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Bowman P, Salvail H. From lab reagent to metabolite: the riboswitch ligand guanidine as a relevant compound in bacterial physiology. J Bacteriol 2025; 207:e0007325. [PMID: 40401924 PMCID: PMC12186494 DOI: 10.1128/jb.00073-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025] Open
Abstract
Efforts of the last 20 years in validating novel riboswitches led to the identification of numerous new motifs recognizing compounds with well-established biological functions. However, the recent characterization of widespread classes of riboswitches binding the nitrogen-rich compound guanidine raised questions regarding its physiological significance that has so far remained elusive. Recent findings established that certain bacterial species assimilate guanidine as a nitrogen source via guanidine-specific enzymes and transporters and that complete ammonium oxidizers can use it as a sole source of energy, reductant, and nitrogen. The frequent association of guanidine riboswitches with genes encoding guanidine efflux transporters also hints that bacteria may experience the burden of guanidine as a stressor during their lifestyle. A major gap in understanding the biology of guanidine resides in its natural source. While metabolic pathways responsible for guanidine synthesis were defined in plants, only a few guanidine-producing enzymes have been identified in bacteria, despite indications that the model organism E. coli may produce guanidine. This review summarizes how riboswitch research unveiled guanidine as an important compound in living organisms and the recent findings advancing our knowledge of guanidine biology. We also highlight open questions that will orient future research aiming at gaining further insights into the biological relevance of guanidine.
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Affiliation(s)
- Payton Bowman
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, USA
| | - Hubert Salvail
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, USA
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2
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Qu S, Dai H. Conjugated STING agonists. MOLECULAR THERAPY. NUCLEIC ACIDS 2025; 36:102530. [PMID: 40291379 PMCID: PMC12032345 DOI: 10.1016/j.omtn.2025.102530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
Abstract
An innate immune system is the first line of defense and prevents the host from infection and attacks the invading pathogens. Stimulator of interferon genes (STING) plays a vital role in the innate immune system. STING activation by STING agonists leads to phosphorylation of TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) with the release of type I interferons and proinflammatory cytokines, further promoting the adaptive immune response and activating T cells by increased antigen presentation. Natural STING agonist cyclic dinucleotides (CDNs) encounter many defects such as high polarity by negative charges, low stability and circulative half-life, off-target systemic toxicity, and low response efficacy in clinical trials. To overcome these challenges, massive efforts have addressed chemical modifications of CDNs, development of non-CDN STING agonists, and delivery of these STING agonists either by conjugation or liposomes/nanoparticles. Considering there have been a great number of reports regarding nanosystem-aided delivery, here, we examine the development of STING agonists, especially for non-CDNs and their delivery specifically by conjugation strategy, with a focus on the STING agonists in clinical trials and current challenges of their potential in cancer immunotherapy.
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Affiliation(s)
- Shuhao Qu
- School of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Hong Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
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3
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López-Pérez M, Balasubramanian D, Campos-Lopez A, Crist C, Grant TA, Haro-Moreno JM, Zaragoza-Solas A, Almagro-Moreno S. Allelic variations and gene cluster modularity act as nonlinear bottlenecks for cholera emergence. Proc Natl Acad Sci U S A 2025; 122:e2417915122. [PMID: 40434643 DOI: 10.1073/pnas.2417915122] [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: 09/11/2024] [Accepted: 04/23/2025] [Indexed: 05/29/2025] Open
Abstract
The underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. The diarrheal disease cholera is caused by strains from a phylogenetically confined group within the Vibrio cholerae species, the pandemic cholera group (PCG), making it an ideal model system to tackle this puzzling phenomenon. Comprehensive analyses of over 1,840 V. cholerae genomes, including environmental isolates from this study, reveal that the species consists of eleven groups, with the PCG belonging to the largest and located within a lineage shared with environmental strains. This hierarchical classification provided us with a framework to unravel the ecoevolutionary dynamics of the genetic determinants associated with the emergence of toxigenic V. cholerae. Our analyses indicate that this phenomenon is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. We determined that certain PCG-associated alleles are essential for successful colonization whereas others provide a nonlinear competitive advantage, acting as a critical bottleneck that clarifies the isolated emergence of PCG. For instance, toxigenic strains encoding non-PCG alleles of a) tcpF or b) a sextuple allelic exchange mutant for genes tcpA, toxT, VC0176, VC1791, rfbT, and ompU, lose their ability to colonize the intestine. Interestingly, these alleles do not play a role in the colonization of newly established model environmental reservoirs. Our study uncovers the evolutionary roots of toxigenic V. cholerae offering a tractable approach for investigating the emergence of pathogenic clones within an environmental population.
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Affiliation(s)
- Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central, Florida, Orlando, FL, 32827
- Microbial Genomics and Evolution Group, División de Microbiología, Universidad Miguel Hernández, Alicante 03550, Spain
| | - Deepak Balasubramanian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central, Florida, Orlando, FL, 32827
- Division of Molecular Microbiology, Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Alicia Campos-Lopez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central, Florida, Orlando, FL, 32827
- Microbial Genomics and Evolution Group, División de Microbiología, Universidad Miguel Hernández, Alicante 03550, Spain
| | - Cole Crist
- Burnett School of Biomedical Sciences, College of Medicine, University of Central, Florida, Orlando, FL, 32827
| | - Trudy-Ann Grant
- Burnett School of Biomedical Sciences, College of Medicine, University of Central, Florida, Orlando, FL, 32827
| | - Jose M Haro-Moreno
- Microbial Genomics and Evolution Group, División de Microbiología, Universidad Miguel Hernández, Alicante 03550, Spain
| | - Asier Zaragoza-Solas
- Microbial Genomics and Evolution Group, División de Microbiología, Universidad Miguel Hernández, Alicante 03550, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central, Florida, Orlando, FL, 32827
- Division of Molecular Microbiology, Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN 38105
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4
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Adams DW, Jaskólska M, Lemopoulos A, Stutzmann S, Righi L, Bader L, Blokesch M. West African-South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems. Nat Microbiol 2025:10.1038/s41564-025-02004-9. [PMID: 40404828 DOI: 10.1038/s41564-025-02004-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 04/03/2025] [Indexed: 05/24/2025]
Abstract
Our understanding of the factors underlying the evolutionary success of different lineages of pandemic Vibrio cholerae remains incomplete. The West African-South American (WASA) lineage of V. cholerae, responsible for the 1991-2001 Latin American cholera epidemic, is defined by two unique genetic signatures. Here we show that these signatures encode multiple distinct anti-phage defence systems. Firstly, the WASA-1 prophage encodes an abortive-infection system, WonAB, that renders the lineage resistant to the major predatory vibriophage ICP1, which, alongside other phages, is thought to restrict cholera epidemics. Secondly, a unique set of genes on the Vibrio seventh pandemic island II encodes an unusual modification-dependent restriction system targeting phages with modified genomes, and a previously undescribed member of the Shedu defence family that defends against vibriophage X29. We propose that these anti-phage defence systems likely contributed to the success of a major epidemic lineage of the ongoing seventh cholera pandemic.
