. [PMID: 37932528 DOI: 10.1038/s41589-023-01479-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Argonaute proteins (Agos), which use small RNAs or DNAs as guides to recognize complementary nucleic acid targets, mediate RNA silencing in eukaryotes. In prokaryotes, Agos are involved in immunity: the short prokaryotic Ago/TIR-APAZ (SPARTA) immune system triggers cell death by degrading NAD+ in response to invading plasmids, but its molecular mechanisms remain unknown. Here we used cryo-electron microscopy to determine the structures of inactive monomeric and active tetrameric Crenotalea thermophila SPARTA complexes, revealing mechanisms underlying SPARTA assembly, RNA-guided recognition of target single-stranded DNA (ssDNA) and subsequent SPARTA tetramerization, as well as tetramerization-dependent NADase activation. The small RNA guides Ago to recognize its ssDNA target, inducing SPARTA tetramerization via both Ago- and TIR-mediated interactions and resulting in a two-stranded, parallel, head-to-tail TIR rearrangement primed for NAD+ hydrolysis. Our findings thus identify the molecular basis for target ssDNA-mediated SPARTA activation, which will facilitate the development of SPARTA-based biotechnological tools.
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Affiliation(s)
- Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xin-Yang Wei
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Ning Cui
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
- Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China.
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28
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Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y. Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system. Nat Chem Biol 2024; 20:512-520. [PMID: 37932527 DOI: 10.1038/s41589-023-01478-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Short prokaryotic Ago accounts for most prokaryotic Argonaute proteins (pAgos) and is involved in defending bacteria against invading nucleic acids. Short pAgo associated with TIR-APAZ (SPARTA) has been shown to oligomerize and deplete NAD+ upon guide-mediated target DNA recognition. However, the molecular basis of SPARTA inhibition and activation remains unknown. In this study, we determined the cryogenic electron microscopy structures of Crenotalea thermophila SPARTA in its inhibited, transient and activated states. The SPARTA monomer is auto-inhibited by its acidic tail, which occupies the guide-target binding channel. Guide-mediated target binding expels this acidic tail and triggers substantial conformational changes to expose the Ago-Ago dimerization interface. As a result, SPARTA assembles into an active tetramer, where the four TIR domains are rearranged and packed to form NADase active sites. Together with biochemical evidence, our results provide a panoramic vision explaining SPARTA auto-inhibition and activation and expand understanding of pAgo-mediated bacterial defense systems.
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Affiliation(s)
- Lijie Guo
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Pingping Huang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhaoxing Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Young-Cheul Shin
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Purui Yan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Meirong Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China.
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29
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Agapov A, Baker KS, Bedekar P, Bhatia RP, Blower TR, Brockhurst MA, Brown C, Chong CE, Fothergill JL, Graham S, Hall JP, Maestri A, McQuarrie S, Olina A, Pagliara S, Recker M, Richmond A, Shaw SJ, Szczelkun MD, Taylor TB, van Houte S, Went SC, Westra ER, White MF, Wright R. Multi-layered genome defences in bacteria. Curr Opin Microbiol 2024; 78:102436. [PMID: 38368839 DOI: 10.1016/j.mib.2024.102436] [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: 11/14/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Bacteria have evolved a variety of defence mechanisms to protect against mobile genetic elements, including restriction-modification systems and CRISPR-Cas. In recent years, dozens of previously unknown defence systems (DSs) have been discovered. Notably, diverse DSs often coexist within the same genome, and some co-occur at frequencies significantly higher than would be expected by chance, implying potential synergistic interactions. Recent studies have provided evidence of defence mechanisms that enhance or complement one another. Here, we review the interactions between DSs at the mechanistic, regulatory, ecological and evolutionary levels.
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Affiliation(s)
- Aleksei Agapov
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Kate S Baker
- Department of Genetics, University of Cambridge, CB2 3EH, UK
| | - Paritosh Bedekar
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Rama P Bhatia
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Michael A Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Cooper Brown
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | | | - Joanne L Fothergill
- Dept of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - James Pj Hall
- Dept of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - Alice Maestri
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Stuart McQuarrie
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Anna Olina
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | | | - Mario Recker
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Anna Richmond
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Steven J Shaw
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | | | - Sam C Went
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Edze R Westra
- ESI, Centre for Ecology and Conservation, University of Exeter, UK.
