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Zhang H, Li Y, Li L, Chen L, Zhu C, Sun L, Dong P, Jing D, Yang J, Fu L, Xiao F, Xia N, Li S, Zheng Q, Wu Y. Structural insights into activation mechanisms on NADase of the bacterial DSR2 anti-phage defense system. SCIENCE ADVANCES 2024; 10:eadn5691. [PMID: 39083599 PMCID: PMC11290490 DOI: 10.1126/sciadv.adn5691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD+) of infected cells, which can be activated by tail tube protein (TTP) and inhibited by DSR anti-defense 1 (DSAD1) of diverse phages. However, the regulating mechanism remains elusive. Here, we determined the cryo-electron microscopy structure of apo DSR2, as well as the respective complex structures with TTP and DSAD1. Structural analyses and biochemical studies reveal that DSR2 forms a tetramer with a SIR2 central core and two distinct conformations. Monomeric TTP preferentially binds to the closed conformation of DSR2, inducing conformational distortions on SIR2 tetramer assembly to activate its NADase activity. DSAD1 combines with the open conformation of DSR2, directly or allosterically inhibiting TTP activation on DSR2 NAD+ hydrolysis. Our findings decipher the detailed molecule mechanisms for DSR2 NADase activity regulation and lay a foundation for in-depth understanding of the DSR2 anti-phage defense system.
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Affiliation(s)
- Hong Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Yu Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Lanlan Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Lifei Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Chunhua Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Panpan Dong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Dingding Jing
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Jinbo Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Lei Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Fangnan Xiao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Qingbing Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen 361102, PR China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
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2
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Liu T, Gao X, Chen R, Tang K, Liu Z, Wang P, Wang X. A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral-associated Halomonas meridiana. Microb Biotechnol 2024; 17:e14524. [PMID: 38980956 PMCID: PMC11232893 DOI: 10.1111/1751-7915.14524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
The coral reef microbiome plays a vital role in the health and resilience of reefs. Previous studies have examined phage therapy for coral pathogens and for modifying the coral reef microbiome, but defence systems against coral-associated bacteria have received limited attention. Phage defence systems play a crucial role in helping bacteria fight phage infections. In this study, we characterized a new defence system, Hma (HmaA-HmaB-HmaC), in the coral-associated Halomonas meridiana derived from the scleractinian coral Galaxea fascicularis. The Swi2/Snf2 helicase HmaA with a C-terminal nuclease domain exhibits antiviral activity against Escherichia phage T4. Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Additionally, HmaA homologues are present in ~1000 bacterial and archaeal genomes. The high frequency of HmaA helicase in Halomonas strains indicates the widespread presence of these phage defence systems, while the insertion of defence genes in the hma region confirms the existence of a defence gene insertion hotspot. These findings offer insights into the diversity of phage defence systems in coral-associated bacteria and these diverse defence systems can be further applied into designing probiotics with high-phage resistance.
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Affiliation(s)
- Tianlang Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xinyu Gao
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
| | - Ziyao Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental EngineeringSouth China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
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3
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Huang J, Zhu K, Gao Y, Ye F, Li Z, Ge Y, Liu S, Yang J, Gao A. Molecular basis of bacterial DSR2 anti-phage defense and viral immune evasion. Nat Commun 2024; 15:3954. [PMID: 38729958 PMCID: PMC11087589 DOI: 10.1038/s41467-024-48291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Defense-associated sirtuin 2 (DSR2) systems are widely distributed across prokaryotic genomes, providing robust protection against phage infection. DSR2 recognizes phage tail tube proteins and induces abortive infection by depleting intracellular NAD+, a process that is counteracted by another phage-encoded protein, DSR Anti Defense 1 (DSAD1). Here, we present cryo-EM structures of Bacillus subtilis DSR2 in its apo, Tube-bound, and DSAD1-bound states. DSR2 assembles into an elongated tetramer, with four NADase catalytic modules clustered in the center and the regulatory-sensing modules distributed at four distal corners. Interestingly, monomeric Tube protein, rather than its oligomeric states, docks at each corner of the DSR2 tetramer to form a 4:4 DSR2-Tube assembly, which is essential for DSR2 NADase activity. DSAD1 competes with Tube for binding to DSR2 by occupying an overlapping region, thereby inhibiting DSR2 immunity. Thus, our results provide important insights into the assembly, activation and inhibition of the DSR2 anti-phage defense system.
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Affiliation(s)
- Jiafeng Huang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Keli Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yina Gao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feng Ye
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhaolong Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yao Ge
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Songqing Liu
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yang
- Department of Neurology, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing, 100049, China.
| | - Ang Gao
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
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4
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Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 2024; 32:557-572.e6. [PMID: 38402614 PMCID: PMC11009048 DOI: 10.1016/j.chom.2024.01.015] [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: 11/12/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.