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Affiliation(s)
- David W Adams
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Milena Jaskólska
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexandre Lemopoulos
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sandrine Stutzmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laurie Righi
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Loriane Bader
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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5
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Uhlig S, Vevik K, Vyver JVD, Dragland IS, Grutle LA, Pain M, Simm R. Separation and Quantification of Cyclic di-AMP, -GMP, and Cyclic GAMP in Bacteria Using LC-MS/MS. J Sep Sci 2025; 48:e70157. [PMID: 40318142 DOI: 10.1002/jssc.70157] [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: 04/03/2025] [Revised: 04/12/2025] [Accepted: 04/17/2025] [Indexed: 05/07/2025]
Abstract
This study summarizes the optimization of a selective method for UHPLC-separation and subsequent tandem mass spectrometric detection of adenosyl- and guanosyl-containing cyclic dinucleotides in bacteria. Cyclic dinucleotides are a class of bacterial second messenger molecules, and their cellular concentrations are tightly regulated by biosynthesis and enzymatic breakdown. Although bacteria, according to present knowledge, only produce 3',3'-linked cyclic dinucleotides, other nucleotide variants also exist, including structural isomers, which may lead to misidentifications. Mixtures of the 2',2'-, 2',3'-, and 3',3'-linked isomers of cyclic di-AMP, cyclic di-GMP, and cyclic GAMP were separated using an octadecylsilane-amide column. Subsequent tandem mass spectrometric detection was based on monitoring the adenosyl- or guanosyl-product ions for quantification, and additional monitoring of up to three product ions for verification. We show the presence of an unidentified putative structural isomer of cyclic di-AMP in several bacterial species. Cyclic di-AMP was quantified using an isotope dilution approach and 15N10-cyclic di-AMP as an internal standard, whereas instrument calibration for other variants was performed using matrix-matched calibration. The combined measurement uncertainty u' for the quantification of the nine cyclic dinucleotide variants in anion-exchanged bacterial extracts was 10%-41%, determined at an extract concentration of 12 nM. Our study also demonstrated the application of total protein measurements in resuspended, nucleotide-extracted, bacterial pellets to normalize nucleotide concentrations.
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Affiliation(s)
- Silvio Uhlig
- Nordic Institute of Dental Materials (NIOM), Oslo, Norway
| | - Kristina Vevik
- Nordic Institute of Dental Materials (NIOM), Oslo, Norway
- Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Joke Van De Vyver
- Nordic Institute of Dental Materials (NIOM), Oslo, Norway
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | | | - Lene A Grutle
- Nordic Institute of Dental Materials (NIOM), Oslo, Norway
| | - Maria Pain
- Nordic Institute of Dental Materials (NIOM), Oslo, Norway
| | - Roger Simm
- Department of Biosciences, University of Oslo, Oslo, Norway
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6
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Wang J, Li Z, Lang H, Fu W, Gao Y, Yin S, Sun P, Li Z, Huang J, Liu S, Zhu Y, Sun F, Li D, Gao P, Ang Gao. Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity. Cell 2025:S0092-8674(25)00457-X. [PMID: 40345202 DOI: 10.1016/j.cell.2025.04.022] [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: 07/17/2024] [Revised: 01/10/2025] [Accepted: 04/16/2025] [Indexed: 05/11/2025]
Abstract
Cyclic-oligonucleotide-based antiphage signaling systems (CBASS), a widespread antiviral bacterial immune system homologous to the mammalian cGAS-STING pathway, synthesizes cyclic nucleotide signals and triggers effector proteins to induce cell death and prevent viral propagation. Among various CBASS effectors, phospholipase effectors are the first to be discovered and are one of the most widespread families that sense cyclic dinucleotides to degrade cell membrane phospholipids. Here, we report that CBASS phospholipases assemble from a dimeric inactive state into active higher-order filamentous oligomers upon sensing cyclic dinucleotides. Using a combined approach of cryo-electron microscopy and X-ray crystallography, we have determined the structures of CBASS phospholipase in the inactive dimeric state, the cyclic-dinucleotide-bound active higher-order state, and the substrate-analog-bound catalytic mimicry state, thereby visualizing the complete conformational reorganization process. Complemented by functional assays of intermolecular binding, phospholipase enzymatic activity, in vitro membrane disruption, and in vivo antiphage efficiency, our work elucidates the mechanisms of assembly and activation of CBASS phospholipases.
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Affiliation(s)
- Jingge Wang
- Department of Radiology, Zhuhai People's Hospital, The Affiliated Hospital of Beijing Institute of Technology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zhao Li
- Department of Radiology, Zhuhai People's Hospital, The Affiliated Hospital of Beijing Institute of Technology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Hao Lang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfeng Fu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yina Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sen Yin
- Department of Radiology, Zhuhai People's Hospital, The Affiliated Hospital of Beijing Institute of Technology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Panpan Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaolong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiafeng Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Songqing Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Dong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pu Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ang Gao
- Department of Radiology, Zhuhai People's Hospital, The Affiliated Hospital of Beijing Institute of Technology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250118, China; Center for Cell and Gene Therapy, The First Hospital of China Medical University, Shenyang 110001, China.
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7
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Drebes Dörr NC, Lemopoulos A, Blokesch M. Exploring Mobile Genetic Elements in Vibrio cholerae. Genome Biol Evol 2025; 17:evaf079. [PMID: 40302206 PMCID: PMC12082036 DOI: 10.1093/gbe/evaf079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 04/22/2025] [Accepted: 04/25/2025] [Indexed: 05/02/2025] Open
Abstract
Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and nonpandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/antiplasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that nonpandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.
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Affiliation(s)
- Natália C Drebes Dörr
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alexandre Lemopoulos
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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8
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Ma Z, Zhou M, Chen H, Shen Q, Zhou J. Deubiquitinase-Targeting Chimeras (DUBTACs) as a Potential Paradigm-Shifting Drug Discovery Approach. J Med Chem 2025; 68:6897-6915. [PMID: 40135978 DOI: 10.1021/acs.jmedchem.4c02975] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2025]
Abstract
Developing proteolysis-targeting chimeras (PROTACs) is well recognized through target protein degradation (TPD) toward promising therapeutics. While a variety of diseases are driven by aberrant ubiquitination and degradation of critical proteins with protective functions, target protein stabilization (TPS) rather than TPD is emerging as a unique therapeutic modality. Deubiquitinase-targeting chimeras (DUBTACs), a class of heterobifunctional protein stabilizers consisting of deubiquitinase (DUB) and protein-of-interest (POI) targeting ligands conjugated with a linker, can rescue such proteins from aberrant elimination. DUBTACs stabilize the levels of POIs in a DUB-dependent manner, removing ubiquitin from polyubiquitylated and degraded proteins. DUBTACs can induce a new interaction between POI and DUB by forming a POI-DUBTAC-DUB ternary complex. Herein, therapeutic benefits of TPS approaches for human diseases are introduced, and recent advances in developing DUBTACs are summarized. Relevant challenges, opportunities, and future perspectives are also discussed.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Mingxiang Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Qiang Shen
- Department of Interdisciplinary Oncology, School of Medicine, LSU LCMC Health Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
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9
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Peng L, Song J, Sun H, Zhang X, Huang Y, Zeng S, Zhou Z, Li X, Zhuo C. Molecular investigation of an epidemic dissemination of vancomycin-resistant Enterococcus faecium sequence type 80 in Guangdong province, China. Int J Antimicrob Agents 2025; 65:107412. [PMID: 39709131 DOI: 10.1016/j.ijantimicag.2024.107412] [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: 11/06/2024] [Revised: 12/04/2024] [Accepted: 12/09/2024] [Indexed: 12/23/2024]
Abstract
BACKGROUND The detection rate of vancomycin-resistant Enterococcus faecium (VREfm) displayed a dramatic increase in Guangdong, China, from 2021 to 2023, for which the molecular epidemiology and genomic characteristics remain largely unexplored. In this study, we investigated the genetic features and epidemiology of VREfm isolates in Guangdong. METHODS A total of 54 Guangdong VREfm isolates were collected from three tertiary hospitals in Guangdong. We preformed antimicrobial susceptibility tests, whole genome sequencing, risk factor analysis, and bioinformatics analysis to conduct this research. RESULTS Our investigation indicated that VREfm isolates were highly clonal and multidrug-resistant ST80 Enterococcus faecium harboring vanA-positive plasmid. Phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) demonstrated that VREfm isolates exhibited minimal genetic similarity to previously reported E. faecium in China, whereas they exhibited high genomic similarity to an India strain A10290 isolated in 2019 and Hiroshima isolates detected in 2020, indicative of a possible exogeneous import. The genetic environment of cps region showed a novel type of wzy gene cluster involved in capsule polysaccharide (CPS) biosynthesis flanked by ISEf1 and IS16 identified in VREfm isolates, which displayed a remarkably divergence from the downstream of putative cpsABCD region in other sequence types (STs) E. faecium. Heat map of plasmid-mediated virulence factors suggested that several predicted proteins including Cag pathogenetic island proteins existed in VREfm isolates at a high frequency. CONCLUSIONS This study highlighted the importance of ongoing surveillance to track the dynamic dissemination of multidrug-resistant ST80 VREfm isolates harboring multiple virulence genes in Guangdong Province, China.
