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Esteves NC, Scharf BE. Serratia marcescens ATCC 274 increases production of the red pigment prodigiosin in response to Chi phage infection. Sci Rep 2024; 14:17750. [PMID: 39085460 PMCID: PMC11291754 DOI: 10.1038/s41598-024-68747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024] Open
Abstract
Serratia marcescens is an opportunistic human pathogen that produces a vibrant red pigment called prodigiosin. Prodigiosin has implications in virulence of S. marcescens and promising clinical applications. We discovered that addition of the virulent flagellotropic bacteriophage χ (Chi) to a culture of S. marcescens stimulates a greater than fivefold overproduction of prodigiosin. Active phage infection is required for the effect, as a χ-resistant strain lacking flagella does not respond to phage presence. Via a reporter fusion assay, we have determined that the addition of a χ-induced S. marcescens cell lysate to an uninfected culture causes a threefold increase in transcription of the pig operon, containing genes essential for pigment biosynthesis. Replacement of the pig promoter with a constitutive promoter abolished the pigmentation increase, indicating that regulatory elements present in the pig promoter likely mediate the phenomenon. We hypothesize that S. marcescens detects the threat of phage-mediated cell death and reacts by producing prodigiosin as a stress response. Our findings are of clinical significance for two main reasons: (i) elucidating complex phage-host interactions is crucial for development of therapeutic phage treatments, and (ii) overproduction of prodigiosin in response to phage could be exploited for its biosynthesis and use as a pharmaceutical.
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Affiliation(s)
- Nathaniel C Esteves
- Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Birgit E Scharf
- Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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2
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Wu Z, Guo L, Wu Y, Yang M, Du S, Shao J, Zhang Z, Zhao Y. Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family. mSphere 2024; 9:e0045824. [PMID: 38926906 PMCID: PMC11288001 DOI: 10.1128/msphere.00458-24] [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: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Bacteriophages play an essential role in shaping the diversity and metabolism of bacterial communities. Marine Roseobacter group is an abundant heterotrophic bacterial group that is involved in many major element cycles, especially carbon and sulfur. Members of the Roseobacter CHUG (Clade Hidden and Underappreciated Globally) lineage are globally distributed and are activated in pelagic marine environments. In this study, we isolated and characterized a phage, CRP-810, that infects the CHUG strain FZCC0198. The genome of CRP-810 was dissimilar to those of other known phages. Additionally, 251 uncultured viral genomes (UViGs) closely related to CRP-810 were obtained from the uncultivated marine viral contig databases. Comparative genomic and phylogenetic analyses revealed that CRP-810 and these related UViGs exhibited conserved genome synteny, representing a new phage family with at least eight subgroups. Most of the CRP-810-type phages contain an integrase gene, and CRP-810 can be integrated into the host genome. Further analysis revealed that three CRP-810-type members were prophages found in the genomes of marine SAR11, Poseidonocella, and Sphingomonadaceae. Finally, viromic read-mapping analysis showed that CRP-810-type phages were globally distributed and displayed distinct biogeographic patterns related to temperature and latitude. Many members with a lower G + C content were mainly distributed in the trade station, whereas members with a higher G + C content were mainly distributed in polar and westerlies station, indicating that the niche differentiation of phages was subject to host adaptation. Collectively, these findings identify a novel phage family and expand our understanding of phylogenetic diversity, evolution, and biogeography of marine phages. IMPORTANCE The Roseobacter CHUG lineage, affiliated with the Pelagic Roseobacter Cluster (PRC), is widely distributed in the global oceans and is active in oligotrophic seawater. However, knowledge of the bacteriophages that infect CHUG members is limited. In this study, a CHUG phage, CRP-810, that infects the CHUG strain FZCC0198, was isolated and shown to have a novel genomic architecture. In addition, 251 uncultured viral genomes closely related to CRP-810 were recovered and included in the analyses. Phylogenomic analyses revealed that the CRP-810-type phages represent a new phage family containing at least eight genus-level subgroups. Members of this family were predicted to infect various marine bacteria. We also demonstrated that the CRP-810-type phages are widely distributed in global oceans and display distinct biogeographic patterns related to latitude. Collectively, this study provides important insights into the genomic organization, diversity, and ecology of a novel phage family that infect ecologically important bacteria in the global ocean.