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Affiliation(s)
- Yi Wu
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anne van den Hurk
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Simran Krishnakant Kushwaha
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Claire M King
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yaqing Ou
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Thomas C Todeschini
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Franklin L Nobrega
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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5
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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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6
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Schaeffer RD, Zhang J, Medvedev KE, Kinch LN, Cong Q, Grishin NV. ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput Biol 2024; 20:e1011586. [PMID: 38416793 PMCID: PMC10927120 DOI: 10.1371/journal.pcbi.1011586] [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: 10/10/2023] [Revised: 03/11/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database. On average, we can provide positive classification (either of domains or other identifiable non-domain regions) for 90% of residues in all proteomes. We classified 746,349 domains from 536,808 proteins comprised of over 226,424,000 amino acid residues. We examine the varying populations of homologous groups in both eukaryotes and bacteria. In addition to containing a higher fraction of disordered regions and unassigned domains, eukaryotes show a higher proportion of repeated proteins, both globular and small repeats. We enumerate those highly populated domains that are shared in both eukaryotes and bacteria, such as the Rossmann domains, TIM barrels, and P-loop domains. Additionally, we compare the sampling of homologous groups from this whole proteome set against our stable ECOD reference and discuss groups that have been enriched by structure predictions. Finally, we discuss the implication of these results for protein target selection for future classification strategies for very large protein sets.
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Affiliation(s)
- R. Dustin Schaeffer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Kirill E. Medvedev
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lisa N. Kinch
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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7
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Burke KA, Urick CD, Mzhavia N, Nikolich MP, Filippov AA. Correlation of Pseudomonas aeruginosa Phage Resistance with the Numbers and Types of Antiphage Systems. Int J Mol Sci 2024; 25:1424. [PMID: 38338703 PMCID: PMC10855318 DOI: 10.3390/ijms25031424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.
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Affiliation(s)
| | | | | | | | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (K.A.B.); (C.D.U.); (N.M.); (M.P.N.)
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8
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Kelly A, Went SC, Mariano G, Shaw LP, Picton DM, Duffner SJ, Coates I, Herdman-Grant R, Gordeeva J, Drobiazko A, Isaev A, Lee YJ, Luyten Y, Morgan RD, Weigele P, Severinov K, Wenner N, Hinton JCD, Blower TR. Diverse Durham collection phages demonstrate complex BREX defense responses. Appl Environ Microbiol 2023; 89:e0062323. [PMID: 37668405 PMCID: PMC10537673 DOI: 10.1128/aem.00623-23] [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: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023] Open
Abstract
Bacteriophages (phages) outnumber bacteria ten-to-one and cause infections at a rate of 1025 per second. The ability of phages to reduce bacterial populations makes them attractive alternative antibacterials for use in combating the rise in antimicrobial resistance. This effort may be hindered due to bacterial defenses such as Bacteriophage Exclusion (BREX) that have arisen from the constant evolutionary battle between bacteria and phages. For phages to be widely accepted as therapeutics in Western medicine, more must be understood about bacteria-phage interactions and the outcomes of bacterial phage defense. Here, we present the annotated genomes of 12 novel bacteriophage species isolated from water sources in Durham, UK, during undergraduate practical classes. The collection includes diverse species from across known phylogenetic groups. Comparative analyses of two novel phages from the collection suggest they may be founding members of a new genus. Using this Durham phage collection, we determined that particular BREX defense systems were likely to confer a varied degree of resistance against an invading phage. We concluded that the number of BREX target motifs encoded in the phage genome was not proportional to the degree of susceptibility. IMPORTANCE Bacteriophages have long been the source of tools for biotechnology that are in everyday use in molecular biology research laboratories worldwide. Phages make attractive new targets for the development of novel antimicrobials. While the number of phage genome depositions has increased in recent years, the expected bacteriophage diversity remains underrepresented. Here we demonstrate how undergraduates can contribute to the identification of novel phages and that a single City in England can provide ample phage diversity and the opportunity to find novel technologies. Moreover, we demonstrate that the interactions and intricacies of the interplay between bacterial phage defense systems such as Bacteriophage Exclusion (BREX) and phages are more complex than originally thought. Further work will be required in the field before the dynamic interactions between phages and bacterial defense systems are fully understood and integrated with novel phage therapies.
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Affiliation(s)
- Abigail Kelly
- Department of Biosciences, Durham University, Durham, UK
| | - Sam C. Went
- Department of Biosciences, Durham University, Durham, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Liam P. Shaw
- Department of Biosciences, Durham University, Durham, UK
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Isabel Coates
- Department of Biosciences, Durham University, Durham, UK
| | | | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yan-Jiun Lee
- New England Biolabs, Ipswich, Massachusetts, USA
| | | | | | | | | | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R. Blower
- Department of Biosciences, Durham University, Durham, UK
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9
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Okin D, Kagan JC. Inflammasomes as regulators of non-infectious disease. Semin Immunol 2023; 69:101815. [PMID: 37506489 PMCID: PMC10527946 DOI: 10.1016/j.smim.2023.101815] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Inflammasomes are cytoplasmic organelles that stimulate inflammation upon cellular detection of infectious or non-infectious stress. While much foundational work has focused on the infection-associated aspects of inflammasome activities, recent studies have highlighted the role of inflammasomes in non-infectious cellular and organismal functions. Herein, we discuss the evolution of inflammasome components and highlight characteristics that permit inflammasome regulation of physiologic processes. We focus on emerging data that highlight the importance of inflammasome proteins in the regulation of reproduction, development, and malignancy. A framework is proposed to contextualize these findings.
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Affiliation(s)
- Daniel Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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