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Wang S, Ma T, Xia X, Zhang L. Evolutionary insights and functional diversity of gasdermin family proteins and homologs in microorganisms. Front Immunol 2024; 15:1371611. [PMID: 38571940 PMCID: PMC10989679 DOI: 10.3389/fimmu.2024.1371611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024] Open
Abstract
The gasdermin protein family and its homologs in microorganisms have gained significant attention due to their roles in programmed cell death, immune defense, and microbial infection. This review summarizes the current research status of gasdermin proteins, their structural features, and functional roles in fungi, bacteria, and viruses. The review presents evolutionary parallels between mammalian and microbial defense systems, highlighting the conserved role of gasdermin proteins in regulating cell death processes and immunity. Additionally, the structural and functional characteristics of gasdermin homologs in microorganisms are summarized, shedding light on their potential as targets for therapeutic interventions. Future research directions in this field are also discussed to provide a roadmap for further investigation.
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Affiliation(s)
- Shule Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, China
| | - Tingbo Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong, China
| | - Xiaoyi Xia
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
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2
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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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3
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Guler P, Bendori SO, Borenstein T, Aframian N, Kessel A, Eldar A. Arbitrium communication controls phage lysogeny through non-lethal modulation of a host toxin-antitoxin defence system. Nat Microbiol 2024; 9:150-160. [PMID: 38177304 DOI: 10.1038/s41564-023-01551-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Temperate Bacillus phages often utilize arbitrium communication to control lysis/lysogeny decisions, but the mechanisms by which this control is exerted remains largely unknown. Here we find that the arbitrium system of Bacillus subtilis phage ϕ3T modulates the host-encoded MazEF toxin-antitoxin system to this aim. Upon infection, the MazF ribonuclease is activated by three phage genes. At low arbitrium signal concentrations, MazF is inactivated by two phage-encoded MazE homologues: the arbitrium-controlled AimX and the later-expressed YosL proteins. At high signal, MazF remains active, promoting lysogeny without harming the bacterial host. MazF cleavage sites are enriched on transcripts of phage lytic genes but absent from the phage repressor in ϕ3T and other Spβ-like phages. Combined with low activation levels of MazF during infections, this pattern explains the phage-specific effect. Our results show how a bacterial toxin-antitoxin system has been co-opted by a phage to control lysis/lysogeny decisions without compromising host viability.
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Affiliation(s)
- Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shira Omer Bendori
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tom Borenstein
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Nitzan Aframian
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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4
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Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023; 51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency-free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
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Affiliation(s)
- Gianlucca G Nicastro
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
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Yerushalmy O, Braunstein R, Alkalay-Oren S, Rimon A, Coppenhagn-Glazer S, Onallah H, Nir-Paz R, Hazan R. Towards Standardization of Phage Susceptibility Testing: The Israeli Phage Therapy Center "Clinical Phage Microbiology"-A Pipeline Proposal. Clin Infect Dis 2023; 77:S337-S351. [PMID: 37932122 DOI: 10.1093/cid/ciad514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Using phages as salvage therapy for nonhealing infections is gaining recognition as a viable solution for patients with such infections. The escalating issue of antibiotic resistance further emphasizes the significance of using phages in treating bacterial infections, encompassing compassionate-use scenarios and clinical trials. Given the high specificity of phages, selecting the suitable phage(s) targeting the causative bacteria becomes critical for achieving treatment success. However, in contrast to conventional antibiotics, where susceptibility-testing procedures were well established for phage therapy, there is a lack of standard frameworks for matching phages from a panel to target bacterial strains and assessing their interactions with antibiotics or other agents. This review discusses and compares published methods for clinical phage microbiology, also known as phage susceptibility testing, and proposes guidelines for establishing a standard pipeline based on our findings over the past 5 years of phage therapy at the Israeli Phage Therapy Center.
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Affiliation(s)
- Ortal Yerushalmy
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Braunstein
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alkalay-Oren
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
- The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Rimon
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shunit Coppenhagn-Glazer
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadil Onallah
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ran Nir-Paz
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ronen Hazan
- The Israeli Phage Therapy Center (IPTC) of Hadassah Medical Center and the Hebrew University, Jerusalem, Israel
- Faculty of Dental Medicine, Institute of Biomedical and Oral Research (IBOR), The Hebrew University of Jerusalem, Jerusalem, Israel
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Fernández-García L, Wood TK. Phage-Defense Systems Are Unlikely to Cause Cell Suicide. Viruses 2023; 15:1795. [PMID: 37766202 PMCID: PMC10535081 DOI: 10.3390/v15091795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
As new phage-defense systems (PDs) are discovered, the overlap between their mechanisms and those of toxin/antitoxin systems (TAs) is becoming clear in that both use similar means to reduce cellular metabolism; for example, both systems have members that deplete energetic compounds (e.g., NAD+, ATP) and deplete nucleic acids, and both have members that inflict membrane damage. Moreover, both TAs and PDs are similar in that rather than altruistically killing the host to limit phage propagation (commonly known as abortive infection), both reduce host metabolism since phages propagate less in slow-growing cells, and slow growth facilitates the interaction of multiple phage-defense systems.
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Affiliation(s)
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA;
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