1
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Mets T, Kurata T, Ernits K, Johansson MJO, Craig SZ, Evora GM, Buttress JA, Odai R, Wallant KC, Nakamoto JA, Shyrokova L, Egorov AA, Doering CR, Brodiazhenko T, Laub MT, Tenson T, Strahl H, Martens C, Harms A, Garcia-Pino A, Atkinson GC, Hauryliuk V. Mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems. Cell Host Microbe 2024:S1931-3128(24)00174-4. [PMID: 38821063 DOI: 10.1016/j.chom.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
Toxin-antitoxins (TAs) are prokaryotic two-gene systems composed of a toxin neutralized by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilizes the antitoxin by recognizing its chaperone addiction (ChAD) element. TACs mediate antiphage defense, but the mechanisms of viral sensing and restriction are unexplored. We identify two Escherichia coli antiphage TAC systems containing host inhibition of growth (HigBA) and CmdTA TA modules, HigBAC and CmdTAC. HigBAC is triggered through recognition of the gpV major tail protein of phage λ. Chaperone HigC recognizes gpV and ChAD via analogous aromatic molecular patterns, with gpV outcompeting ChAD to trigger toxicity. For CmdTAC, the CmdT ADP-ribosyltransferase toxin modifies mRNA to halt protein synthesis and limit phage propagation. Finally, we establish the modularity of TACs by creating a hybrid broad-spectrum antiphage system combining the CmdTA TA warhead with a HigC chaperone phage sensor. Collectively, these findings reveal the potential of TAC systems in broad-spectrum antiphage defense.
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Affiliation(s)
- Toomas Mets
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Karin Ernits
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Marcus J O Johansson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Sophie Z Craig
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Gabriel Medina Evora
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Jessica A Buttress
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Roni Odai
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Kyo Coppieters't Wallant
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Jose A Nakamoto
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Lena Shyrokova
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | | | | | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Building BC, 1050 Bruxelles, Belgium
| | - Alexander Harms
- ETH Zurich, Institute of Food, Nutrition and Health, 8092 Zürich, Switzerland
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), Campus La Plaine, Building BC, Room 1C4203, Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; Virus Centre, Lund University, Lund, Sweden.
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia; Virus Centre, Lund University, Lund, Sweden; Science for Life Laboratory, Lund, Sweden.
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2
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Sprenger M, Siemers M, Krautwurst S, Papenfort K. Small RNAs direct attack and defense mechanisms in a quorum sensing phage and its host. Cell Host Microbe 2024; 32:727-738.e6. [PMID: 38579715 DOI: 10.1016/j.chom.2024.03.010] [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: 11/21/2023] [Revised: 02/02/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Many, if not all, bacteria use quorum sensing (QS) to control collective behaviors, and more recently, QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or "listen in" on the host's communication processes, to switch between lytic and lysogenic modes of infection. Here, we study the interaction of Vibrio cholerae with the lysogenic phage VP882, which is activated by the QS molecule DPO. We discover that induction of VP882 results in the binding of phage transcripts to the major RNA chaperone Hfq, which in turn outcompetes and downregulates host-encoded small RNAs (sRNAs). VP882 itself also encodes Hfq-binding sRNAs, and we demonstrate that one of these sRNAs, named VpdS, promotes phage replication by regulating host and phage mRNA levels. We further show that host-encoded sRNAs can antagonize phage replication by downregulating phage mRNA expression and thus might be part of the host's phage defense arsenal.
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Affiliation(s)
- Marcel Sprenger
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
| | - Malte Siemers
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
| | | | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany.
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3
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Martínez M, Rizzuto I, Molina R. Knowing Our Enemy in the Antimicrobial Resistance Era: Dissecting the Molecular Basis of Bacterial Defense Systems. Int J Mol Sci 2024; 25:4929. [PMID: 38732145 PMCID: PMC11084316 DOI: 10.3390/ijms25094929] [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: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Bacteria and their phage adversaries are engaged in an ongoing arms race, resulting in the development of a broad antiphage arsenal and corresponding viral countermeasures. In recent years, the identification and utilization of CRISPR-Cas systems have driven a renewed interest in discovering and characterizing antiphage mechanisms, revealing a richer diversity than initially anticipated. Currently, these defense systems can be categorized based on the bacteria's strategy associated with the infection cycle stage. Thus, bacterial defense systems can degrade the invading genetic material, trigger an abortive infection, or inhibit genome replication. Understanding the molecular mechanisms of processes related to bacterial immunity has significant implications for phage-based therapies and the development of new biotechnological tools. This review aims to comprehensively cover these processes, with a focus on the most recent discoveries.