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Rosanna Wright
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
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30
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Tamulaitiene G, Sabonis D, Sasnauskas G, Ruksenaite A, Silanskas A, Avraham C, Ofir G, Sorek R, Zaremba M, Siksnys V. Activation of Thoeris antiviral system via SIR2 effector filament assembly. Nature 2024; 627:431-436. [PMID: 38383786 DOI: 10.1038/s41586-024-07092-x] [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: 02/13/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024]
Abstract
To survive bacteriophage (phage) infections, bacteria developed numerous anti-phage defence systems1-7. Some of them (for example, type III CRISPR-Cas, CBASS, Pycsar and Thoeris) consist of two modules: a sensor responsible for infection recognition and an effector that stops viral replication by destroying key cellular components8-12. In the Thoeris system, a Toll/interleukin-1 receptor (TIR)-domain protein, ThsB, acts as a sensor that synthesizes an isomer of cyclic ADP ribose, 1''-3' glycocyclic ADP ribose (gcADPR), which is bound in the Smf/DprA-LOG (SLOG) domain of the ThsA effector and activates the silent information regulator 2 (SIR2)-domain-mediated hydrolysis of a key cell metabolite, NAD+ (refs. 12-14). Although the structure of ThsA has been solved15, the ThsA activation mechanism remained incompletely understood. Here we show that 1''-3' gcADPR, synthesized in vitro by the dimeric ThsB' protein, binds to the ThsA SLOG domain, thereby activating ThsA by triggering helical filament assembly of ThsA tetramers. The cryogenic electron microscopy (cryo-EM) structure of activated ThsA revealed that filament assembly stabilizes the active conformation of the ThsA SIR2 domain, enabling rapid NAD+ depletion. Furthermore, we demonstrate that filament formation enables a switch-like response of ThsA to the 1''-3' gcADPR signal.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Dziugas Sabonis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Audrone Ruksenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Carmel Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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31
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Li Y, Shen Z, Zhang M, Yang XY, Cleary SP, Xie J, Marathe IA, Kostelic M, Greenwald J, Rish AD, Wysocki VH, Chen C, Chen Q, Fu TM, Yu Y. PtuA and PtuB assemble into an inflammasome-like oligomer for anti-phage defense. Nat Struct Mol Biol 2024; 31:413-423. [PMID: 38177683 DOI: 10.1038/s41594-023-01172-8] [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: 02/22/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show that PtuA and PtuB form a stable complex with a 6:2 stoichiometry. Cryo-electron microscopy structure of PtuAB reveals a distinctive horseshoe-like configuration. PtuA adopts a hexameric arrangement, organized as an asymmetric trimer of dimers, contrasting the ring-like structure by other ATPases. Notably, the three pairs of PtuA dimers assume distinct conformations and fulfill unique roles in recruiting PtuB. Our functional assays have further illuminated the importance of the oligomeric assembly of PtuAB in anti-phage defense. Moreover, we have uncovered that ATP molecules can directly bind to PtuA and inhibit the activities of PtuAB. Together, the assembly and function of the Septu system shed light on understanding other ATPase-containing systems in bacterial immunity.
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Affiliation(s)
- Yuanyuan Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mengyuan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Sean P Cleary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jiale Xie
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Ila A Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Marius Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jacelyn Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Anthony D Rish
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chong Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China.
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.
| | - Yamei Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China.
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32
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Finocchio G, Koopal B, Potocnik A, Heijstek C, Westphal AH, Jinek M, Swarts DC. Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Res 2024; 52:2012-2029. [PMID: 38224450 PMCID: PMC10899771 DOI: 10.1093/nar/gkad1248] [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: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
In both prokaryotic and eukaryotic innate immune systems, TIR domains function as NADases that degrade the key metabolite NAD+ or generate signaling molecules. Catalytic activation of TIR domains requires oligomerization, but how this is achieved varies in distinct immune systems. In the Short prokaryotic Argonaute (pAgo)/TIR-APAZ (SPARTA) immune system, TIR NADase activity is triggered upon guide RNA-mediated recognition of invading DNA by an unknown mechanism. Here, we describe cryo-EM structures of SPARTA in the inactive monomeric and target DNA-activated tetrameric states. The monomeric SPARTA structure reveals that in the absence of target DNA, a C-terminal tail of TIR-APAZ occupies the nucleic acid binding cleft formed by the pAgo and TIR-APAZ subunits, inhibiting SPARTA activation. In the active tetrameric SPARTA complex, guide RNA-mediated target DNA binding displaces the C-terminal tail and induces conformational changes in pAgo that facilitate SPARTA-SPARTA dimerization. Concurrent release and rotation of one TIR domain allow it to form a composite NADase catalytic site with the other TIR domain within the dimer, and generate a self-complementary interface that mediates cooperative tetramerization. Combined, this study provides critical insights into the structural architecture of SPARTA and the molecular mechanism underlying target DNA-dependent oligomerization and catalytic activation.