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Affiliation(s)
- Zuqing Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Luyuan Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiabing Shao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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3
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Li X, Zhang C, Li S, Liang S, Xu X, Zhao Z. Quorum sensing positively regulates CPS-dependent Autographiviridae phage infection in Vibrio alginolyticus. Appl Environ Microbiol 2024:e0221023. [PMID: 39072624 DOI: 10.1128/aem.02210-23] [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: 12/11/2023] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Quorum sensing (QS) orchestrates many bacterial behaviors, including virulence and biofilm formation, across bacterial populations. Nevertheless, the underlying mechanism by which QS regulates capsular polysaccharide (CPS)-dependent phage-bacterium interactions remains unclear. In this study, we report that QS upregulates the expression of CPS-dependent phage receptors, thus increasing phage adsorption and infection rates in Vibrio alginolyticus. We found that QS upregulated the expression of the ugd gene, leading to increased synthesis of Autographiviridae phage receptor CPS synthesis in V. alginolyticus. The signal molecule autoinducer-2 released by Vibrio from different sources can potentially enhance CPS-dependent phage infections. Therefore, our data suggest that inhibiting QS may reduce, rather than improve, the therapeutic efficacy of CPS-specific phages. IMPORTANCE Phage resistance is a direct threat to phage therapy, and understanding phage-host interactions, especially how bacteria block phage infection, is essential for developing successful phage therapy. In the present study, we demonstrate for the first time that Vibrio alginolyticus uses quorum sensing (QS) to promote capsular polysaccharide (CPS)-specific phage infection by upregulating ugd expression, which is necessary for the synthesis of Autographiviridae phage receptor CPS. Although increased CPS-specific phage susceptibility is a novel trade-off mediated by QS, it results in the upregulation of virulence factors, promoting biofilm development and enhanced capsular polysaccharide production in V. alginolyticus. This suggests that inhibiting QS may improve the effectiveness of antibiotic treatment, but it may also reduce the efficacy of phage therapy.
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Affiliation(s)
- Xixi Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Chen Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Shenao Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Sixuan Liang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Xuefei Xu
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
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4
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Beggs GA, Bassler BL. Phage small proteins play large roles in phage-bacterial interactions. Curr Opin Microbiol 2024; 80:102519. [PMID: 39047312 DOI: 10.1016/j.mib.2024.102519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/05/2024] [Accepted: 07/07/2024] [Indexed: 07/27/2024]
Abstract
Phages have wide influence on bacterial physiology, and likewise, bacterial processes impinge on phage biology. Key to these interactions are phage small proteins (<100 aa). Long underappreciated, recent work has revealed millions of phage small proteins, and increasingly, mechanisms by which they function to dictate phage and/or bacterial behavior and evolution. Here, we describe select phage small proteins that mediate phage-bacterial interactions by modulating phage lifestyle decision-making components or by altering host gene expression.
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Affiliation(s)
- Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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5
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Debatisse K, Lopez P, Poli M, Rousseau P, Campos M, Coddeville M, Cocaign-Bousquet M, Le Bourgeois P. Redefining the bacteriophage mv4 site-specific recombination system and the sequence specificity of its attB and core-attP sites. Mol Microbiol 2024; 121:1200-1216. [PMID: 38705589 DOI: 10.1111/mmi.15275] [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: 04/10/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024]
Abstract
Through their involvement in the integration and excision of a large number of mobile genetic elements, such as phages and integrative and conjugative elements (ICEs), site-specific recombination systems based on heterobivalent tyrosine recombinases play a major role in genome dynamics and evolution. However, despite hundreds of these systems having been identified in genome databases, very few have been described in detail, with none from phages that infect Bacillota (formerly Firmicutes). In this study, we reanalyzed the recombination module of Lactobacillus delbrueckii subsp. bulgaricus phage mv4, previously considered atypical compared with classical systems. Our results reveal that mv4 integrase is a 369 aa protein with all the structural hallmarks of recombinases from the Tn916 family and that it cooperatively interacts with its recombination sites. Using randomized DNA libraries, NGS sequencing, and other molecular approaches, we show that the 21-bp core-attP and attB sites have structural similarities to classical systems only if considering the nucleotide degeneracy, with two 7-bp inverted regions corresponding to mv4Int core-binding sites surrounding a 7-bp strand-exchange region. We also examined the different compositional constraints in the core-binding regions, which define the sequence space of permissible recombination sites.