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Affiliation(s)
| | | | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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4
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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] [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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5
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Krüger L, Gaskell-Mew L, Graham S, Shirran S, Hertel R, White MF. Reversible conjugation of a CBASS nucleotide cyclase regulates bacterial immune response to phage infection. Nat Microbiol 2024:10.1038/s41564-024-01670-5. [PMID: 38589469 DOI: 10.1038/s41564-024-01670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/07/2024] [Indexed: 04/10/2024]
Abstract
Prokaryotic antiviral defence systems are frequently toxic for host cells and stringent regulation is required to ensure survival and fitness. These systems must be readily available in case of infection but tightly controlled to prevent activation of an unnecessary cellular response. Here we investigate how the bacterial cyclic oligonucleotide-based antiphage signalling system (CBASS) uses its intrinsic protein modification system to regulate the nucleotide cyclase. By integrating a type II CBASS system from Bacillus cereus into the model organism Bacillus subtilis, we show that the protein-conjugating Cap2 (CBASS associated protein 2) enzyme links the cyclase exclusively to the conserved phage shock protein A (PspA) in the absence of phage. The cyclase-PspA conjugation is reversed by the deconjugating isopeptidase Cap3 (CBASS associated protein 3). We propose a model in which the cyclase is held in an inactive state by conjugation to PspA in the absence of phage, with conjugation released upon infection, priming the cyclase for activation.
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Affiliation(s)
- Larissa Krüger
- School of Biology, University of St Andrews, St Andrews, UK.
| | | | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews, UK
| | - Sally Shirran
- School of Biology, University of St Andrews, St Andrews, UK
| | - Robert Hertel
- Genomic and Applied Microbiology, Göttingen Centre for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews, UK.
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6
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Cossart P, Hacker J, Holden DH, Normark S, Vogel J. Meeting report 'Microbiology 2023: from single cell to microbiome and host', an international interacademy conference in Würzburg. MICROLIFE 2024; 5:uqae008. [PMID: 38665235 PMCID: PMC11044969 DOI: 10.1093/femsml/uqae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
On September 20-22 September 2023, the international conference 'Microbiology 2023: from single cell to microbiome and host' convened microbiologists from across the globe for a very successful symposium, showcasing cutting-edge research in the field. Invited lecturers delivered exceptional presentations covering a wide range of topics, with a major emphasis on phages and microbiomes, on the relevant bacteria within these ecosystems, and their multifaceted roles in diverse environments. Discussions also spanned the intricate analysis of fundamental bacterial processes, such as cell division, stress resistance, and interactions with phages. Organized by four renowned Academies, the German Leopoldina, the French Académie des sciences, the Royal Society UK, and the Royal Swedish Academy of Sciences, the symposium provided a dynamic platform for experts to share insights and discoveries, leaving participants inspired and eager to integrate new knowledge into their respective projects. The success of Microbiology 2023 prompted the decision to host the next quadrennial academic meeting in Sweden. This choice underscores the commitment to fostering international collaboration and advancing the frontiers of microbiological knowledge. The transition to Sweden promises to be an exciting step in the ongoing global dialogue and specific collaborations on microbiology, a field where researchers will continue to push the boundaries of knowledge, understanding, and innovation not only in health and disease but also in ecology.
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Affiliation(s)
| | - Jörg Hacker
- German National Academy of Science Leopoldina, Jägerberg 1, D-06108 Halle, Germany
| | - David H Holden
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Flowers Building, South Kensington Campus, Exhibition Road, Imperial College London, London SW7 2AZ, United Kingdom
| | - Staffan Normark
- Karolinska Institute, Tumor-och-cellbiologi, C1 Microbial Pathogenesis, 17177 Stockholm, Sweden
| | - Jörg Vogel
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str2/Gebaude D15; É. D-97080 Würzburg, Germany
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7
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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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8
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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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9
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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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10
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Li Y, Wei Y, Guo X, Li X, Lu L, Hu L, He Z. Insertion sequence transposition activates antimycobacteriophage immunity through an lsr2-silenced lipid metabolism gene island. MLIFE 2024; 3:87-100. [PMID: 38827510 PMCID: PMC11139207 DOI: 10.1002/mlf2.12106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 06/04/2024]
Abstract
Insertion sequences (ISs) exist widely in bacterial genomes, but their roles in the evolution of bacterial antiphage defense remain to be clarified. Here, we report that, under the pressure of phage infection, the IS1096 transposition of Mycobacterium smegmatis into the lsr2 gene can occur at high frequencies, which endows the mutant mycobacterium with a broad-spectrum antiphage ability. Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes. The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium, thus defending against phage infection. Strikingly, a phage that has evolved mutations in two tail-filament genes can re-escape from the lsr2 inactivation-triggered host defense. This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by IS transposition and provided insight into the natural evolution of bacterial antiphage defense.
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Affiliation(s)
- Yakun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Yuyun Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Xiao Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Xiaohui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Lining Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
| | - Zheng‐Guo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and TechnologyGuangxi UniversityNanningChina
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11
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Ledvina HE, Whiteley AT. Conservation and similarity of bacterial and eukaryotic innate immunity. Nat Rev Microbiol 2024:10.1038/s41579-024-01017-1. [PMID: 38418927 DOI: 10.1038/s41579-024-01017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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12
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Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. SCIENCE ADVANCES 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
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13
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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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14
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Kumar V, Stewart JH. cGLRs Join Their Cousins of Pattern Recognition Receptor Family to Regulate Immune Homeostasis. Int J Mol Sci 2024; 25:1828. [PMID: 38339107 PMCID: PMC10855445 DOI: 10.3390/ijms25031828] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Pattern recognition receptors (PRRs) recognize danger signals such as PAMPs/MAMPs and DAMPs to initiate a protective immune response. TLRs, NLRs, CLRs, and RLRs are well-characterized PRRs of the host immune system. cGLRs have been recently identified as PRRs. In humans, the cGAS/STING signaling pathway is a part of cGLRs. cGAS recognizes cytosolic dsDNA as a PAMP or DAMP to initiate the STING-dependent immune response comprising type 1 IFN release, NF-κB activation, autophagy, and cellular senescence. The present article discusses the emergence of cGLRs as critical PRRs and how they regulate immune responses. We examined the role of cGAS/STING signaling, a well-studied cGLR system, in the activation of the immune system. The following sections discuss the role of cGAS/STING dysregulation in disease and how immune cross-talk with other PRRs maintains immune homeostasis. This understanding will lead to the design of better vaccines and immunotherapeutics for various diseases, including infections, autoimmunity, and cancers.