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Affiliation(s)
- Giada Finocchio
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Balwina Koopal
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Ana Potocnik
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Clint Heijstek
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
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33
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Patel PH, Taylor VL, Zhang C, Getz LJ, Fitzpatrick AD, Davidson AR, Maxwell KL. Anti-phage defence through inhibition of virion assembly. Nat Commun 2024; 15:1644. [PMID: 38388474 PMCID: PMC10884400 DOI: 10.1038/s41467-024-45892-x] [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: 11/21/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Bacteria have evolved diverse antiviral defence mechanisms to protect themselves against phage infection. Phages integrated into bacterial chromosomes, known as prophages, also encode defences that protect the bacterial hosts in which they reside. Here, we identify a type of anti-phage defence that interferes with the virion assembly pathway of invading phages. The protein that mediates this defence, which we call Tab (for 'Tail assembly blocker'), is constitutively expressed from a Pseudomonas aeruginosa prophage. Tab allows the invading phage replication cycle to proceed, but blocks assembly of the phage tail, thus preventing formation of infectious virions. While the infected cell dies through the activity of the replicating phage lysis proteins, there is no release of infectious phage progeny, and the bacterial community is thereby protected from a phage epidemic. Prophages expressing Tab are not inhibited during their own lytic cycle because they express a counter-defence protein that interferes with Tab function. Thus, our work reveals an anti-phage defence that operates by blocking virion assembly, thereby both preventing formation of phage progeny and allowing destruction of the infected cell due to expression of phage lysis genes.
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Affiliation(s)
| | | | - Chi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Landon J Getz
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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34
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Gu L, Zheng J, Zhang Y, Wang D, Liu J. Selection and Characterization of DNA Aptamers for Cytidine and Uridine. Chembiochem 2024; 25:e202300656. [PMID: 38180305 DOI: 10.1002/cbic.202300656] [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: 09/25/2023] [Revised: 11/30/2023] [Indexed: 01/06/2024]
Abstract
Cytidine and uridine are two essential pyrimidine ribonucleotides, and accurate detection of these nucleosides holds significant biological importance. While many aptamers were reported to bind purines, little success was achieved for pyrimidine binding. This study employs the library-immobilization capture-SELEX technique to isolate aptamers capable of selectively binding to cytidine and uridine. First, a selection was performed using a mixture of cytidine and uridine as the target. This selection led to the isolation of a highly selective aptamer for cytidine with a dissociation constant (Kd ) of 0.9 μM as determined by isothermal titration calorimetry (ITC). In addition, a dual-recognition aptamer was also discovered, which exhibited selective binding to both cytidine and uridine. Subsequently, a separate selection was carried out using uridine as the sole target, and the resulting uridine aptamer displayed a Kd of 4 μM based on a thioflavin T fluorescence assay and a Kd of 102 μM based on ITC. These aptamers do not have a strict requirement of metal ions for binding, and they showed excellent selectivity since no binding was observed with their nucleobases or nucleotides. This study has resulted three aptamers for pyrimidines, which can be employed in biosensors and DNA switches.
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Affiliation(s)
- Lide Gu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Jiajie Zheng
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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35
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Burke KA, Urick CD, Mzhavia N, Nikolich MP, Filippov AA. Correlation of Pseudomonas aeruginosa Phage Resistance with the Numbers and Types of Antiphage Systems. Int J Mol Sci 2024; 25:1424. [PMID: 38338703 PMCID: PMC10855318 DOI: 10.3390/ijms25031424] [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: 12/14/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.