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Affiliation(s)
- Lianghui Peng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Jingjie Song
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hongli Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiwei Zhang
- Department of Clinical Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Yulan Huang
- Department of Clinical Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Shihan Zeng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Zhuoyang Zhou
- Department of Clinical Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China
| | - Xiaoyan Li
- Department of Clinical Laboratory, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, China.
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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10
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Xu X, Gu P. Overview of Phage Defense Systems in Bacteria and Their Applications. Int J Mol Sci 2024; 25:13316. [PMID: 39769080 PMCID: PMC11676413 DOI: 10.3390/ijms252413316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2024] [Revised: 12/07/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
As natural parasites of bacteria, phages have greatly contributed to bacterial evolution owing to their persistent threat. Diverse phage resistance systems have been developed in bacteria during the coevolutionary process with phages. Conversely, phage contamination has a devastating effect on microbial fermentation, resulting in fermentation failure and substantial economic loss. Accordingly, natural defense systems derived from bacteria can be employed to obtain robust phage-resistant host cells that can overcome the threats posed by bacteriophages during industrial bacterial processes. In this review, diverse phage resistance mechanisms, including the remarkable research progress and potential applications, are systematically summarized. In addition, the development prospects and challenges of phage-resistant bacteria are discussed. This review provides a useful reference for developing phage-resistant bacteria.
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Affiliation(s)
| | - Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
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11
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Yadav M, Ghosh S, Sen U. Crystal structure of the complex between cyclic-di-inosine monophosphate and the Vibrio cholerae standalone phosphodiesterase (VcEAL) at 2.2 Å. Biochem Biophys Res Commun 2024; 737:150535. [PMID: 39137586 DOI: 10.1016/j.bbrc.2024.150535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 08/15/2024]
Abstract
Cyclic dinucleotides (CDNs) are a significant and expanding class of secondary messengers that influence several vital bacterial physiological functions. Therefore, an understanding of the process by which CDNs are degraded by their cognate PDEs is crucial for comprehending a variety of cellular processes, such as the formation and dissemination of biofilms. As an alternative, it might be beneficial to create and/or identify non-hydrolyzable CDN derivatives to employ them as chemical probes of cyclic-di-GMP (c-di-GMP) signaling. Cyclic-di-inosine monophosphate, or c-di-IMP, is not a naturally occurring signaling molecule in biological systems, but it has strong adjuvant effects on metazoans and functions as an immunological modulator and stimulant. Here we report the first structural details of c-di-IMP and EAL interaction through high-resolution (2.2 Å) crystal structure of VcEAL in complex with c-di-IMP + Ca2+. Comparison of the VcEAL structures bound with cyclic-di-GMP (c-di-GMP), 3',5'-cyclic-AMP-GMP (cGAMP) and c-di-IMP and the structural variations at the chemical level between these CDNs provides their structural basis of recognition and rate of hydrolysis.
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Affiliation(s)
- Malti Yadav
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata, 700064, India
| | - Shrestha Ghosh
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata, 700064, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata, 700064, India.
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Samir S, Elshereef AA, Alva V, Hahn J, Dubnau D, Galperin MY, Selim KA. ComFB, a new widespread family of c-di-NMP receptor proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.10.622515. [PMID: 39574629 PMCID: PMC11581024 DOI: 10.1101/2024.11.10.622515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Cyclic dimeric GMP (c-di-GMP) is a widespread bacterial second messenger that controls a variety of cellular functions, including protein and polysaccharide secretion, motility, cell division, cell development, and biofilm formation, and contributes to the virulence of some important bacterial pathogens. While the genes for diguanylate cyclases and c-di-GMP hydrolases (active or mutated) can be easily identified in microbial genomes, the list of c-di-GMP receptor domains is quite limited, and only two of them, PliZ and MshEN, are found across multiple bacterial phyla. Recently, a new c-di-GMP receptor protein, named CdgR or ComFB, has been identified in cyanobacteria and shown to regulate their cell size and, more recently, natural competence. Sequence and structural analysis indicated that CdgR is part of a widespread ComFB protein family, named after the "late competence development protein ComFB" from Bacillus subtilis. This prompted the suggestion that ComFB and ComFB-like proteins could also be c-di-GMP receptors. Indeed, we revealed that ComFB proteins from Gram-positive B. subtilis and Thermoanaerobacter brockii were able to bind c-di-GMP with high-affinity. The ability to bind c-di-GMP was also demonstrated for the ComFB proteins from clinically relevant Gram-negative bacteria Vibrio cholerae and Treponema denticola. These observations indicate that the ComFB family serves as yet another widespread family of bacterial c-di-GMP receptors. Incidentally, some ComFB proteins were also capable of c-di-AMP binding, identifying them as a unique family of c-di-NMP receptor proteins. The overexpression of comFB in B. subtilis, combined with an elevated concentration of c-di-GMP, suppressed motility, attesting to the biological relevance of ComFB as a c-di-GMP binding protein.
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Affiliation(s)
- Sherihan Samir
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence “Controlling Microbes to Fight Infections”, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Abdalla A. Elshereef
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence “Controlling Microbes to Fight Infections”, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Germany
| | - Jeanette Hahn
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, New Jersey, USA
| | - David Dubnau
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, New Jersey, USA
| | - Michael Y. Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Khaled A. Selim
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence “Controlling Microbes to Fight Infections”, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
- Institute of Phototroph Microbiology, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
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13
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Li D, Xiao Y, Fedorova I, Xiong W, 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 signals from TIR and cGAS-like enzymes. Nature 2024; 635:719-727. [PMID: 39478223 DOI: 10.1038/s41586-024-08122-4] [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: 11/08/2023] [Accepted: 09/26/2024] [Indexed: 11/06/2024]
Abstract
Prokaryotic anti-phage immune systems use TIR and cGAS-like enzymes to produce 1''-3'-glycocyclic ADP-ribose (1''-3'-gcADPR) and cyclic dinucleotide (CDN) and cyclic trinucleotide (CTN) signalling molecules, respectively, which limit phage replication1-3. However, how phages neutralize these distinct and common systems is largely unclear. Here we show that the Thoeris anti-defence proteins Tad14 and Tad25 both achieve anti-cyclic-oligonucleotide-based anti-phage signalling system (anti-CBASS) activity by simultaneously sequestering CBASS cyclic oligonucleotides. Apart from binding to the Thoeris signals 1''-3'-gcADPR and 1''-2'-gcADPR, Tad1 also binds to numerous CBASS CDNs and CTNs with high affinity, inhibiting CBASS systems that use these molecules in vivo and in vitro. The hexameric Tad1 has six binding sites for CDNs or gcADPR, which are independent of the two high-affinity binding sites for CTNs. Tad2 forms a tetramer that also sequesters various CDNs in addition to gcADPR molecules, using distinct binding sites to simultaneously bind to these signals. Thus, Tad1 and Tad2 are both two-pronged inhibitors that, alongside anti-CBASS protein 2 (Acb26-8), establish a paradigm of phage proteins that use distinct binding sites to flexibly sequester a considerable breadth of cyclic nucleotides.
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Affiliation(s)
- Dong Li
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yu Xiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Iana Fedorova
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Weijia Xiong
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yu Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xi Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 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, China
| | - Zirui Gao
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xingyu Zhao
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xueli Cao
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yi Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Yue Feng
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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14
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Liu X, Zou L, Li B, Di Martino P, Rittschof D, Yang JL, Maki J, Liu W, Gu JD. Chemical signaling in biofilm-mediated biofouling. Nat Chem Biol 2024; 20:1406-1419. [PMID: 39349970 DOI: 10.1038/s41589-024-01740-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/14/2024] [Indexed: 10/27/2024]
Abstract
Biofouling is the undesirable accumulation of living organisms and their metabolites on submerged surfaces. Biofouling begins with adhesion of biomacromolecules and/or microorganisms and can lead to the subsequent formation of biofilms that are predominantly regulated by chemical signals, such as cyclic dinucleotides and quorum-sensing molecules. Biofilms typically release chemical cues that recruit or repel other invertebrate larvae and algal spores. As such, harnessing the biochemical mechanisms involved is a promising avenue for controlling biofouling. Here, we discuss how chemical signaling affects biofilm formation and dispersion in model species. We also examine how this translates to marine biofouling. Both inductive and inhibitory effects of chemical cues from biofilms on macrofouling are also discussed. Finally, we outline promising mitigation strategies by targeting chemical signaling to foster biofilm dispersion or inhibit biofouling.