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Affiliation(s)
- Vijay Kumar
- Laboratory of Tumor Immunology and Immunotherapy, Department of Surgery, Morehouse School of Medicine, Atlanta, GA 30310, USA;
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15
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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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16
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Yan Y, Zheng J, Zhang X, Yin Y. dbAPIS: a database of anti-prokaryotic immune system genes. Nucleic Acids Res 2024; 52:D419-D425. [PMID: 37889074 PMCID: PMC10767833 DOI: 10.1093/nar/gkad932] [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: 08/11/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS (https://bcb.unl.edu/dbAPIS), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome/virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.
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Affiliation(s)
- Yuchen Yan
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
| | | | - Xinpeng Zhang
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE 68588, USA
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17
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Jiang A, Liu Z, Lv X, Zhou C, Ran T, Tan Z. Prospects and Challenges of Bacteriophage Substitution for Antibiotics in Livestock and Poultry Production. BIOLOGY 2024; 13:28. [PMID: 38248459 PMCID: PMC10812986 DOI: 10.3390/biology13010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024]
Abstract
The overuse and misuse of antibiotics in the livestock and poultry industry has led to the development of multi-drug resistance in animal pathogens, and antibiotic resistance genes (ARGs) in bacteria transfer from animals to humans through the consumption of animal products, posing a serious threat to human health. Therefore, the use of antibiotics in livestock production has been strictly controlled. As a result, bacteriophages have attracted increasing research interest as antibiotic alternatives, since they are natural invaders of bacteria. Numerous studies have shown that dietary bacteriophage supplementation could regulate intestinal microbial composition, enhance mucosal immunity and the physical barrier function of the intestinal tract, and play an important role in maintaining intestinal microecological stability and normal body development of animals. The effect of bacteriophages used in animals is influenced by factors such as species, dose, and duration. However, as a category of mobile genetic elements, the high frequency of gene exchange of bacteriophages also poses risks of transmitting ARGs among bacteria. Hence, we summarized the mechanism and efficacy of bacteriophage therapy, and highlighted the feasibility and challenges of bacteriophage utilization in farm animal production, aiming to provide a reference for the safe and effective application of bacteriophages as an antibiotic alternative in livestock and poultry.
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Affiliation(s)
- Aoyu Jiang
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (A.J.); (Z.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zixin Liu
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (A.J.); (Z.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiaokang Lv
- College of Animal Science, Anhui Science and Technology University, Bengbu 233100, China;
| | - Chuanshe Zhou
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (A.J.); (Z.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Tao Ran
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
| | - Zhiliang Tan
- CAS Key Laboratory for Agri-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (A.J.); (Z.L.); (Z.T.)
- University of Chinese Academy of Sciences, Beijing 101408, China
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18
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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 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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19
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Blower TR, van Houte S. Viruses wrap up bacterial defence systems. Nature 2024; 625:250-251. [PMID: 38114828 DOI: 10.1038/d41586-023-03796-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
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20
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Brenzinger S, Airoldi M, Ogunleye AJ, Jugovic K, Amstalden MK, Brochado AR. The Vibrio cholerae CBASS phage defence system modulates resistance and killing by antifolate antibiotics. Nat Microbiol 2024; 9:251-262. [PMID: 38172623 DOI: 10.1038/s41564-023-01556-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: 06/14/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Toxic bacterial modules such as toxin-antitoxin systems hold antimicrobial potential, though successful applications are rare. Here we show that in Vibrio cholerae the cyclic-oligonucleotide-based anti-phage signalling system (CBASS), another example of a toxic module, increases sensitivity to antifolate antibiotics up to 10×, interferes with their synergy and ultimately enables bacterial lysis by these otherwise classic bacteriostatic antibiotics. Cyclic-oligonucleotide production by the CBASS nucleotidyltransferase DncV upon antifolate treatment confirms full CBASS activation under these conditions, and suggests that antifolates release DncV allosteric inhibition by folates. Consequently, the CBASS-antifolate interaction is specific to CBASS systems with closely related nucleotidyltransferases and similar folate-binding pockets. Last, antifolate resistance genes abolish the CBASS-antifolate interaction by bypassing the effects of on-target antifolate activity, thereby creating potential for their coevolution with CBASS. Altogether, our findings illustrate how toxic modules can impact antibiotic activity and ultimately confer bactericidal activity to classical bacteriostatic antibiotics.
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Affiliation(s)
- Susanne Brenzinger
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martina Airoldi
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | | | - Karl Jugovic
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Ana Rita Brochado
- Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.