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Affiliation(s)
| | | | | | | | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (K.A.B.); (C.D.U.); (N.M.); (M.P.N.)
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36
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Cao X, Xiao Y, Huiting E, Cao X, Li D, Ren J, Fedorova I, Wang H, Guan L, Wang Y, Li L, Bondy-Denomy J, Feng Y. Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides. Mol Cell 2024; 84:375-385.e7. [PMID: 38103556 PMCID: PMC11102597 DOI: 10.1016/j.molcel.2023.11.026] [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: 05/22/2023] [Revised: 10/09/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
Cyclic-oligonucleotide-based anti-phage signaling system (CBASS) is a common immune system that uses cyclic oligonucleotide signals to limit phage replication. In turn, phages encode anti-CBASS (Acb) proteins such as Acb2, which can sequester some cyclic dinucleotides (CDNs) and limit downstream effector activation. Here, we identified that Acb2 sequesters many CDNs produced by CBASS systems and inhibits stimulator of interferon genes (STING) activity in human cells. Surprisingly, the Acb2 hexamer also binds with high affinity to CBASS cyclic trinucleotides (CTNs) 3'3'3'-cyclic AMP-AMP-AMP and 3'3'3'-cAAG at a distinct site from CDNs. One Acb2 hexamer can simultaneously bind two CTNs and three CDNs. Phage-encoded Acb2 provides protection from type III-C CBASS that uses cA3 signaling molecules. Moreover, phylogenetic analysis of >2,000 Acb2 homologs encoded by diverse phages and prophages revealed that most are expected to bind both CTNs and CDNs. Altogether, Acb2 sequesters nearly all known CBASS signaling molecules through two distinct binding pockets and therefore serves as a broad-spectrum inhibitor of cGAS-based immunity.
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Affiliation(s)
- Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yu Xiao
- 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, Beijing 100084, China
| | - Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xujun Cao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Arc Institute, Palo Alto, CA 94304, USA
| | - Dong Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Iana Fedorova
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hao Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Linlin Guan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yu Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingyin Li
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Arc Institute, Palo Alto, CA 94304, 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 94720, USA.
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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37
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Jenson JM, Chen ZJ. cGAS goes viral: A conserved immune defense system from bacteria to humans. Mol Cell 2024; 84:120-130. [PMID: 38181755 PMCID: PMC11168419 DOI: 10.1016/j.molcel.2023.12.005] [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: 10/12/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024]
Abstract
To survive, all organisms need the ability to accurately recognize and neutralize pathogens. As a result, many of the fundamental strategies that our innate immune system uses to fight infection have deep evolutionary roots. The innate immune sensor cyclic-GMP-AMP synthase (cGAS), an enzyme that plays a critical role in our bodies by sensing and signaling in response to microbial infection, is broadly conserved and has functional homologs in many vertebrates, invertebrates, and even bacteria. In this review, we will provide an overview of cGAS and cGAS-like signaling in eukaryotes before discussing cGAS-like homologs in bacteria.
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Affiliation(s)
- Justin M Jenson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
| | - Zhijian J Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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38
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Chen Y, Ying Y, Lalsiamthara J, Zhao Y, Imani S, Li X, Liu S, Wang Q. From bacteria to biomedicine: Developing therapies exploiting NAD + metabolism. Bioorg Chem 2024; 142:106974. [PMID: 37984103 DOI: 10.1016/j.bioorg.2023.106974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD+) serves as a critical cofactor in cellular metabolism and redox reactions. Bacterial pathways rely on NAD+ participation, where its stability and concentration govern essential homeostasis and functions. This review delves into the role and metabolic regulation of NAD+ in bacteria, highlighting its influence on physiology and virulence. Notably, we explore enzymes linked to NAD+ metabolism as antibacterial drug targets and vaccine candidates. Moreover, we scrutinize NAD+'s medical potential, offering insights for its application in biomedicine. This comprehensive assessment informs future research directions in the dynamic realm of NAD+ and its biomedical significance.
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Affiliation(s)
- Yu Chen
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Yuanyuan Ying
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Jonathan Lalsiamthara
- Molecular Microbiology & Immunology, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Yuheng Zhao
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang 310015, China
| | - Saber Imani
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Xin Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Sijing Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Qingjing Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China.