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Affiliation(s)
- Kevin Debatisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Pierre Lopez
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Maryse Poli
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Philippe Rousseau
- CBI, LMGM, Université de Toulouse, CNRS, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Manuel Campos
- CBI, LMGM, Université de Toulouse, CNRS, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Michèle Coddeville
- CBI, LMGM, Université de Toulouse, CNRS, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
| | | | - Pascal Le Bourgeois
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Université Toulouse III - Paul Sabatier, Toulouse, France
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6
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de Melo AG, Morency C, Moineau S. Virulence-associated factors as targets for phage infection. Curr Opin Microbiol 2024; 79:102471. [PMID: 38569419 DOI: 10.1016/j.mib.2024.102471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
Bacterial pathogens can infect a wide range of hosts and pose a threat to public and animal health as well as to agriculture. The emergence of antibiotic-resistant strains has increased this risk by making the treatment of bacterial infections even more challenging. Pathogenic bacteria thrive in various ecological niches, but they can also be specifically targeted and killed by bacteriophages (phages). Lytic phages are now investigated and even used, in some cases, as alternatives or complements to antibiotics for preventing or treating bacterial infections (phage therapy). As such, it is key to identify factors responsible for phage specificity and efficiency. Here, we review recent advances in virulence-associated factors that are targeted by phages. We highlight components of the bacterial cell surface, effector systems, and motility structures exploited by phages and the effects of phages on cell aggregation and communication. We also look at the fitness trade-off of phage resistance.
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Affiliation(s)
- Alessandra G de Melo
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Carlee Morency
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Québec City, QC G1V 0A6, Canada; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC G1V 0A6, Canada.
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7
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Al-Faliti M, Wang P, Smith AL, Delgado Vela J. Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors. WATER RESEARCH 2024; 256:121620. [PMID: 38677036 DOI: 10.1016/j.watres.2024.121620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
Phage emit communication signals that inform their lytic and lysogenic life cycles. However, little is known regarding the abundance and diversity of the genes associated with phage communication systems in wastewater treatment microbial communities. This study focused on phage communities within two distinct biochemical wastewater environments, specifically aerobic membrane bioreactors (AeMBRs) and anaerobic membrane bioreactors (AnMBRs) exposed to varying antibiotic concentrations. Metagenomic data from the bench-scale systems were analyzed to explore phage phylogeny, life cycles, and genetic capacity for antimicrobial resistance and quorum sensing. Two dominant phage families, Schitoviridae and Peduoviridae, exhibited redox-dependent dynamics. Schitoviridae prevailed in anaerobic conditions, while Peduoviridae dominated in aerobic conditions. Notably, the abundance of lytic and lysogenic proteins varied across conditions, suggesting the coexistence of both life cycles. Furthermore, the presence of antibiotic resistance genes (ARGs) within viral contigs highlighted the potential for phage to transfer ARGs in AeMBRs. Finally, quorum sensing genes in the virome of AeMBRs indicated possible molecular signaling between phage and bacteria. Overall, this study provides insights into the dynamics of viral communities across varied redox conditions in MBRs. These findings shed light on phage life cycles, and auxiliary genetic capacity such as antibiotic resistance and bacterial quorum sensing within wastewater treatment microbial communities.
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Affiliation(s)
- Mitham Al-Faliti
- Department of Civil and Environmental Engineering, Howard University, Washington, D.C., USA
| | - Phillip Wang
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, D.C., USA.
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8
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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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9
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Wienhausen G, Moraru C, Bruns S, Tran DQ, Sultana S, Wilkes H, Dlugosch L, Azam F, Simon M. Ligand cross-feeding resolves bacterial vitamin B 12 auxotrophies. Nature 2024; 629:886-892. [PMID: 38720071 DOI: 10.1038/s41586-024-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/08/2024] [Indexed: 05/24/2024]
Abstract
Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes1,2. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics2-4. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Stefan Bruns
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.