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21
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Antine SP, Johnson AG, Mooney SE, Leavitt A, Mayer ML, Yirmiya E, Amitai G, Sorek R, Kranzusch PJ. Structural basis of Gabija anti-phage defence and viral immune evasion. Nature 2024; 625:360-365. [PMID: 37992757 PMCID: PMC10781630 DOI: 10.1038/s41586-023-06855-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation1-5. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes1,6,7, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
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Affiliation(s)
- Sadie P Antine
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah E Mooney
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Megan L Mayer
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA, USA
| | - Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
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22
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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: 8] [Impact Index Per Article: 8.0] [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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23
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Sasaki T, Takita S, Fujishiro T, Shintani Y, Nojiri S, Yasui R, Yonesaki T, Otsuka Y. Phage single-stranded DNA-binding protein or host DNA damage triggers the activation of the AbpAB phage defense system. mSphere 2023; 8:e0037223. [PMID: 37882551 PMCID: PMC10732053 DOI: 10.1128/msphere.00372-23] [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: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Although numerous phage defense systems have recently been discovered in bacteria, how these systems defend against phage propagation or sense phage infections remains unclear. The Escherichia coli AbpAB defense system targets several lytic and lysogenic phages harboring DNA genomes. A phage-encoded single-stranded DNA-binding protein, Gp32, activates this system similar to other phage defense systems such as Retron-Eco8, Hachiman, ShosTA, Nhi, and Hna. DNA replication inhibitors or defects in DNA repair factors activate the AbpAB system, even without phage infection. This is one of the few examples of activating phage defense systems without phage infection or proteins. The AbpAB defense system may be activated by sensing specific DNA-protein complexes.
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Affiliation(s)
- Takaomi Sasaki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Saya Takita
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yunosuke Shintani
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Satoki Nojiri
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryota Yasui
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tetsuro Yonesaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuichi Otsuka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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24
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Forti F, Bertoli C, Cafora M, Gilardi S, Pistocchi A, Briani F. Identification and impact on Pseudomonas aeruginosa virulence of mutations conferring resistance to a phage cocktail for phage therapy. Microbiol Spectr 2023; 11:e0147723. [PMID: 37966242 PMCID: PMC10714927 DOI: 10.1128/spectrum.01477-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE In this work, we identified the putative receptors of 16 Pseudomonas phages and evaluated how resistance to phages recognizing different bacterial receptors may affect the virulence. Our findings are relevant for the implementation of phage therapy of Pseudomonas aeruginosa infections, which are difficult to treat with antibiotics. Overall, our results highlight the need to modify natural phages to enlarge the repertoire of receptors exploited by therapeutic phages and suggest that phages using the PAO1-type T4P as receptor may have limited value for the therapy of the cystic fibrosis infection.
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Affiliation(s)
- Francesca Forti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Claudia Bertoli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Marco Cafora
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Sara Gilardi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Federica Briani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
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25
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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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26
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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: 0] [Impact Index Per Article: 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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27
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Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2023; 623:1001-1008. [PMID: 37968393 PMCID: PMC10686824 DOI: 10.1038/s41586-023-06743-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.
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Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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28
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Wang J, Li G, Wu M. Dissolving self to protect community: cGAS ubiquitin-like mechanism for bacteria to fight against phages. Sci Bull (Beijing) 2023; 68:2132-2134. [PMID: 37633829 DOI: 10.1016/j.scib.2023.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Affiliation(s)
- Junyi Wang
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu 610000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau SAR 999078, China.
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Department of Pulmonary and Critical Care Medicine, Chengdu Institute of Respiratory Health, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu 610000, China.
| | - Min Wu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China.
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29
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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30
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Slavik KM, Kranzusch PJ. CBASS to cGAS-STING: The Origins and Mechanisms of Nucleotide Second Messenger Immune Signaling. Annu Rev Virol 2023; 10:423-453. [PMID: 37380187 DOI: 10.1146/annurev-virology-111821-115636] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Host defense against viral pathogens is an essential function for all living organisms. In cell-intrinsic innate immunity, dedicated sensor proteins recognize molecular signatures of infection and communicate to downstream adaptor or effector proteins to activate immune defense. Remarkably, recent evidence demonstrates that much of the core machinery of innate immunity is shared across eukaryotic and prokaryotic domains of life. Here, we review a pioneering example of evolutionary conservation in innate immunity: the animal cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) signaling pathway and its ancestor in bacteria, CBASS (cyclic nucleotide-based antiphage signaling system) antiphage defense. We discuss the unique mechanism by which animal cGLRs (cGAS-like receptors) and bacterial CD-NTases (cGAS/dinucleotide-cyclase in Vibrio (DncV)-like nucleotidyltransferases) in these pathways link pathogen detection with immune activation using nucleotide second messenger signals. Comparing the biochemical, structural, and mechanistic details of cGAS-STING, cGLR signaling, and CBASS, we highlight emerging questions in the field and examine evolutionary pressures that may have shaped the origins of nucleotide second messenger signaling in antiviral defense.