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Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. Mol Microbiol 2024; 121:152-166. [PMID: 38104967 PMCID: PMC10842292 DOI: 10.1111/mmi.15206] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
Small proteins (<50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance, are poorly understood. Here, we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene neighborhoods support that MntS evolved from the signal peptide of an ancestral SitA protein, acquiring a life of its own with a distinct function in Mn homeostasis.
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Affiliation(s)
- Zachary Wright
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Mackenzie Seymour
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Kalista Paszczak
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Taylor Truttmann
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Katherine Senn
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Samuel Stilp
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Nickolas Jansen
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Magdalyn Gosz
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Lindsay Goeden
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lauren S. Waters
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
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40
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Zhuang Z, Cheng YY, Deng J, Cai Z, Zhong L, Qu JX, Wang K, Yang L. Genomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates. Microbiol Res 2024; 278:127528. [PMID: 37918082 DOI: 10.1016/j.micres.2023.127528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 11/04/2023]
Abstract
Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial 'defense islands' in prophage. Our study provides novel insights into the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends our understanding of bacterial-phage interactions and might guide the application of phage therapy in combating S. maltophilia infections.
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Affiliation(s)
- Zilin Zhuang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China
| | - Ying-Ying Cheng
- Shenzhen Institute of Respiratory Diseases, Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, PR China; BGI Forensic, Shenzhen 518083, PR China; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, PR China
| | - Jie Deng
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China
| | - Zhao Cai
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China
| | - Lin Zhong
- Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, PR China
| | - Jiu-Xin Qu
- Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, PR China
| | - Ke Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, PR China.
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China; Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Disease, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, PR China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, Guangdong, PR China.
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41
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Yirmiya E, Leavitt A, Lu A, Ragucci AE, Avraham C, Osterman I, Garb J, Antine SP, Mooney SE, Hobbs SJ, Kranzusch PJ, Amitai G, Sorek R. Phages overcome bacterial immunity via diverse anti-defence proteins. Nature 2024; 625:352-359. [PMID: 37992756 DOI: 10.1038/s41586-023-06869-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
It was recently shown that bacteria use, apart from CRISPR-Cas and restriction systems, a considerable diversity of phage resistance systems1-4, but it is largely unknown how phages cope with this multilayered bacterial immunity. Here we analysed groups of closely related Bacillus phages that showed differential sensitivity to bacterial defence systems, and discovered four distinct families of anti-defence proteins that inhibit the Gabija, Thoeris and Hachiman systems. We show that these proteins Gad1, Gad2, Tad2 and Had1 efficiently cancel the defensive activity when co-expressed with the respective defence system or introduced into phage genomes. Homologues of these anti-defence proteins are found in hundreds of phages that infect taxonomically diverse bacterial species. We show that the anti-Gabija protein Gad1 blocks the ability of the Gabija defence complex to cleave phage-derived DNA. Our data further reveal that the anti-Thoeris protein Tad2 is a 'sponge' that sequesters the immune signalling molecules produced by Thoeris TIR-domain proteins in response to phage infection. Our results demonstrate that phages encode an arsenal of anti-defence proteins that can disable a variety of bacterial defence mechanisms.
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Affiliation(s)
- Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Allen Lu
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adelyn E Ragucci
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carmel Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Osterman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jeremy Garb
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - 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
| | - 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
| | - Samuel J Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - 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
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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42
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Hou MH, Wang YC, Yang CS, Liao KF, Chang JW, Shih O, Yeh YQ, Sriramoju MK, Weng TW, Jeng US, Hsu STD, Chen Y. Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING. Nat Commun 2023; 14:8519. [PMID: 38129386 PMCID: PMC10739871 DOI: 10.1038/s41467-023-44052-x] [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: 05/22/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
The cyclic GMP-AMP synthase (cGAS)/stimulator of interferon gene (STING) signaling pathway plays a critical protective role against viral infections. Metazoan STING undergoes multilayers of regulation to ensure specific signal transduction. However, the mechanisms underlying the regulation of bacterial STING remain unclear. In this study, we determined the crystal structure of anti-parallel dimeric form of bacterial STING, which keeps itself in an inactive state by preventing cyclic dinucleotides access. Conformational transition between inactive and active states of bacterial STINGs provides an on-off switch for downstream signaling. Some bacterial STINGs living in extreme environment contain an insertion sequence, which we show codes for an additional long lid that covers the ligand-binding pocket. This lid helps regulate anti-phage activities. Furthermore, bacterial STING can bind cyclic di-AMP in a triangle-shaped conformation via a more compact ligand-binding pocket, forming spiral-shaped protofibrils and higher-order fibril filaments. Based on the differences between cyclic-dinucleotide recognition, oligomerization, and downstream activation of different bacterial STINGs, we proposed a model to explain structure-function evolution of bacterial STINGs.