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Affiliation(s)
- Xiaobo Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China.
| | - Ling Zou
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Boqiao Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Patrick Di Martino
- Groupe Biofilm et Comportement Microbien aux Interfaces, Laboratoire ERRMECe, Cergy Paris Université, Cergy-Pontoise, France
| | - Daniel Rittschof
- Duke Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
| | - Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - James Maki
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
| | - Ji-Dong Gu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou, China.
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, China.
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15
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Menendez-Gil P, Veleva D, Virgo M, Zhang J, Ramalhete R, Ho BT. Modulation of Vibrio cholerae gene expression through conjugative delivery of engineered regulatory small RNAs. J Bacteriol 2024; 206:e0014224. [PMID: 39292012 PMCID: PMC11500501 DOI: 10.1128/jb.00142-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
The increase in antibiotic resistance in bacteria has prompted the efforts in developing new alternative strategies for pathogenic bacteria. We explored the feasibility of targeting Vibrio cholerae by neutralizing bacterial cellular processes rather than outright killing the pathogen. We investigated the efficacy of delivering engineered regulatory small RNAs (sRNAs) to modulate gene expression through DNA conjugation. As a proof of concept, we engineered several sRNAs targeting the type VI secretion system (T6SS), several of which were able to successfully knockdown the T6SS activity at different degrees. Using the same strategy, we modulated exopolysaccharide production and motility. Lastly, we delivered an sRNA targeting T6SS into V. cholerae via conjugation and observed a rapid knockdown of the T6SS activity. Coupling conjugation with engineered sRNAs represents a novel way of modulating gene expression in V. cholerae opening the door for the development of novel prophylactic and therapeutic applications. IMPORTANCE Given the prevalence of antibiotic resistance, there is an increasing need to develop alternative approaches to managing pathogenic bacteria. In this work, we explore the feasibility of modulating the expression of various cellular systems in Vibrio cholerae using engineered regulatory sRNAs delivered into cells via DNA conjugation. These sRNAs are based on regulatory sRNAs found in V. cholerae and exploit its native regulatory machinery. By delivering these sRNAs conjugatively along with a real-time marker for DNA transfer, we found that complete knockdown of a targeted cellular system could be achieved within one cell division cycle after sRNA gene delivery. These results indicate that conjugative delivery of engineered regulatory sRNAs is a rapid and robust way of precisely targeting V. cholerae.
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Affiliation(s)
- Pilar Menendez-Gil
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
| | - Diana Veleva
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Mollie Virgo
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
| | - Jige Zhang
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Rita Ramalhete
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
| | - Brian T. Ho
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
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16
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Sudaryo V, Carvalho DR, Lee JM, Carozza JA, Cao X, Cordova AF, Li L. Toxicity of extracellular cGAMP and its analogs to T cells is due to SLC7A1-mediated import. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.21.614248. [PMID: 39386698 PMCID: PMC11463533 DOI: 10.1101/2024.09.21.614248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
STING agonists are promising innate immune therapies and can synergize with adaptive immune checkpoint blockade therapies for cancer treatment, but their effectiveness is limited by the toxicity to activated T cells. An important class of STING agonists are analogs of the endogenous STING agonist, cGAMP, and while transporters for these small molecules are known in some cell types, how they enter and kill T cells remains unknown. Here, we identify the cationic amino acid transporter SLC7A1 as the dominant transporter of cGAMP and its analogs in activated primary mouse and human T cells. T cells upregulate this transporter upon activation and rapid proliferation to meet their high metabolic demand, but this comes at the cost of enabling increased transport and toxicity of cGAMP. To circumvent the essentiality of SLC7A1 to proliferating T cells, we found that the residues responsible for cGAMP transport are separate from the arginine binding pocket allowing us to perturb cGAMP transport and STING-activation mediated killing without impacting arginine transport. These results suggest that SLC7A1 is a potential target for alleviating T cell toxicity associated with cGAMP and its analogs.
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17
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Vizzarro G, Lemopoulos A, Adams DW, Blokesch M. Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems. J Bacteriol 2024; 206:e0014524. [PMID: 39133004 PMCID: PMC11411939 DOI: 10.1128/jb.00145-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/15/2024] [Indexed: 08/13/2024] Open
Abstract
In response to predation by bacteriophages and invasion by other mobile genetic elements such as plasmids, bacteria have evolved specialized defense systems that are often clustered together on genomic islands. The O1 El Tor strains of Vibrio cholerae responsible for the ongoing seventh cholera pandemic (7PET) contain a characteristic set of genomic islands involved in host colonization and disease, many of which contain defense systems. Notably, Vibrio pathogenicity island 2 contains several characterized defense systems as well as a putative type I restriction-modification (T1RM) system, which, interestingly, is interrupted by two genes of unknown function. Here, we demonstrate that the T1RM system is active, methylates the host genomes of a representative set of 7PET strains, and identify a specific recognition sequence that targets non-methylated plasmids for restriction. We go on to show that the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes. Indeed, we show that this system has potent anti-phage activity against diverse members of the Tevenvirinae, a subfamily of bacteriophages with hypermodified genomes. Taken together, these results expand our understanding of how this highly conserved genomic island contributes to the defense of pandemic V. cholerae against foreign DNA. IMPORTANCE Defense systems are immunity systems that allow bacteria to counter the threat posed by bacteriophages and other mobile genetic elements. Although these systems are numerous and highly diverse, the most common types are restriction enzymes that can specifically recognize and degrade non-self DNA. Here, we show that the Vibrio pathogenicity island 2, present in the pathogen Vibrio cholerae, encodes two types of restriction systems that use distinct mechanisms to sense non-self DNA. The first system is a classical Type I restriction-modification system, and the second is a novel modification-dependent type IV restriction system that recognizes hypermodified cytosines. Interestingly, these systems are embedded within each other, suggesting that they are complementary to each other by targeting both modified and non-modified phages.
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Affiliation(s)
- Grazia Vizzarro
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexandre Lemopoulos
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - David William Adams
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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18
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Ma J, Xu H, Hou K, Cao Y, Xie D, Yan J, Dong W, Jiang T, Chen CP. Design and Synthesis of Cyclic Dinucleotide Analogues Containing Triazolyl C-Nucleosides. J Org Chem 2024; 89:11380-11393. [PMID: 39069788 DOI: 10.1021/acs.joc.4c01055] [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: 07/30/2024]
Abstract
Natural cyclic dinucleotide (CDN) is the secondary messenger involved in bacterial hemostasis, human innate immunity, and bacterial antiphage immunity. Synthetic CDN and its analogues are key molecular probes and potential immunotherapeutic agents. Several CDN analogues are under clinical research for antitumor immunotherapy. A myriad of synthetic methods have been developed and reported for the preparation of CDN and its analogues. However, most of the protocols require multiple steps, and only one CDN or its analogue is prepared at a time. In this study, a strategy based on a macrocyclic ribose phosphate skeleton containing a 1'-alkynyl group was designed and developed to prepare CDN analogues containing triazolyl C-nucleosides by click chemistry. Combinatorial application of click chemistry and the sulfenylation cascade to the macrocyclic skeleton expanded the diversity of the CDN analogues. This macrocyclic skeleton strategy rapidly and efficiently provides CDN analogues to facilitate research on microbiology, immunology, and immunotherapy.