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Affiliation(s)
- Kailey M Slavik
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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31
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Chen K, Liao J, Patel DJ, Xie W. Advances in structure-guided mechanisms impacting on the cGAS-STING innate immune pathway. Adv Immunol 2023; 159:1-32. [PMID: 37996205 DOI: 10.1016/bs.ai.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The metazoan cGAS-STING innate immunity pathway is triggered in response to cytoplasmic double-stranded DNA (dsDNA), thereby providing host defense against microbial pathogens. This pathway also impacts on autoimmune diseases, cellular senescence and anti-tumor immunity. The cGAS-STING pathway was also observed in the bacterial antiviral immune response, known as the cyclic oligonucleotide (CDN)-based anti-phage signaling system (CBASS). This review highlights a structure-based mechanistic perspective of recent advances in metazoan and bacterial cGAS-STING innate immune signaling by focusing on the cGAS sensor, cGAMP second messenger and STING adaptor components, thereby elucidating the specificity, activation, regulation and signal transduction features of the pathway.
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Affiliation(s)
- Kexin Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Jialing Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China; School of Biomedical Engineering, Hubei University of Medicine, Shiyan, Hubei, P.R. China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, United States.
| | - Wei Xie
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P.R. China.
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32
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Jiang S, Chen K, Wang Y, Zhang Y, Tang Y, Huang W, Xiong X, Chen S, Chen C, Wang L. A DNA phosphorothioation-based Dnd defense system provides resistance against various phages and is compatible with the Ssp defense system. mBio 2023; 14:e0093323. [PMID: 37260233 PMCID: PMC10470545 DOI: 10.1128/mbio.00933-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 06/02/2023] Open
Abstract
DndABCDE-catalyzed DNA phosphorothioation (PT), in which the nonbridging oxygen is swapped with a sulfur atom, was first identified in the bacterial genome. Usually, this modification gene cluster is paired with a restriction module consisting of DndF, DndG, and DndH. Although the mechanisms for the antiphage activity conferred by this Dnd-related restriction and modification (R-M) system have been well characterized, several features remain unclear, including the antiphage spectrum and potential interference with DNA methylation. Recently, a novel PT-related R-M system, composed of the modification module SspABCD paired with a single restriction enzyme, SspE, was revealed to be widespread in the bacterial kingdom, which aroused our interest in the interaction between Dnd- and Ssp-based R-M systems. In this study, we discussed the action of Dnd-related R-M systems against phages and demonstrated that the host could benefit from the protection provided by Dnd-related R-M systems against infection by various lytic phages as well as temperate phages. However, this defense barrier would fail against lysogenic phages. Interestingly, DNA methylation, even in the consensus sequence recognized by the Dnd system, could not weaken the restriction efficiency. Finally, we explored the interaction between Dnd- and Ssp-based R-M systems and found that these two systems were compatible. This study not only expands our knowledge of Dnd-associated R-M systems but also reveals a complex interaction between different defense barriers that coexist in the cell. IMPORTANCE Recently, we decoded the mechanism of Dnd-related R-M systems against genetic parasites. In the presence of exogenous DNA that lacks PT, the macromolecular machine consisting of DndF, DndG, and DndH undergoes conformational changes to perform DNA binding, translocation, and DNA nicking activities and scavenge the foreign DNA. However, several questions remain unanswered, including questions regarding the antiphage spectrum, potential interference by DNA methylation, and interplay with other PT-dependent R-M systems. Here, we revealed that the host could benefit from Dnd-related R-M systems for a broad range of antiphage activities, regardless of the presence of DNA methylation. Furthermore, we demonstrated that the convergence of Dnd- and Ssp-related R-M systems could confer to the host a stronger antiphage ability through the additive suppression of phage replication. This study not only deepens our understanding of PT-related defense barriers but also expands our knowledge of the arms race between bacteria and their predators.
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Affiliation(s)
- Susu Jiang
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Ke Chen
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Yingying Wang
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yueying Zhang
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yaru Tang
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wanqiu Huang
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Xiaolin Xiong
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Shi Chen
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Chao Chen
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Lianrong Wang
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
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33
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Andriianov A, Trigüis S, Drobiazko A, Sierro N, Ivanov NV, Selmer M, Severinov K, Isaev A. Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase. Cell Rep 2023; 42:112972. [PMID: 37578860 DOI: 10.1016/j.celrep.2023.112972] [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: 02/23/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Bacteriophage T3 encodes a SAMase that, through cleavage of S-adenosyl methionine (SAM), circumvents the SAM-dependent type I restriction-modification (R-M) defense. We show that SAMase also allows T3 to evade the BREX defense. Although SAM depletion weakly affects BREX methylation, it completely inhibits the defensive function of BREX, suggesting that SAM could be a co-factor for BREX-mediated exclusion of phage DNA, similar to its anti-defense role in type I R-M. The anti-BREX activity of T3 SAMase is mediated not just by enzymatic degradation of SAM but also by direct inhibition of MetK, the host SAM synthase. We present a 2.8 Å cryoelectron microscopy (cryo-EM) structure of the eight-subunit T3 SAMase-MetK complex. Structure-guided mutagenesis reveals that this interaction stabilizes T3 SAMase in vivo, further stimulating its anti-BREX activity. This work provides insights in the versatility of bacteriophage counterdefense mechanisms and highlights the role of SAM as a co-factor of diverse bacterial immunity systems.
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Affiliation(s)
| | - Silvia Trigüis
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, 751 24 Uppsala, Sweden
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchatel, Switzerland
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, 751 24 Uppsala, Sweden.
| | | | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia.