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Grants
- National Science and Technology Council, Taiwan, 109-2311-B241-001 National Science and Technology Council, Taiwan, 111-2311-B-039-001-MY3
- National Science and Technology Council, Taiwan, 111-2811-M-001-125
- National Science and Technology Council, Taiwan, 110-2113-M-001-050-MY3 National Science and Technology Council, Taiwan, 110-2311-B-001-013-MY3 Academia Sinica intramural fund, an Academia Sinica Career Development Award, Academia Sinica, AS-CDA-109-L08 Infectious Disease Research Supporting Grant, AS-IDR-110-08.
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Affiliation(s)
- Mei-Hui Hou
- Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan
| | - Yu-Chuan Wang
- Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan
| | - Chia-Shin Yang
- Genomics BioSci. & Tech. Co. Ltd., New Taipei, 221411, Taiwan
| | - Kuei-Fen Liao
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | - Je-Wei Chang
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
| | | | - Tzu-Wen Weng
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu Science Park, Hsinchu, 300092, Taiwan
- Department of Chemical Engineering & College of Semiconductor Research, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan
| | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 402202, Taiwan.
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43
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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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44
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Giengkam S, Kullapanich C, Wongsantichon J, Adcox HE, Gillespie JJ, Salje J. Orientia tsutsugamushi: comprehensive analysis of the mobilome of a highly fragmented and repetitive genome reveals the capacity for ongoing lateral gene transfer in an obligate intracellular bacterium. mSphere 2023; 8:e0026823. [PMID: 37850800 PMCID: PMC10732058 DOI: 10.1128/msphere.00268-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/22/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Obligate intracellular bacteria, or those only capable of growth inside other living cells, have limited opportunities for horizontal gene transfer with other microbes due to their isolated replicative niche. The human pathogen Ot, an obligate intracellular bacterium causing scrub typhus, encodes an unusually high copy number of a ~40 gene mobile genetic element that typically facilitates genetic transfer across microbes. This proliferated element is heavily degraded in Ot and previously assumed to be inactive. Here, we conducted a detailed analysis of this element in eight Ot strains and discovered two strains with at least one intact copy. This implies that the element is still capable of moving across Ot populations and suggests that the genome of this bacterium may be even more dynamic than previously appreciated. Our work raises questions about intracellular microbial evolution and sounds an alarm for gene-based efforts focused on diagnosing and combatting scrub typhus.
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Affiliation(s)
- Suparat Giengkam
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chitrasak Kullapanich
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Haley E. Adcox
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, Virginia, USA
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland, USA
| | - Jeanne Salje
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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45
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Yang CC, Wang ZY, Cheng CM. Insights into Superinfection Immunity Regulation of Xanthomonas axonopodis Filamentous Bacteriophage cf. Curr Microbiol 2023; 81:42. [PMID: 38112972 DOI: 10.1007/s00284-023-03539-y] [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: 01/31/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023]
Abstract
Filamentous bacteriophage cf infects Xanthomonas axonopodis pv. citri, a serious plant pathogen which causes citrus canker. To understand the immunity regulation of bacteria infected with bacteriophage cf, we applied DNA shuffling to mutate the cf intergenic region. One of the immunity mutants, cf-m3 (NCBI Taxonomy ID: 3050368) expressed a 106-109 fold greater superinfection ability compared with wild type cf. Nine mutations were identified on the cf-m3 phage, four of which were located within the coding region of an open reading frame (ORF165) for a hypothetical repressor, PT, and five located upstream of the PT coding region. A set of phages with mutations to the predicted PT protein or the upstream coding region were generated. All showed similarly low superinfection efficiency to wild type cf and no superinfection ability on cf lysogens. The results indicate that rather than superinfection inhibition, the PT protein and the un-transcribed cis element function individually as positive regulators of cf superinfection immunity. Greater superinfection ability depends on the simultaneous presence of both elements. This work yields further insight into the possible control of citrus canker disease through phages that overcome host superinfection immunity.