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Affiliation(s)
- Jinliang Ma
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Hui Xu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Ke Hou
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Yaru Cao
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Di Xie
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Jiayin Yan
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Wenpei Dong
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Tao Jiang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Chang-Po Chen
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
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19
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Ledvina HE, Whiteley AT. Conservation and similarity of bacterial and eukaryotic innate immunity. Nat Rev Microbiol 2024; 22:420-434. [PMID: 38418927 PMCID: PMC11389603 DOI: 10.1038/s41579-024-01017-1] [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] [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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20
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Li H, Di X, Wang S, Li Q, Weng S, He J, Li C. Nucleic Acid Sensing by STING Induces an IFN-like Antiviral Response in a Marine Invertebrate. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1945-1957. [PMID: 38700419 DOI: 10.4049/jimmunol.2300669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/09/2024] [Indexed: 05/05/2024]
Abstract
The cytosolic detection of pathogen-derived nucleic acids has evolved as an essential strategy for host innate immune defense in mammals. One crucial component in this process is the stimulator of IFN genes (STING), which acts as a vital signaling adaptor, connecting the cytosolic detection of DNA by cyclic GMP-AMP (cGAMP) synthase (cGAS) to the downstream type I IFN signaling pathway. However, this process remains elusive in invertebrates. In this study, we present evidence demonstrating that STING, an ortholog found in a marine invertebrate (shrimp) called Litopenaeus vannamei, can directly detect DNA and initiate an IFN-like antiviral response. Unlike its homologs in other eukaryotic organisms, which exclusively function as sensors for cyclic dinucleotides, shrimp STING has the ability to bind to both double-stranded DNA and cyclic dinucleotides, including 2'3'-cGAMP. In vivo, shrimp STING can directly sense DNA nucleic acids from an infected virus, accelerate IFN regulatory factor dimerization and nuclear translocation, induce the expression of an IFN functional analog protein (Vago4), and finally establish an antiviral state. Taken together, our findings unveil a novel double-stranded DNA-STING-IKKε-IRF-Vago antiviral axis in an arthropod, providing valuable insights into the functional origins of DNA-sensing pathways in evolution.
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Affiliation(s)
- Haoyang Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Xuanzheng Di
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Sheng Wang
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Qinyao Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol/Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering/Guangdong Provincial Key Laboratory of Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangzhou, China
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21
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Yan Y, Xiao J, Huang F, Xian W, Yu B, Cheng R, Wu H, Lu X, Wang X, Huang W, Li J, Oyejobi GK, Robinson CV, Wu H, Wu D, Liu X, Wang L, Zhu B. Phage defence system CBASS is regulated by a prokaryotic E2 enzyme that imitates the ubiquitin pathway. Nat Microbiol 2024; 9:1566-1578. [PMID: 38649411 DOI: 10.1038/s41564-024-01684-z] [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: 10/15/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
The cyclic-oligonucleotide-based anti-phage signalling system (CBASS) is a type of innate prokaryotic immune system. Composed of a cyclic GMP-AMP synthase (cGAS) and CBASS-associated proteins, CBASS uses cyclic oligonucleotides to activate antiviral immunity. One major class of CBASS contains a homologue of eukaryotic ubiquitin-conjugating enzymes, which is either an E1-E2 fusion or a single E2. However, the functions of single E2s in CBASS remain elusive. Here, using biochemical, genetic, cryo-electron microscopy and mass spectrometry investigations, we discover that the E2 enzyme from Serratia marcescens regulates cGAS by imitating the ubiquitination cascade. This includes the processing of the cGAS C terminus, conjugation of cGAS to a cysteine residue, ligation of cGAS to a lysine residue, cleavage of the isopeptide bond and poly-cGASylation. The poly-cGASylation activates cGAS to produce cGAMP, which acts as an antiviral signal and leads to cell death. Thus, our findings reveal a unique regulatory role of E2 in CBASS.
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Affiliation(s)
- Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Xiao
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.
| | - Wei Xian
- Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjing Huang
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jing Li
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Greater Kayode Oyejobi
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Xiaoyun Liu
- Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China.
| | - Longfei Wang
- Department of Cardiovascular Surgery, Taikang Center for Life and Medical Sciences Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China.
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22
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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; 9:1579-1592. [PMID: 38589469 PMCID: PMC11153139 DOI: 10.1038/s41564-024-01670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [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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23
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Manisha Y, Srinivasan M, Jobichen C, Rosenshine I, Sivaraman J. Sensing for survival: specialised regulatory mechanisms of Type III secretion systems in Gram-negative pathogens. Biol Rev Camb Philos Soc 2024; 99:837-863. [PMID: 38217090 DOI: 10.1111/brv.13047] [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] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/15/2024]
Abstract
For centuries, Gram-negative pathogens have infected the human population and been responsible for numerous diseases in animals and plants. Despite advancements in therapeutics, Gram-negative pathogens continue to evolve, with some having developed multi-drug resistant phenotypes. For the successful control of infections caused by these bacteria, we need to widen our understanding of the mechanisms of host-pathogen interactions. Gram-negative pathogens utilise an array of effector proteins to hijack the host system to survive within the host environment. These proteins are secreted into the host system via various secretion systems, including the integral Type III secretion system (T3SS). The T3SS spans two bacterial membranes and one host membrane to deliver effector proteins (virulence factors) into the host cell. This multifaceted process has multiple layers of regulation and various checkpoints. In this review, we highlight the multiple strategies adopted by these pathogens to regulate or maintain virulence via the T3SS, encompassing the regulation of small molecules to sense and communicate with the host system, as well as master regulators, gatekeepers, chaperones, and other effectors that recognise successful host contact. Further, we discuss the regulatory links between the T3SS and other systems, like flagella and metabolic pathways including the tricarboxylic acid (TCA) cycle, anaerobic metabolism, and stringent cell response.
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Affiliation(s)
- Yadav Manisha
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Mahalashmi Srinivasan
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Chacko Jobichen
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - J Sivaraman
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
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24
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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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25
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Ma XY, Chen MM, Meng LH. Second messenger 2'3'-cyclic GMP-AMP (2'3'-cGAMP): the cell autonomous and non-autonomous roles in cancer progression. Acta Pharmacol Sin 2024; 45:890-899. [PMID: 38177693 PMCID: PMC11053103 DOI: 10.1038/s41401-023-01210-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024]
Abstract
Cytosolic double-stranded DNA (dsDNA) is frequently accumulated in cancer cells due to chromosomal instability or exogenous stimulation. Cyclic GMP-AMP synthase (cGAS) acts as a cytosolic DNA sensor, which is activated upon binding to dsDNA to synthesize the crucial second messenger 2'3'-cyclic GMP-AMP (2'3'-cGAMP) that in turn triggers stimulator of interferon genes (STING) signaling. The canonical role of cGAS-cGAMP-STING pathway is essential for innate immunity and viral defense. Recent emerging evidence indicates that 2'3'-cGAMP plays an important role in cancer progression via cell autonomous and non-autonomous mechanisms. Beyond its role as an intracellular messenger to activate STING signaling in tumor cells, 2'3'-cGAMP also serves as an immunotransmitter produced by cancer cells to modulate the functions of non-tumor cells especially immune cells in the tumor microenvironment by activating STING signaling. In this review, we summarize the synthesis, transmission, and degradation of 2'3'-cGAMP as well as the dual functions of 2'3'-cGAMP in a STING-dependent manner. Additionally, we discuss the potential therapeutic strategies that harness the cGAMP-mediated antitumor response for cancer therapy.
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Affiliation(s)
- Xiao-Yu Ma
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Man-Man Chen
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling-Hua Meng
- Division of Anti-tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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26
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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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27
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Li Q, Wu P, Du Q, Hanif U, Hu H, Li K. cGAS-STING, an important signaling pathway in diseases and their therapy. MedComm (Beijing) 2024; 5:e511. [PMID: 38525112 PMCID: PMC10960729 DOI: 10.1002/mco2.511] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Since cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway was discovered in 2013, great progress has been made to elucidate the origin, function, and regulating mechanism of cGAS-STING signaling pathway in the past decade. Meanwhile, the triggering and transduction mechanisms have been continuously illuminated. cGAS-STING plays a key role in human diseases, particularly DNA-triggered inflammatory diseases, making it a potentially effective therapeutic target for inflammation-related diseases. Here, we aim to summarize the ancient origin of the cGAS-STING defense mechanism, as well as the triggers, transduction, and regulating mechanisms of the cGAS-STING. We will also focus on the important roles of cGAS-STING signal under pathological conditions, such as infections, cancers, autoimmune diseases, neurological diseases, and visceral inflammations, and review the progress in drug development targeting cGAS-STING signaling pathway. The main directions and potential obstacles in the regulating mechanism research and therapeutic drug development of the cGAS-STING signaling pathway for inflammatory diseases and cancers will be discussed. These research advancements expand our understanding of cGAS-STING, provide a theoretical basis for further exploration of the roles of cGAS-STING in diseases, and open up new strategies for targeting cGAS-STING as a promising therapeutic intervention in multiple diseases.