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34
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Andryka-Cegielski K, Soler S, Bartok E. Unexpected bonds: Ubiquitin-like conjugation of cGAS/CD-NTases supports their enzymatic activity and antiphage defense. Signal Transduct Target Ther 2023; 8:308. [PMID: 37620346 PMCID: PMC10449767 DOI: 10.1038/s41392-023-01549-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/29/2023] [Accepted: 06/24/2023] [Indexed: 08/26/2023] Open
Affiliation(s)
- Katarzyna Andryka-Cegielski
- Institute of Experimental Haematology and Transfusion Medicine, University Hospital, University of Bonn, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Bonn, Germany
| | - Sofía Soler
- Institute of Experimental Haematology and Transfusion Medicine, University Hospital, University of Bonn, Bonn, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Bonn, Germany
| | - Eva Bartok
- Institute of Experimental Haematology and Transfusion Medicine, University Hospital, University of Bonn, Bonn, Germany.
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Bonn, Germany.
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35
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Huiting E, Bondy-Denomy J. Defining the expanding mechanisms of phage-mediated activation of bacterial immunity. Curr Opin Microbiol 2023; 74:102325. [PMID: 37178480 PMCID: PMC11080646 DOI: 10.1016/j.mib.2023.102325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/07/2023] [Accepted: 04/08/2023] [Indexed: 05/15/2023]
Abstract
Due to recent discovery efforts, over 100 immune systems encoded by bacteria that antagonize bacteriophage (phage) replication have been uncovered. These systems employ direct and indirect mechanisms to detect phage infection and activate bacterial immunity. The most well-studied mechanisms are direct detection and activation by phage-associated molecular patterns (PhAMPs), such as phage DNA and RNA sequences, and expressed phage proteins that directly activate abortive infection systems. Phage effectors may also inhibit host processes and, therefore, indirectly activate immunity. Here, we discuss our current understanding of these protein PhAMPs and effectors expressed during various stages of the phage life cycle that activate immunity. Immune activators are predominantly identified from genetic approaches that isolate phage mutants that escape a bacterial immune system, coupled with biochemical validation. Although the mechanism of phage-mediated activation remains uncertain for most systems, it has become clear that each stage of the phage life cycle has the potential to induce a bacterial immune response.
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Affiliation(s)
- Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Innovative Genomics Institute, Berkeley, CA, USA.
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36
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Rousset F, Sorek R. The evolutionary success of regulated cell death in bacterial immunity. Curr Opin Microbiol 2023; 74:102312. [PMID: 37030143 DOI: 10.1016/j.mib.2023.102312] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/09/2023]
Abstract
Bacteria employ a complex arsenal of immune mechanisms to defend themselves against phages. Recent studies demonstrate that these immune mechanisms frequently involve regulated cell death in response to phage infection. By sacrificing infected cells, this strategy prevents the spread of phages within the surrounding population. In this review, we discuss the principles of regulated cell death in bacterial defense, and show that over 70% of sequenced prokaryotes employ this strategy as part of their defensive arsenals. We highlight the modularity of defense systems involving regulated cell death, explaining how shuffling between phage-sensing and cell-killing protein domains dominates their evolution. Some of these defense systems are the evolutionary ancestors of key components of eukaryotic immunity, highlighting their importance in shaping the evolutionary trajectory of immune systems across the tree of life.
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37
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Wang L, Zhang L. The arms race between bacteria CBASS and bacteriophages. Front Immunol 2023; 14:1224341. [PMID: 37575224 PMCID: PMC10419184 DOI: 10.3389/fimmu.2023.1224341] [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: 05/17/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
The Bacterial Cyclic oligonucleotide-Based Anti-phage Signaling System (CBASS) is an innate immune system that induces cell suicide to defend against phage infections. This system relies on cGAS/DncV-like nucleotidyltransferases (CD-NTase) to synthesize cyclic oligonucleotides (cOs) and CD-NTase-associated proteins (Caps) to execute cell death through DNA cleavage, membrane damage, and NAD depletion, thereby inhibiting phage replication. Ancillary proteins expressed in CBASS, in combination with CD-NTase, ensure the normal synthesis of cOs and prepare CD-NTase for full activation by binding to phage genomes, proteins, or other unknown products. To counteract cell death induced by CBASS, phage genes encode immune evasion proteins that curb Cap recognition of cOs, allowing for phage replication, assembly, and propagation in bacterial cells. This review provides a comprehensive understanding of CBASS immunity, comparing it with different bacterial immune systems and highlighting the interplay between CBASS and phage. Additionally, it explores similar immune escape methods based on shared proteins and action mechanisms between prokaryotic and eukaryotic viruses.