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Affiliation(s)
- Chia-Chin Yang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Zih-Yun Wang
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan
| | - Ching-Ming Cheng
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan.
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46
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Amaya I, Edwards K, Wise BM, Bhattacharyya A, Pablo CHD, Mushrush E, Coats AN, Dao S, Dittmar G, Gore T, Jarva TM, Kenkebashvili G, Rathan-Kumar S, Reyes GM, Watts GL, Watts VK, Dubrow D, Lewis G, Stone BH, Xue B, Cresawn SG, Mavrodi D, Sivanathan V, Heller D. A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy. G3 (BETHESDA, MD.) 2023; 13:jkad240. [PMID: 37934806 PMCID: PMC10700055 DOI: 10.1093/g3journal/jkad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023]
Abstract
During infection, bacteriophages produce diverse gene products to overcome bacterial antiphage defenses, to outcompete other phages, and to take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing ∼25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known antimycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
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Affiliation(s)
- Isabel Amaya
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Kaylia Edwards
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Bethany M Wise
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Ember Mushrush
- Department of Biology, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Amber N Coats
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sara Dao
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Grace Dittmar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Taylor Gore
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Taiya M Jarva
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Giorgi Kenkebashvili
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Sudiksha Rathan-Kumar
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Gabriella M Reyes
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Garrett L Watts
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Victoria Kalene Watts
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Deena Dubrow
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Gabrielle Lewis
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Benjamin H Stone
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Bingjie Xue
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Steven G Cresawn
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Dmitri Mavrodi
- School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Viknesh Sivanathan
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
| | - Danielle Heller
- Center for the Advancement of Science Leadership and Culture, Howard Hughes Medical Institute, Chevy Chase, MD 20185, USA
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47
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Fung DK, Trinquier AE, Wang JD. Crosstalk between (p)ppGpp and other nucleotide second messengers. Curr Opin Microbiol 2023; 76:102398. [PMID: 37866203 PMCID: PMC10842992 DOI: 10.1016/j.mib.2023.102398] [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: 08/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023]
Abstract
In response to environmental cues, bacteria produce intracellular nucleotide messengers to regulate a wide variety of cellular processes and physiology. Studies on individual nucleotide messengers, such as (p)ppGpp or cyclic (di)nucleotides, have established their respective regulatory themes. As research on nucleotide signaling networks expands, recent studies have begun to uncover various crosstalk mechanisms between (p)ppGpp and other nucleotide messengers, including signal conversion, allosteric regulation, and target competition. The multiple layers of crosstalk implicate that (p)ppGpp is intricately linked to different nucleotide signaling pathways. From a physiological perspective, (p)ppGpp crosstalk enables fine-tuning and feedback regulation with other nucleotide messengers to achieve optimal adaptation.
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Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aude E Trinquier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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48
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Kulkarni M, Hardwick JM. Programmed Cell Death in Unicellular Versus Multicellular Organisms. Annu Rev Genet 2023; 57:435-459. [PMID: 37722687 DOI: 10.1146/annurev-genet-033123-095833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Programmed cell death (self-induced) is intrinsic to all cellular life forms, including unicellular organisms. However, cell death research has focused on animal models to understand cancer, degenerative disorders, and developmental processes. Recently delineated suicidal death mechanisms in bacteria and fungi have revealed ancient origins of animal cell death that are intertwined with immune mechanisms, allaying earlier doubts that self-inflicted cell death pathways exist in microorganisms. Approximately 20 mammalian death pathways have been partially characterized over the last 35 years. By contrast, more than 100 death mechanisms have been identified in bacteria and a few fungi in recent years. However, cell death is nearly unstudied in most human pathogenic microbes that cause major public health burdens. Here, we consider how the current understanding of programmed cell death arose through animal studies and how recently uncovered microbial cell death mechanisms in fungi and bacteria resemble and differ from mechanisms of mammalian cell death.