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Affiliation(s)
- Qijie Li
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
| | - Ping Wu
- Department of Occupational DiseasesThe Second Affiliated Hospital of Chengdu Medical College (China National Nuclear Corporation 416 Hospital)ChengduSichuanChina
| | - Qiujing Du
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
| | - Ullah Hanif
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
| | - Hongbo Hu
- Center for Immunology and HematologyState Key Laboratory of BiotherapyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Ka Li
- Sichuan province Medical and Engineering Interdisciplinary Research Center of Nursing & Materials/Nursing Key Laboratory of Sichuan ProvinceWest China Hospital, Sichuan University/West China School of NursingSichuan UniversityChengduSichuanChina
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28
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Liu C, Shi R, Jensen MS, Zhu J, Liu J, Liu X, Sun D, Liu W. The global regulation of c-di-GMP and cAMP in bacteria. MLIFE 2024; 3:42-56. [PMID: 38827514 PMCID: PMC11139211 DOI: 10.1002/mlf2.12104] [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: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/09/2023] [Indexed: 06/04/2024]
Abstract
Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in bacteria. The best-studied examples are cyclic AMP (cAMP) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), which both act as global regulators. Global regulatory frameworks of c-di-GMP and cAMP in bacteria show several parallels but also significant variances. In this review, we illustrate the global regulatory models of the two nucleotide second messengers, compare the different regulatory frameworks between c-di-GMP and cAMP, and discuss the mechanisms and physiological significance of cross-regulation between c-di-GMP and cAMP. c-di-GMP responds to numerous signals dependent on a great number of metabolic enzymes, and it regulates various signal transduction pathways through its huge number of effectors with varying activities. In contrast, due to the limited quantity, the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse signals. cAMP performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein (CRP) in most bacteria. This review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes, providing theoretical guidelines for future research.
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Affiliation(s)
- Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Rui Shi
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Marcus S. Jensen
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Xiaobo Liu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information TechnologyNanjing University of Science and TechnologyNanjingChina
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
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29
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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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30
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Jusufovic N, Krusenstjerna AC, Savage CR, Saylor TC, Brissette CA, Zückert WR, Schlax PJ, Motaleb MA, Stevenson B. Borrelia burgdorferi PlzA is a cyclic-di-GMP dependent DNA and RNA binding protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.30.526351. [PMID: 36778503 PMCID: PMC9915621 DOI: 10.1101/2023.01.30.526351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The PilZ domain-containing protein, PlzA, is the only known cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here we report that PlzA can bind DNA and RNA and that nucleic acid binding requires c-di-GMP, with the affinity of PlzA for nucleic acids increasing as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. We also determined that PlzA interacts predominantly with the major groove of DNA and that sequence length plays a role in DNA binding affinity. PlzA is a dual-domain protein with a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle direct PlzA binding to regulatory targets.
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Affiliation(s)
- Nerina Jusufovic
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Andrew C. Krusenstjerna
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Christina R. Savage
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Timothy C. Saylor
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58203-9061, USA
| | - Wolfram R. Zückert
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Paula J. Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240-6030, USA
| | - Md A. Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834-435, USA
| | - Brian Stevenson
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
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31
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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: 19] [Impact Index Per Article: 19.0] [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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Jenson JM, Chen ZJ. cGAS goes viral: A conserved immune defense system from bacteria to humans. Mol Cell 2024; 84:120-130. [PMID: 38181755 PMCID: PMC11168419 DOI: 10.1016/j.molcel.2023.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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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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: 3] [Impact Index Per Article: 3.0] [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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34
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Cancino-Diaz ME, Guerrero-Barajas C, Betanzos-Cabrera G, Cancino-Diaz JC. Nucleotides as Bacterial Second Messengers. Molecules 2023; 28:7996. [PMID: 38138485 PMCID: PMC10745434 DOI: 10.3390/molecules28247996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In addition to comprising monomers of nucleic acids, nucleotides have signaling functions and act as second messengers in both prokaryotic and eukaryotic cells. The most common example is cyclic AMP (cAMP). Nucleotide signaling is a focus of great interest in bacteria. Cyclic di-AMP (c-di-AMP), cAMP, and cyclic di-GMP (c-di-GMP) participate in biological events such as bacterial growth, biofilm formation, sporulation, cell differentiation, motility, and virulence. Moreover, the cyclic-di-nucleotides (c-di-nucleotides) produced in pathogenic intracellular bacteria can affect eukaryotic host cells to allow for infection. On the other hand, non-cyclic nucleotide molecules pppGpp and ppGpp are alarmones involved in regulating the bacterial response to nutritional stress; they are also considered second messengers. These second messengers can potentially be used as therapeutic agents because of their immunological functions on eukaryotic cells. In this review, the role of c-di-nucleotides and cAMP as second messengers in different bacterial processes is addressed.
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Affiliation(s)
- Mario E. Cancino-Diaz
- Departamentos Microbiología and Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, Ciudad de México 11350, Mexico
| | - Claudia Guerrero-Barajas
- Departamento de Bioprocesos, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto, La Laguna Ticoman, Gustavo A. Madero, Ciudad de México 07340, Mexico;
| | - Gabriel Betanzos-Cabrera
- Área Académica de Nutrición y Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Actopan Camino a Tilcuautla s/n, Pueblo San Juan Tilcuautla, Pachuca Hidalgo 42160, Mexico;
| | - Juan C. Cancino-Diaz
- Departamentos Microbiología and Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, Ciudad de México 11350, Mexico
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35
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Fung DK, Trinquier AE, Wang JD. Crosstalk between (p)ppGpp and other nucleotide second messengers. Curr Opin Microbiol 2023; 76:102398. [PMID: 37866203 PMCID: PMC10842992 DOI: 10.1016/j.mib.2023.102398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023]
Abstract
In response to environmental cues, bacteria produce intracellular nucleotide messengers to regulate a wide variety of cellular processes and physiology. Studies on individual nucleotide messengers, such as (p)ppGpp or cyclic (di)nucleotides, have established their respective regulatory themes. As research on nucleotide signaling networks expands, recent studies have begun to uncover various crosstalk mechanisms between (p)ppGpp and other nucleotide messengers, including signal conversion, allosteric regulation, and target competition. The multiple layers of crosstalk implicate that (p)ppGpp is intricately linked to different nucleotide signaling pathways. From a physiological perspective, (p)ppGpp crosstalk enables fine-tuning and feedback regulation with other nucleotide messengers to achieve optimal adaptation.