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10
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Guo X, Wang X, Shi J, Ren J, Zeng J, Li J, Li Y. A review and new perspective on oral bacteriophages: manifestations in the ecology of oral diseases. J Oral Microbiol 2024; 16:2344272. [PMID: 38698893 PMCID: PMC11064738 DOI: 10.1080/20002297.2024.2344272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/05/2024] Open
Abstract
Objective To explore the manifestations of bacteriophages in different oral disease ecologies, including periodontal diseases, dental caries, endodontic infections, and oral cancer, as well as to propel phage therapy for safer and more effective clinical application in the field of dentistry. Methods In this literature review, we outlined interactions between bacteriophages, bacteria and even oral cells in the oral ecosystem, especially in disease states. We also analyzed the current status and future prospects of phage therapy in the perspective of different oral diseases. Results Various oral bacteriophages targeting at periodontal pathogens as Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola and Aggregatibacter actinomycetemcomitans, cariogenic pathogen Streptococcus mutans, endodontic pathogen Enterococcus faecalis were predicted or isolated, providing promising options for phage therapy. In the realm of oral cancer, aside from displaying tumor antigens or participating in tumor-targeted therapies, phage-like particle vaccines demonstrated the potential to prevent oral infections caused by human papillomaviruses (HPVs) associated with head-and-neck cancers. Conclusion Due to their intricate interactions with bacteria and oral cells, bacteriophages are closely linked to the progression and regression of diverse oral diseases. And there is an urgent need for research to explore additional possibilities of bacteriophages in the management of oral diseases.
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Affiliation(s)
- Xinyu Guo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaowan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiayi Ren
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Center for Archaeological Science, Sichuan University, Chengdu, China
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11
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Baaziz H, Makhlouf R, McClelland M, Hsu BB. Bacterial resistance to temperate phage is influenced by the frequency of lysogenic establishment. iScience 2024; 27:109595. [PMID: 38623331 PMCID: PMC11016777 DOI: 10.1016/j.isci.2024.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024] Open
Abstract
Temperate phages can shape bacterial community dynamics and evolution through lytic and lysogenic life cycles. In response, bacteria that resist phage infection can emerge. This study explores phage-based factors that influence bacterial resistance using a model system of temperate P22 phage and Salmonella both inside and outside the mammalian host. Phages that remained functional despite gene deletions had minimal impact on lysogeny and phage resistance except for deletions in the immI region that substantially reduced lysogeny and increased phage resistance to levels comparable to that observed with an obligately lytic P22. This immI deletion does not make the lysogen less competitive but instead increases the frequency of bacterial lysis. Thus, subtle changes in the balance between lysis and lysogeny during the initial stages of infection can significantly influence the extent of phage resistance in the bacterial population. Our work highlights the complex nature of the phage-bacteria-mammalian host triad.
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Affiliation(s)
- Hiba Baaziz
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rita Makhlouf
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Bryan B. Hsu
- Department of Biological Sciences, Fralin Life Sciences Institute, Center for Emerging, and Zoonotic, Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
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12
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Roughgarden J. Lytic/Lysogenic Transition as a Life-History Switch. Virus Evol 2024; 10:veae028. [PMID: 38756985 PMCID: PMC11097211 DOI: 10.1093/ve/veae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.
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Affiliation(s)
- Joan Roughgarden
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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13
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Schmidtke DT, Hickey AS, Liachko I, Sherlock G, Bhatt AS. Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585998. [PMID: 38562748 PMCID: PMC10983915 DOI: 10.1101/2024.03.20.585998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The prototypic crAssphage (Carjivirus communis) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris, revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.
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Affiliation(s)
- Danica T. Schmidtke
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA, USA
- Senior author
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Division of Hematology), Stanford University, Stanford, CA, USA
- Lead corresponding author
- Senior author
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14
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Zhou Q, Mi K, Ma W, Feng F, Huo M, Sun Y, Huang L. Metagenomic analysis reveals impact of acyl homoserine endolipid-like signaling molecules on the aqueous sediment resistome under florfenicol stress. BIORESOURCE TECHNOLOGY 2024; 395:130318. [PMID: 38219924 DOI: 10.1016/j.biortech.2024.130318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
Quorum sensing potentially helps microorganisms adapt to antibiotic stress encountered in the environment. This experiment investigated the effect of acyl homoserine endolipid-like signaling molecules on microbial antibiotic resistance gene structures in aqueous sediments under florfenicol stress. Additional acyl homoserine endolipid-like signaling molecules (AHLs) alter the structure of multidrug resistance genes in florfenicol-stressed sediments, particularly the multidrug resistance efflux pump gene family. Prophages and integrative and conjugative elements (ICEs) determined the resistance genes structure, and pathways related to mobile genetic elements (MGEs) transfer may play an essential role in this process. The practical application of AHLs to regulate quorum sensing systems may alter bacterial stress responses to environmental florfenicol residues, thereby reducing the development of antibiotic resistance in the environment.