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Affiliation(s)
- Madhura Kulkarni
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; ,
| | - J Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA; ,
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Li X, Yin W, Lin JD, Zhang Y, Guo Q, Wang G, Chen X, Cui B, Wang M, Chen M, Li P, He YW, Qian W, Luo H, Zhang LH, Liu XW, Song S, Deng Y. Regulation of the physiology and virulence of Ralstonia solanacearum by the second messenger 2',3'-cyclic guanosine monophosphate. Nat Commun 2023; 14:7654. [PMID: 37996405 PMCID: PMC10667535 DOI: 10.1038/s41467-023-43461-2] [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: 03/09/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Previous studies have demonstrated that bis-(3',5')-cyclic diguanosine monophosphate (bis-3',5'-c-di-GMP) is a ubiquitous second messenger employed by bacteria. Here, we report that 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) controls the important biological functions, quorum sensing (QS) signaling systems and virulence in Ralstonia solanacearum through the transcriptional regulator RSp0980. This signal specifically binds to RSp0980 with high affinity and thus abolishes the interaction between RSp0980 and the promoters of target genes. In-frame deletion of RSp0334, which contains an evolved GGDEF domain with a LLARLGGDQF motif required to catalyze 2',3'-cGMP to (2',5')(3',5')-cyclic diguanosine monophosphate (2',3'-c-di-GMP), altered the abovementioned important phenotypes through increasing the intracellular 2',3'-cGMP levels. Furthermore, we found that 2',3'-cGMP, its receptor and the evolved GGDEF domain with a LLARLGGDEF motif also exist in the human pathogen Salmonella typhimurium. Together, our work provides insights into the unusual function of the GGDEF domain of RSp0334 and the special regulatory mechanism of 2',3'-cGMP signal in bacteria.
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Affiliation(s)
- Xia Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wenfang Yin
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Junjie Desmond Lin
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yong Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Quan Guo
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Gerun Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xiayu Chen
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Binbin Cui
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Min Chen
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Peng Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institution of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haibin Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Lian-Hui Zhang
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Xue-Wei Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Shihao Song
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China.
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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50
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Li D, Xiao Y, Xiong W, Fedorova I, Wang Y, Liu X, Huiting E, Ren J, Gao Z, Zhao X, Cao X, Zhang Y, Bondy-Denomy J, Feng Y. Single phage proteins sequester TIR- and cGAS-generated signaling molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567273. [PMID: 38014003 PMCID: PMC10680739 DOI: 10.1101/2023.11.15.567273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Prokaryotic anti-phage immune systems use TIR (toll/interleukin-1 receptor) and cGAS (cyclic GMP-AMP synthase) enzymes to produce 1"-3'/1"-2' glycocyclic ADPR (gcADPR) and cyclid di-/trinucleotides (CDNs and CTNs) signaling molecules that limit phage replication, respectively 1-3. However, how phages neutralize these common systems is largely unknown. Here, we show that Thoeris anti-defense proteins Tad1 4 and Tad2 5 both have anti-CBASS activity by simultaneously sequestering CBASS cyclic oligonucleotides. Strikingly, apart from binding Thoeris signals 1"-3' and 1"-2' gcADPR, Tad1 also binds numerous CBASS CDNs/CTNs with high affinity, inhibiting CBASS systems using these molecules in vivo and in vitro. The hexameric Tad1 has six binding sites for CDNs or gcADPR, which are independent from two high affinity binding sites for CTNs. Tad2 also sequesters various CDNs in addition to gcADPR molecules, inhibiting CBASS systems using these CDNs. However, the binding pockets for CDNs and gcADPR are different in Tad2, whereby a tetramer can bind two CDNs and two gcADPR molecules simultaneously. Taken together, Tad1 and Tad2 are both two-pronged inhibitors that, alongside anti-CBASS protein 2, establish a paradigm of phage proteins that flexibly sequester a remarkable breadth of cyclic nucleotides involved in TIR- and cGAS-based anti-phage immunity.
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Affiliation(s)
- Dong Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Authors contributed equally
| | - Yu Xiao
- 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, Beijing 100084, China
- Authors contributed equally
| | - Weijia Xiong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Authors contributed equally
| | - Iana Fedorova
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Authors contributed equally
| | - Yu Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Authors contributed equally
| | - Xi Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Authors contributed equally
| | - Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jie Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zirui Gao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xingyu Zhao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xueli Cao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - 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 94720, USA
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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