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Affiliation(s)
- Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aude E Trinquier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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36
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Li D, Xiao Y, Xiong W, Fedorova I, Wang Y, Liu X, Huiting E, Ren J, Gao Z, Zhao X, Cao X, Zhang Y, Bondy-Denomy J, Feng Y. Single phage proteins sequester TIR- and cGAS-generated signaling molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567273. [PMID: 38014003 PMCID: PMC10680739 DOI: 10.1101/2023.11.15.567273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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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Zhang Q, Alter T, Strauch E, Hammerl JA, Schwartz K, Borowiak M, Deneke C, Fleischmann S. Genetic and Phenotypic Virulence Potential of Non-O1/Non-O139 Vibrio cholerae Isolated from German Retail Seafood. Microorganisms 2023; 11:2751. [PMID: 38004762 PMCID: PMC10672755 DOI: 10.3390/microorganisms11112751] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Non-O1 and non-O139 Vibrio cholerae (NOVC) can cause gastrointestinal infections in humans. Contaminated food, especially seafood, is an important source of human infections. In this study, the virulence potential of 63 NOVC strains isolated from retail seafood were characterized at the genotypic and phenotypic levels. Although no strain encoded the cholera toxin (CTX) and the toxin-coregulated pilus (TCP), several virulence factors, including the HlyA hemolysin, the cholix toxin ChxA, the heat-stable enterotoxin Stn, and genes coding for the type 3 and type 6 secretion systems, were detected. All strains showed hemolytic activity against human and sheep erythrocytes: 90% (n = 57) formed a strong biofilm, 52% (n = 33) were highly motile at 37 °C, and only 8% (n = 5) and 14% (n = 9) could resist ≥60% and ≥40% human serum, respectively. Biofilm formation and toxin regulation genes were also detected. cgMLST analysis demonstrated that NOVC strains from seafood cluster with clinical NOVC strains. Antimicrobial susceptibility testing (AST) results in the identification of five strains that developed non-wildtype phenotypes (medium and resistant) against the substances of the classes of beta-lactams (including penicillin, carbapenem, and cephalosporin), polymyxins, and sulphonamides. The phenotypic resistance pattern could be partially attributed to the acquired resistance determinants identified via in silico analysis. Our results showed differences in the virulence potential of the analyzed NOVC isolated from retail seafood products, which may be considered for further pathogenicity evaluation and the risk assessment of NOVC isolates in future seafood monitoring.
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Affiliation(s)
- Quantao Zhang
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Eckhard Strauch
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Jens Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Keike Schwartz
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Maria Borowiak
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Susanne Fleischmann
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
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38
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Huang Y, Liu B, Sinha SC, Amin S, Gan L. Mechanism and therapeutic potential of targeting cGAS-STING signaling in neurological disorders. Mol Neurodegener 2023; 18:79. [PMID: 37941028 PMCID: PMC10634099 DOI: 10.1186/s13024-023-00672-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/10/2023] Open
Abstract
DNA sensing is a pivotal component of the innate immune system that is responsible for detecting mislocalized DNA and triggering downstream inflammatory pathways. Among the DNA sensors, cyclic GMP-AMP synthase (cGAS) is a primary player in detecting cytosolic DNA, including foreign DNA from pathogens and self-DNA released during cellular damage, culminating in a type I interferon (IFN-I) response through stimulator of interferon genes (STING) activation. IFN-I cytokines are essential in mediating neuroinflammation, which is widely observed in CNS injury, neurodegeneration, and aging, suggesting an upstream role for the cGAS DNA sensing pathway. In this review, we summarize the latest developments on the cGAS-STING DNA-driven immune response in various neurological diseases and conditions. Our review covers the current understanding of the molecular mechanisms of cGAS activation and highlights cGAS-STING signaling in various cell types of central and peripheral nervous systems, such as resident brain immune cells, neurons, and glial cells. We then discuss the role of cGAS-STING signaling in different neurodegenerative conditions, including tauopathies, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, as well as aging and senescence. Finally, we lay out the current advancements in research and development of cGAS inhibitors and assess the prospects of targeting cGAS and STING as therapeutic strategies for a wide spectrum of neurological diseases.
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Affiliation(s)
- Yige Huang
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Bangyan Liu
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Subhash C Sinha
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Sadaf Amin
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
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39
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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: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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40
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Severin GB, Ramliden MS, Ford KC, Van Alst AJ, Sanath-Kumar R, Decker KA, Hsueh BY, Chen G, Yoon SH, Demey LM, O'Hara BJ, Rhoades CR, DiRita VJ, Ng WL, Waters CM. Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion. mBio 2023; 14:e0087523. [PMID: 37623317 PMCID: PMC10653837 DOI: 10.1128/mbio.00875-23] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE To counteract infection with phage, bacteria have evolved a myriad of molecular defense systems. Some of these systems initiate a process called abortive infection, in which the infected cell kills itself to prevent phage propagation. However, such systems must be inhibited in the absence of phage infection to prevent spurious death of the host. Here, we show that the cyclic oligonucleotide based anti-phage signaling system (CBASS) accomplishes this by sensing intracellular folate molecules and only expressing this system in a group. These results enhance our understanding of the evolution of the seventh Vibrio cholerae pandemic and more broadly how bacteria defend themselves against phage infection.
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Affiliation(s)
- Geoffrey B. Severin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Miriam S. Ramliden
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Kathryne C. Ford
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Andrew J. Van Alst
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Ram Sanath-Kumar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Kaitlin A. Decker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Brian Y. Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Gong Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Soo Hun Yoon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Lucas M. Demey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Brendan J. O'Hara
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christopher R. Rhoades
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Victor J. DiRita
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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41
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Römling U. Cyclic di-GMP signaling-Where did you come from and where will you go? Mol Microbiol 2023; 120:564-574. [PMID: 37427497 DOI: 10.1111/mmi.15119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
Abstract
Microbes including bacteria are required to respond to their often continuously changing ecological niches in order to survive. While many signaling molecules are produced as seemingly circumstantial byproducts of common biochemical reactions, there are a few second messenger signaling systems such as the ubiquitous cyclic di-GMP second messenger system that arise through the synthesis of dedicated multidomain enzymes triggered by multiple diverse external and internal signals. Being one of the most numerous and widespread signaling system in bacteria, cyclic di-GMP signaling contributes to adjust physiological and metabolic responses in all available ecological niches. Those niches range from deep-sea and hydrothermal springs to the intracellular environment in human immune cells such as macrophages. This outmost adaptability is possible by the modularity of the cyclic di-GMP turnover proteins which enables coupling of enzymatic activity to the diversity of sensory domains and the flexibility in cyclic di-GMP binding sites. Nevertheless, commonly regulated fundamental microbial behavior include biofilm formation, motility, and acute and chronic virulence. The dedicated domains carrying out the enzymatic activity indicate an early evolutionary origin and diversification of "bona fide" second messengers such as cyclic di-GMP which is estimated to have been present in the last universal common ancestor of archaea and bacteria and maintained in the bacterial kingdom until today. This perspective article addresses aspects of our current view on the cyclic di-GMP signaling system and points to knowledge gaps that still await answers.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Song X, Wang M, Liu S, Liu H, Jiang A, Zou Y, Deng Y, Qin Q, Song Y, Zheng Y. A sequential scheme including PTT and 2'3'-cGAMP/CQ-LP reveals the antitumor immune function of PTT through the type I interferon pathway. Pharmacol Res 2023; 196:106939. [PMID: 37758101 DOI: 10.1016/j.phrs.2023.106939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/30/2023]
Abstract
Photothermal therapy (PTT) is a promising antitumor treatment that is easy to implement, minimally invasive, and precisely controllable, and evokes strong antitumor immunity. We believe that a thorough elucidation of its underlying antitumor immune mechanisms would contribute to the rational design of combination treatments with other antitumor strategies and consequently potentiate clinical use. In this study, PTT using indocyanine green (ICG) induced STING-dependent type I interferon (IFN) production in macrophages (RAW264.7 and bone marrow-derived macrophages (BMDMs)), as proven by the use of a STING inhibitor (C178), and triggered STING-independent type I IFN generation in tumor cells (CT26 and 4T1), which was inhibited by DNase pretreatment. A novel liposome coloaded with the STING agonist 2'3'-cGAMP (cGAMP) and chloroquine (CQ) was constructed to achieve synergistic effect with PTT, in which CQ increased cGAMP entrapment efficiency and prevented STING degradation after IFN signaling activation. The sequential combination treatment caused a significant increase in tumor cell apoptosis, probably due to interferon stimulating gene products 15 and 54 (ISG15 and ISG 54), and achieved a more striking antitumor inhibition effect in the CT26 tumor model than the 4T1 model, likely due to higher STAT1 expression and consequently more intense IFN signal transduction. In the tumor microenvironment, the combination treatment increased infiltrating CD8+T cells (4-fold) and M1-like TAMs (10-fold), and decreased M-MDSCs (over 2-fold) and M2-like TAMs (over 4-fold). Above all, in-depth exploration of the antitumor mechanism of PTT provides guidance for selecting sensitive tumor models and designing reasonable clinical schemes.