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Affiliation(s)
- Qin Zhou
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products,Whan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China|
| | - Kun Mi
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan 430070, China
| | - Wenjin Ma
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China
| | - Fenglin Feng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China|
| | - Meixia Huo
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China|
| | - Lingli Huang
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products,Whan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China.
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15
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Winans JB, Garcia SL, Zeng L, Nadell CD. Spatial propagation of temperate phages within and among biofilms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.571119. [PMID: 38187755 PMCID: PMC10769212 DOI: 10.1101/2023.12.20.571119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bacteria form groups comprised of cells and secreted adhesive matrix that controls their spatial organization. These groups - termed biofilms - can act as refuges from environmental disturbance and from biotic threats, including phages. Despite the ubiquity of temperate phages and bacterial biofilms, temperate phage propagation within biofilms has never been characterized on multicellular spatial scales. Here, we leverage several approaches to track temperate phages and distinguish between lytic and lysogenic infections. We determine that lysogeny within E. coli biofilms most often occurs within a predictable region of cell group architecture. Because lysogens are generally found on the periphery of large groups, where lytic viral activity also reduces local structural integrity, lysogens are predisposed to disperse and are over-represented in biofilms formed downstream of the original biofilm-phage system. Comparing our results with those for virulent phages reveals that the temperate phages possess previously unknown advantages for propagation in architecturally heterogeneous biofilm communities.
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16
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Dahan Y, Wingreen NS, Meir Y. The value of information gathering in phage-bacteria warfare. PNAS NEXUS 2024; 3:pgad431. [PMID: 38196923 PMCID: PMC10776245 DOI: 10.1093/pnasnexus/pgad431] [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: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Phages-viruses that infect bacteria-have evolved over billions of years to overcome bacterial defenses. Temperate phage, upon infection, can "choose" between two pathways: lysis-in which the phage create multiple new phage particles, which are then liberated by cell lysis, and lysogeny-where the phage's genetic material is added to the bacterial DNA and transmitted to the bacterial progeny. It was recently discovered that some phages can read information from the environment related to the density of bacteria or the number of nearby infection attempts. Such information may help phage make the right choice between the two pathways. Here, we develop a theoretical model that allows an infecting phage to change its strategy (i.e. the ratio of lysis to lysogeny) depending on an outside signal, and we find the optimal strategy that maximizes phage proliferation. While phages that exploit extra information naturally win in competition against phages with a fixed strategy, there may be costs to information, e.g. as the necessary extra genes may affect the growth rate of a lysogen or the burst size of new phage for the lysis pathway. Surprisingly, even when phages pay a large price for information, they can still maintain an advantage over phages that lack this information, indicating the high benefit of intelligence gathering in phage-bacteria warfare.
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Affiliation(s)
- Yuval Dahan
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yigal Meir
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
- Department of Physics, Princeton University, Princeton, NJ 08544, USA
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17
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Schwartzkopf CM, Taylor VL, Groleau MC, Faith DR, Schmidt AK, Lamma TL, Brooks DM, Déziel E, Maxwell KL, Secor PR. Inhibition of PQS signaling by the Pf bacteriophage protein PfsE enhances viral replication in Pseudomonas aeruginosa. Mol Microbiol 2024; 121:116-128. [PMID: 38038061 PMCID: PMC10842821 DOI: 10.1111/mmi.15202] [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: 08/29/2023] [Revised: 10/24/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023]
Abstract
Quorum sensing, a bacterial signaling system that coordinates group behaviors as a function of cell density, plays an important role in regulating viral (phage) defense mechanisms in bacteria. The opportunistic pathogen Pseudomonas aeruginosa is a model system for the study of quorum sensing. P. aeruginosa is also frequently infected by Pf prophages that integrate into the host chromosome. Upon induction, Pf phages suppress host quorum sensing systems; however, the physiological relevance and mechanism of suppression are unknown. Here, we identify the Pf phage protein PfsE as an inhibitor of Pseudomonas Quinolone Signal (PQS) quorum sensing. PfsE binds to the host protein PqsA, which is essential for the biosynthesis of the PQS signaling molecule. Inhibition of PqsA increases the replication efficiency of Pf virions when infecting a new host and when the Pf prophage switches from lysogenic replication to active virion replication. In addition to inhibiting PQS signaling, our prior work demonstrates that PfsE also binds to PilC and inhibits type IV pili extension, protecting P. aeruginosa from infection by type IV pili-dependent phages. Overall, this work suggests that the simultaneous inhibition of PQS signaling and type IV pili by PfsE may be a viral strategy to suppress host defenses to promote Pf replication while at the same time protecting the susceptible host from competing phages.