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Affiliation(s)
- Lan Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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38
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Tak U, Walth P, Whiteley AT. Bacterial cGAS-like enzymes produce 2',3'-cGAMP to activate an ion channel that restricts phage replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.550367. [PMID: 37546940 PMCID: PMC10402079 DOI: 10.1101/2023.07.24.550367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The mammalian innate immune system uses cyclic GMP-AMP synthase (cGAS) to synthesize the cyclic dinucleotide 2',3'-cGAMP during antiviral and antitumor immune responses. 2',3'-cGAMP is a nucleotide second messenger that initiates inflammatory signaling by binding to and activating the stimulator of interferon genes (STING) receptor. Bacteria also encode cGAS/DncV-like nucleotidyltransferases (CD-NTases) that produce nucleotide second messengers to initiate antiviral (antiphage) signaling. Bacterial CD-NTases produce a wide range of cyclic oligonucleotides but have not been documented to produce 2',3'-cGAMP. Here we discovered bacterial CD-NTases that produce 2',3'-cGAMP to restrict phage replication. Bacterial 2',3'-cGAMP binds to CD-NTase associated protein 14 (Cap14), a transmembrane protein of unknown function. Using electrophysiology, we show that Cap14 is a chloride-selective ion channel that is activated by 2',3'-cGAMP binding. Cap14 adopts a modular architecture, with an N-terminal transmembrane domain and a C-terminal nucleotide-binding SAVED domain. Domain-swapping experiments demonstrated the Cap14 transmembrane region could be substituted with a nuclease, thereby generating a biosensor that is selective for 2',3'-cGAMP. This study reveals that 2',3'-cGAMP signaling extends beyond metazoa to bacteria. Further, our findings suggest that transmembrane proteins of unknown function in bacterial immune pathways may broadly function as nucleotide-gated ion channels.
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Affiliation(s)
- Uday Tak
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Peace Walth
- 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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39
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Mayo-Muñoz D, Pinilla-Redondo R, Birkholz N, Fineran PC. A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Rep 2023; 42:112672. [PMID: 37347666 DOI: 10.1016/j.celrep.2023.112672] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and plasmids. However, MGEs can also impose a fitness cost due to their often parasitic nature and differing evolutionary trajectories. In response, prokaryotes have evolved diverse immune mechanisms against MGEs. Recently, our understanding of the abundance and diversity of prokaryotic immune systems has greatly expanded. These defense systems can degrade the invading genetic material, inhibit genome replication, or trigger abortive infection, leading to population protection. In this review, we highlight these strategies, focusing on the most recent discoveries. The study of prokaryotic defenses not only sheds light on microbial evolution but also uncovers novel enzymatic activities with promising biotechnological applications.
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Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
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40
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Gao Z, Feng Y. Bacteriophage strategies for overcoming host antiviral immunity. Front Microbiol 2023; 14:1211793. [PMID: 37362940 PMCID: PMC10286901 DOI: 10.3389/fmicb.2023.1211793] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023] Open
Abstract
Phages and their bacterial hosts together constitute a vast and diverse ecosystem. Facing the infection of phages, prokaryotes have evolved a wide range of antiviral mechanisms, and phages in turn have adopted multiple tactics to circumvent or subvert these mechanisms to survive. An in-depth investigation into the interaction between phages and bacteria not only provides new insight into the ancient coevolutionary conflict between them but also produces precision biotechnological tools based on anti-phage systems. Moreover, a more complete understanding of their interaction is also critical for the phage-based antibacterial measures. Compared to the bacterial antiviral mechanisms, studies into counter-defense strategies adopted by phages have been a little slow, but have also achieved important advances in recent years. In this review, we highlight the numerous intracellular immune systems of bacteria as well as the countermeasures employed by phages, with an emphasis on the bacteriophage strategies in response to host antiviral immunity.
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41
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Cao X, Xiao Y, Huiting E, Cao X, Li D, Ren J, Guan L, Wang Y, Li L, Bondy-Denomy J, Feng Y. Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543220. [PMID: 37398474 PMCID: PMC10312549 DOI: 10.1101/2023.06.01.543220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
CBASS is a common anti-phage immune system that uses cyclic oligonucleotide signals to activate effectors and limit phage replication. In turn, phages encode anti-CBASS (Acb) proteins. We recently uncovered a widespread phage anti-CBASS protein Acb2 that acts as a "sponge" by forming a hexamer complex with three cGAMP molecules. Here, we identified that Acb2 binds and sequesters many CBASS and cGAS-produced cyclic dinucleotides in vitro and inhibits cGAMP-mediated STING activity in human cells. Surprisingly, Acb2 also binds CBASS cyclic trinucleotides 3'3'3'-cyclic AMP-AMP-AMP (cA3) and 3'3'3'-cAAG with high affinity. Structural characterization identified a distinct binding pocket within the Acb2 hexamer that binds two cyclic trinucleotide molecules and another binding pocket that binds to cyclic dinucleotides. Binding in one pocket does not allosterically alter the other, such that one Acb2 hexamer can simultaneously bind two cyclic trinucleotides and three cyclic dinucleotides. Phage-encoded Acb2 provides protection from Type III-C CBASS that uses cA3 signaling molecules in vivo and blocks cA3-mediated activation of the endonuclease effector in vitro. 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
- 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
| | - Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Authors contributed equally
| | - 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
| | - 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
- Lead Contact
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42
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Ho P, Chen Y, Biswas S, Canfield E, Abdolvahabi A, Feldman DE. Bacteriophage antidefense genes that neutralize TIR and STING immune responses. Cell Rep 2023; 42:112305. [PMID: 36952342 DOI: 10.1016/j.celrep.2023.112305] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/09/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Programmed cell suicide of infected bacteria, known as abortive infection (Abi), serves as an immune defense strategy to prevent the propagation of bacteriophage viruses. Many Abi systems utilize bespoke cyclic nucleotide immune messengers generated upon infection to mobilize cognate death effectors. Here, we identify a family of bacteriophage nucleotidyltransferases (NTases) that synthesize competitor cyclic dinucleotide (CDN) ligands and inhibit TIR NADase effectors activated via a linked STING CDN sensor domain (TIR-STING). Through a functional screen of NTase-adjacent phage genes, we uncover candidate inhibitors of cell suicide induced by heterologous expression of tonically active TIR-STING. Among these, we demonstrate that a virus MazG-like nucleotide pyrophosphohydrolase, Atd1, depletes the starvation alarmone (p)ppGpp, revealing a potential role for the alarmone-activated host toxin MazF as an executioner of TIR-driven Abi. Phage NTases and counterdefenses like Atd1 preserve host viability to ensure virus propagation and represent tools to modulate TIR and STING immune responses.