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Affiliation(s)
- Xiaoshuang Song
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mao Wang
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Simeng Liu
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Huimin Liu
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ailing Jiang
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yu Zou
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuchuan Deng
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qin Qin
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yiran Song
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yu Zheng
- Department of Biotherapy,Cancer Center and State Key Laboratory of Biotherapy,West China Hospital, Sichuan University, Chengdu 610041, China.
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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: 36] [Impact Index Per Article: 18.0] [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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44
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Chen S, He X, Qin Z, Li G, Wang W, Nai Z, Tian Y, Liu D, Jiang X. Loss in the Antibacterial Ability of a PyrR Gene Regulating Pyrimidine Biosynthesis after Using CRISPR/Cas9-Mediated Knockout for Metabolic Engineering in Lactobacillus casei. Microorganisms 2023; 11:2371. [PMID: 37894029 PMCID: PMC10609543 DOI: 10.3390/microorganisms11102371] [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: 09/01/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Lactobacillus casei (L. casei) has four possible mechanisms: antimicrobial antagonism, competitional adhesion, immunoregulation, and the inhibition of bacterial toxins. To delineate the metabolic reactions of nucleotides from L. casei that are associated with mechanisms of inhibiting pathogens and immunoregulation, we report that a PyrR-deficient L. casei strain was constructed using the CRISPR-Cas9D10A tool. Furthermore, there were some changes in its basic biological characterization, such as its growth curve, auxotroph, and morphological damage. The metabolic profiles of the supernatant between the PyrR-deficient and wild strains revealed the regulation of the synthesis of genetic material and of certain targeting pathways and metabolites. In addition, the characteristics of the PyrR-deficient strain were significantly altered as it lost the ability to inhibit the growth of pathogens. Moreover, we identified PyrR-regulating pyrimidine biosynthesis, which further improved its internalization and colocalization with macrophages. Evidence shows that the PyrR gene is a key active component in L. casei supernatants for the regulation of pyrimidine biosynthesis against a wide range of pathogens.
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Affiliation(s)
- Shaojun Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Ziliang Qin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Gang Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Wentao Wang
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Zida Nai
- College of Agriculture, Yanbian University, Yanji 133002, China
| | - Yaguang Tian
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Di Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Xinpeng Jiang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
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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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46
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Yang CS, Ko TP, Chen CJ, Hou MH, Wang YC, Chen Y. Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases. Nat Commun 2023; 14:5078. [PMID: 37604815 PMCID: PMC10442399 DOI: 10.1038/s41467-023-40787-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023] Open
Abstract
Purine-containing nucleotide second messengers regulate diverse cellular activities. Cyclic di-pyrimidines mediate anti-phage functions in bacteria; however, the synthesis mechanism remains elusive. Here, we determine the high-resolution structures of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases (CD-NTases) in clade E (CdnE) in its apo, substrate-, and intermediate-bound states. A conserved (R/Q)xW motif controlling the pyrimidine specificity of donor nucleotide is identified. Mutation of Trp or Arg from the (R/Q)xW motif to Ala rewires its specificity to purine nucleotides, producing mixed purine-pyrimidine cyclic dinucleotides (CDNs). Preferential binding of uracil over cytosine bases explains the product specificity of cyclic di-pyrimidine-synthesizing CdnE to cyclic di-UMP (cUU). Based on the intermediate-bound structures, a synthetic pathway for cUU containing a unique 2'3'-phosphodiester linkage through intermediate pppU[3'-5']pU is deduced. Our results provide a framework for pyrimidine selection and establish the importance of conserved residues at the C-terminal loop for the specificity determination of CD-NTases.
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Affiliation(s)
- Chia-Shin Yang
- Genomics BioSci & Tech Co. Ltd., New Taipei, 221, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, 406, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, 404, Taiwan
| | - Mei-Hui Hou
- Genomics BioSci & Tech Co. Ltd., New Taipei, 221, Taiwan
| | | | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.
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Coyle NM, O'Toole C, Thomas JCL, Ryder D, Feil EJ, Geary M, Bean TP, Joseph AW, Waine A, Cheslett D, Verner-Jeffreys DW. Vibrio aestuarianus clade A and clade B isolates are associated with Pacific oyster ( Magallana gigas) disease outbreaks across Ireland. Microb Genom 2023; 9:mgen001078. [PMID: 37540224 PMCID: PMC10483421 DOI: 10.1099/mgen.0.001078] [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: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Bacteria from the family Vibrionaceae have been implicated in mass mortalities of farmed Pacific oysters (Magallana gigas) in multiple countries, leading to substantial impairment of growth in the sector. In Ireland there has been concern that Vibrio have been involved in serious summer outbreaks. There is evidence that Vibrio aestuarianus is increasingly becoming the main pathogen of concern for the Pacific oyster industry in Ireland. While bacteria belonging to the Vibrio splendidus clade are also detected frequently in mortality episodes, their role in the outbreaks of summer mortality is not well understood. To identify and characterize strains involved in these outbreaks, 43 Vibrio isolates were recovered from Pacific oyster summer mass mortality episodes in Ireland from 2008 to 2015 and these were whole-genome sequenced. Among these, 25 were found to be V. aestuarianus (implicated in disease) and 18 were members of the V. splendidus species complex (role in disease undetermined). Two distinct clades of V. aestuarianus - clade A and clade B - were found that had previously been described as circulating within French oyster culture. The high degree of similarity between the Irish and French V. aestuarianus isolates points to translocation of the pathogen between Europe's two major oyster-producing countries, probably via trade in spat and other age classes. V. splendidus isolates were more diverse, but the data reveal a single clone of this species that has spread across oyster farms in Ireland. This underscores that Vibrio could be transmitted readily across oyster farms. The presence of V. aestuarianus clades A and B in not only France but also Ireland adds weight to growing concern that this pathogen is spreading and impacting Pacific oyster production within Europe.
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Affiliation(s)
- Nicola M. Coyle
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Ciar O'Toole
- Marine Institute, Oranmore, Co. Galway H91 R673, Ireland
| | - Jennifer C. L. Thomas
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - David Ryder
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Michelle Geary
- Marine Institute, Oranmore, Co. Galway H91 R673, Ireland
| | - Timothy P. Bean
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | | | - Ava Waine
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
- Newcastle University, School of Natural and Environmental Sciences, Newcastle Upon Tyne, NE1 7RU, UK
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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: 6] [Impact Index Per Article: 3.0] [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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49
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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: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [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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50
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Ghandour R, Papenfort K. Small regulatory RNAs in Vibrio cholerae. MICROLIFE 2023; 4:uqad030. [PMID: 37441523 PMCID: PMC10335731 DOI: 10.1093/femsml/uqad030] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Vibrio cholerae is a major human pathogen causing the diarrheal disease, cholera. Regulation of virulence in V. cholerae is a multifaceted process involving gene expression changes at the transcriptional and post-transcriptional level. Whereas various transcription factors have been reported to modulate virulence in V. cholerae, small regulatory RNAs (sRNAs) have now been established to also participate in virulence control and the regulation of virulence-associated processes, such as biofilm formation, quorum sensing, stress response, and metabolism. In most cases, these sRNAs act by base-pairing with multiple target transcripts and this process typically requires the aid of an RNA-binding protein, such as the widely conserved Hfq protein. This review article summarizes the functional roles of sRNAs in V. cholerae, their underlying mechanisms of gene expression control, and how sRNAs partner with transcription factors to modulate complex regulatory programs. In addition, we will discuss regulatory principles discovered in V. cholerae that not only apply to other Vibrio species, but further extend into the large field of RNA-mediated gene expression control in bacteria.
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Affiliation(s)
- Rabea Ghandour
- Friedrich Schiller University Jena, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Corresponding author. Institute of Microbiology, General Microbiology, Friedrich Schiller University Jena, Winzerlaer Straße 2, 07745 Jena, Germany. Tel: +49-3641-949-311; E-mail:
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