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Affiliation(s)
| | | | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Amelia K. Schmidt
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Tyrza L. Lamma
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Diane M. Brooks
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Karen L. Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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18
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Zamora-Caballero S, Chmielowska C, Quiles-Puchalt N, Brady A, Gallego Del Sol F, Mancheño-Bonillo J, Felipe-Ruíz A, Meijer WJJ, Penadés JR, Marina A. Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision. Nat Microbiol 2024; 9:161-172. [PMID: 38177302 PMCID: PMC10769878 DOI: 10.1038/s41564-023-01550-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Phages can use a small-molecule communication arbitrium system to coordinate lysis-lysogeny decisions, but the underlying mechanism remains unknown. Here we determined that the arbitrium system in Bacillus subtilis phage phi3T modulates the bacterial toxin-antitoxin system MazE-MazF to regulate the phage life cycle. We show that phi3T expresses AimX and YosL, which bind to and inactivate MazF. AimX also inhibits the function of phi3T_93, a protein that promotes lysogeny by binding to MazE and releasing MazF. Overall, these mutually exclusive interactions promote the lytic cycle of the phage. After several rounds of infection, the phage-encoded AimP peptide accumulates intracellularly and inactivates the phage antiterminator AimR, a process that eliminates aimX expression from the aimP promoter. Therefore, when AimP increases, MazF activity promotes reversion back to lysogeny, since AimX is absent. Altogether, our study reveals the evolutionary strategy used by arbitrium to control lysis-lysogeny by domesticating and fine-tuning a phage-defence mechanism.
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Grants
- Wellcome Trust
- Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- NYSE Euronext
- European Commission NextGenerationEU fund (EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud Global). Block allocation group (BAG) DLS Proposal MX28394, ALBA Proposal 2020074406 and ESRF proposal MX-2452
- grants PID2019-108541GB-I00 and PID2022-137201NB-I00 from Spanish Government (Ministerio de Ciencia e Innovación), PROMETEO/2020/012 by Valencian Government
- MR/M003876/1, MR/V000772/1 and MR/S00940X/1 from the Medical Research Council (UK), BB/N002873/1, BB/V002376/1 and BB/S003835/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), ERC-ADG-2014 Proposal n° 670932 Dut-signal (from EU), and Wellcome Trust 201531/Z/16/Z
- RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- RCUK | Medical Research Council (MRC)
- Wellcome Trust (Wellcome)
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
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Affiliation(s)
- Sara Zamora-Caballero
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Cora Chmielowska
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nuria Quiles-Puchalt
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain
| | - Aisling Brady
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Javier Mancheño-Bonillo
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Alonso Felipe-Ruíz
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Cantoblanco, Madrid, Spain
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain.
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19
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Cortés-Martín A, Denise R, Guerin E, Stockdale SR, Draper LA, Ross RP, Shkoporov AN, Hill C. Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. Gut Microbes 2024; 16:2298254. [PMID: 38178369 PMCID: PMC10773633 DOI: 10.1080/19490976.2023.2298254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
The human gut microbiome plays a significant role in health and disease. The viral component (virome) is predominantly composed of bacteriophages (phages) and has received significantly less attention in comparison to the bacteriome. This knowledge gap is largely due to challenges associated with the isolation and characterization of novel gut phages, and bioinformatic hurdles such as the lack of a universal phage marker gene and the absence of sufficient numbers of homologs in viral databases. Here, we describe the isolation from human feces of a novel lytic phage with siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, and classified within a newly proposed Sagittacolavirus genus. In silico and biological characterization of this phage is presented in this study. Key to the isolation of φPDS1 was the antibiotic-driven selective enrichment of the bacterial host in a fecal fermenter. Despite producing plaques and lacking genes associated with lysogeny, φPDS1 demonstrates the ability to coexist in liquid culture for multiple days without affecting the abundance of its host. Multiple studies have shown that changes in Parabacteroides distasonis abundance can be linked to various disease states, rendering this novel phage-host pair and their interactions of particular interest.