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Affiliation(s)
- Peiyin Ho
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Department of Health Sciences Libraries, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Subarna Biswas
- Department of Surgery, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Ethan Canfield
- University of Southern California, School of Pharmacy, Los Angeles, CA 90033, USA
| | - Alireza Abdolvahabi
- University of Southern California, School of Pharmacy, Los Angeles, CA 90033, USA
| | - Douglas E Feldman
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA.
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43
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Richmond-Buccola D, Kranzusch PJ. Viral sponges sequester nucleotide signals to inactivate immunity. Trends Microbiol 2023; 31:552-553. [PMID: 37100632 DOI: 10.1016/j.tim.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
Bacteria synthesize specialized nucleotide signals to control anti-phage defense. Two papers - by Huiting et al. and Jenson et al. - now reveal that bacteriophages encode protein 'sponges' that sequester cyclic oligonucleotide immune signals and inactivate host antiviral immunity.
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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
| | - 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.
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44
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Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, Sorek R. Discovery of phage determinants that confer sensitivity to bacterial immune systems. Cell 2023; 186:1863-1876.e16. [PMID: 37030292 DOI: 10.1016/j.cell.2023.02.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/09/2023] [Accepted: 02/20/2023] [Indexed: 04/10/2023]
Abstract
Over the past few years, numerous anti-phage defense systems have been discovered in bacteria. Although the mechanism of defense for some of these systems is understood, a major unanswered question is how these systems sense phage infection. To systematically address this question, we isolated 177 phage mutants that escape 15 different defense systems. In many cases, these escaper phages were mutated in the gene sensed by the defense system, enabling us to map the phage determinants that confer sensitivity to bacterial immunity. Our data identify specificity determinants of diverse retron systems and reveal phage-encoded triggers for multiple abortive infection systems. We find general themes in phage sensing and demonstrate that mechanistically diverse systems have converged to sense either the core replication machinery of the phage, phage structural components, or host takeover mechanisms. Combining our data with previous findings, we formulate key principles on how bacterial immune systems sense phage invaders.
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Affiliation(s)
- Avigail Stokar-Avihail
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Taya Fedorenko
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jens Hör
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jeremy Garb
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gabriela Shulman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nicole Wojtania
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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45
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Jenson JM, Li T, Du F, Ea CK, Chen ZJ. Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence. Nature 2023; 616:326-331. [PMID: 36848932 PMCID: PMC10097602 DOI: 10.1038/s41586-023-05862-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
cGAS is an evolutionarily conserved enzyme that has a pivotal role in immune defence against infection1-3. In vertebrate animals, cGAS is activated by DNA to produce cyclic GMP-AMP (cGAMP)4,5, which leads to the expression of antimicrobial genes6,7. In bacteria, cyclic dinucleotide (CDN)-based anti-phage signalling systems (CBASS) have been discovered8-11. These systems are composed of cGAS-like enzymes and various effector proteins that kill bacteria on phage infection, thereby stopping phage spread. Of the CBASS systems reported, approximately 39% contain Cap2 and Cap3, which encode proteins with homology to ubiquitin conjugating (E1/E2) and deconjugating enzymes, respectively8,12. Although these proteins are required to prevent infection of some bacteriophages8, the mechanism by which the enzymatic activities exert an anti-phage effect is unknown. Here we show that Cap2 forms a thioester bond with the C-terminal glycine of cGAS and promotes conjugation of cGAS to target proteins in a process that resembles ubiquitin conjugation. The covalent conjugation of cGAS increases the production of cGAMP. Using a genetic screen, we found that the phage protein Vs.4 antagonized cGAS signalling by binding tightly to cGAMP (dissociation constant of approximately 30 nM) and sequestering it. A crystal structure of Vs.4 bound to cGAMP showed that Vs.4 formed a hexamer that was bound to three molecules of cGAMP. These results reveal a ubiquitin-like conjugation mechanism that regulates cGAS activity in bacteria and illustrates an arms race between bacteria and viruses through controlling CDN levels.
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Affiliation(s)
- Justin M Jenson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tuo Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fenghe Du
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chee-Kwee Ea
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhijian J Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Bondy-Denomy J, Maxwell KL, Davidson AR. Anti-CRISPR Proteins. J Mol Biol 2023; 435:168058. [PMID: 36958604 DOI: 10.1016/j.jmb.2023.168058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- Joseph Bondy-Denomy
- Department of Microbiology, University of California San Francisco, San Francisco, CA, USA. https://twitter.com/@joeBondyDenomy
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. https://twitter.com/@theMaxwellLab
| | - Alan R Davidson
- Department of Biochemistry, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. https://twitter.com/@ARDavidson_UofT
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