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Affiliation(s)
- Adrián Cortés-Martín
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Rémi Denise
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Emma Guerin
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Stephen R. Stockdale
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Lorraine A. Draper
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N. Shkoporov
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
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20
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Brady A, Cabello-Yeves E, Gallego Del Sol F, Chmielowska C, Mancheño-Bonillo J, Zamora-Caballero S, Omer SB, Torres-Puente M, Eldar A, Quiles-Puchalt N, Marina A, Penadés JR. Characterization of a unique repression system present in arbitrium phages of the SPbeta family. Cell Host Microbe 2023; 31:2023-2037.e8. [PMID: 38035880 DOI: 10.1016/j.chom.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/25/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
Arbitrium-coding phages use peptides to communicate and coordinate the decision between lysis and lysogeny. However, the mechanism by which these phages establish lysogeny remains unknown. Here, focusing on the SPbeta phage family's model phages phi3T and SPβ, we report that a six-gene operon called the "SPbeta phages repressor operon" (sro) expresses not one but two master repressors, SroE and SroF, the latter of which folds like a classical phage integrase. To promote lysogeny, these repressors bind to multiple sites in the phage genome. SroD serves as an auxiliary repressor that, with SroEF, forms the repression module necessary for lysogeny establishment and maintenance. Additionally, the proteins SroABC within the operon are proposed to constitute the transducer module, connecting the arbitrium communication system to the activity of the repression module. Overall, this research sheds light on the intricate and specialized repression system employed by arbitrium SPβ-like phages in making lysis-lysogeny decisions.
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Affiliation(s)
- Aisling Brady
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Elena Cabello-Yeves
- Instituto de Biomedicina de Valencia (IBV-CSIC), 46010 Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV-CSIC), 46010 Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Cora Chmielowska
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Javier Mancheño-Bonillo
- Instituto de Biomedicina de Valencia (IBV-CSIC), 46010 Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Sara Zamora-Caballero
- Instituto de Biomedicina de Valencia (IBV-CSIC), 46010 Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - Shira Bendori Omer
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Nuria Quiles-Puchalt
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Department of Biomedical Sciences, Faculty of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca 46115, Spain
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV-CSIC), 46010 Valencia, Spain; CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
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21
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Xu Z, Ding Z, Shi L, Xie Y, Zhang Y, Wang Z, Liu Q. Coevolution between marine Aeromonas and phages reveals temporal trade-off patterns of phage resistance and host population fitness. THE ISME JOURNAL 2023; 17:2200-2209. [PMID: 37814126 PMCID: PMC10689771 DOI: 10.1038/s41396-023-01529-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023]
Abstract
Coevolution of bacteria and phages is an important host and parasite dynamic in marine ecosystems, contributing to the understanding of bacterial community diversity. On the time scale, questions remain concerning what is the difference between phage resistance patterns in marine bacteria and how advantageous mutations gradually accumulate during coevolution. In this study, marine Aeromonas was co-cultured with its phage for 180 days and their genetic and phenotypic dynamics were measured every 30 days. We identified 11 phage resistance genes and classified them into three categories: lipopolysaccharide (LPS), outer membrane protein (OMP), and two-component system (TCS). LPS shortening and OMP mutations are two distinct modes of complete phage resistance, while TCS mutants mediate incomplete resistance by repressing the transcription of phage genes. The co-mutation of LPS and OMP was a major mode for bacterial resistance at a low cost. The mutations led to significant reductions in the growth and virulence of bacterial populations during the first 60 days of coevolution, with subsequent leveling off. Our findings reveal the marine bacterial community dynamics and evolutionary trade-offs of phage resistance during coevolution, thus granting further understanding of the interaction of marine microbes.
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Affiliation(s)
- Zhenhe Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Zihan Ding
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Lijia Shi
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuzhen Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519000, Zhuhai, China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China
| | - Zhuang Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China.
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, China.
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22
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Barrero-Canosa J, Wang L, Oyugi A, Klaes S, Fischer P, Adrian L, Szewzyk U, Cooper M. Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host. Microorganisms 2023; 11:2688. [PMID: 38004701 PMCID: PMC10673088 DOI: 10.3390/microorganisms11112688] [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: 10/05/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage-host interactions at the protein level.
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Affiliation(s)
- Jimena Barrero-Canosa
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Luyao Wang
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Angelah Oyugi
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Simon Klaes
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Pascal Fischer
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Lorenz Adrian
- Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany; (S.K.)
- Helmholtz Centre for Environmental Research GmbH—UFZ, Department of Environmental Biotechnology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Ulrich Szewzyk
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
| | - Myriel Cooper
- Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany; (L.W.); (A.O.); (P.F.); (U.S.); (M.C.)
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23
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Ren X, Zhou J, Liu T, Zhong C, Wang Y, Yan H, Feng J. Antibacterial activity and action mechanism of curcusionol from Carex siderosticta Hance against Ralstonia nicotianae. PEST MANAGEMENT SCIENCE 2023; 79:4607-4616. [PMID: 37436717 DOI: 10.1002/ps.7661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND Tobacco bacterial wilt is a typical soil-borne disease caused by Ralstonia nicotianae, which causes huge losses in tobacco production every year. The crude extract of Carex siderosticta Hance was shown to have antibacterial activity against R. nicotianae during our search, and the natural antibacterial components were sought after using bioassay-guided fractionation of the compounds. RESULT Ethanol extract of Carex siderosticta Hance with the minimum inhibitory concentration (MIC) value of 100 μg/mL against R. nicotianae in vitro. The potential of these compounds as antibactericides against R. nicotianae were assessed. Curcusionol (1), showed the highest antibacterial activity against R. nicotianae with MIC value of 12.5 μg/mL in vitro. In the protective effect tests, the control effect of curcusionol (1) was 92.31 and 72.60%, respectively, after application of 7 and 14 days, at a concentration of 1500 μg/mL, being comparable to that of streptomycin sulfate at a concentration of 500 μg/mL, confirming that curcusionol (1) showed the potential for the development of new antibacterial drugs. RNA-sequencing, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis confirmed that curcusionol mainly destroys R. nicotianae cell membrane structure and affects quorum sensing (QS) to inhibit pathogenic bacteria. CONCLUSION This study revealed that the antibacterial activity of Carex siderosticta Hance makes it a botanical bactericide against R. nicotianae, while curcusionol as lead structures for antibacterial development is obvious by its potent antibacterial activity. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xingyu Ren
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
| | - Juan Zhou
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
| | - Ting Liu
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
| | - Chenquan Zhong
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
| | - Yong Wang
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
| | - He Yan
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
| | - Juntao Feng
- College of Plant Protection, Northwest A&F University, Xianyang, China
- Provincial Center for Bio-Pesticide Engineering, Northwest A&F University, Xianyang, China
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24
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Xuan G, Tan L, Yang Y, Kong J, Lin H, Wang J. Quorum sensing autoinducers AHLs protect Shewanella baltica against phage infection. Int J Food Microbiol 2023; 403:110304. [PMID: 37429117 DOI: 10.1016/j.ijfoodmicro.2023.110304] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/30/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Quorum sensing (QS) plays an important role in phage-host interactions. Shewanella baltica can't produce the N-acyl-homoserine lactones (AHLs) signal molecules but can eavesdrop on exogenous AHLs through its LuxR receptor. However, no clear evidence exists regarding the involvement of AHLs-mediated QS systems in S. baltica in regulating phage infection. Here, we report that AHLs modulated the phage resistance of S. baltica OS155. Specifically, we characterized a S. baltica phage vB_Sb_QDWS and preliminarily identified that lipopolysaccharide (LPS) is an important receptor for phage vB_Sb_QDWS. AHLs could protect S. baltica against phage infection by decreasing LPS-mediated phage adsorption. The expression of genes galU and tkt, which are essential for LPS synthesis, down-regulated significantly in response to AHLs autoinducers. Our finding confirms the important roles of QS in virus-host interactions and would be helpful to develop novel phage strategies for food spoilage control.
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Affiliation(s)
- Guanhua Xuan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Lin Tan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jiuna Kong
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
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25
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Igler C, Brockhurst M. Bacteriophage ecology: Getting a head start on genomic competitors. Curr Biol 2023; 33:R1011-R1013. [PMID: 37816320 DOI: 10.1016/j.cub.2023.08.077] [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: 10/12/2023]
Abstract
Temperate bacteriophages can actively replicate in bacterial host cells or lie dormant as prophages. Prophages inhabiting the same cell will then compete for cellular resources. A recent study indicates that prophages could circumvent this competition by responding to distinct activation cues.
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Affiliation(s)
- Claudia Igler
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK.
| | - Michael Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK
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26
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Moraskie M, Roshid MHO, O'Connor G, Artola Zavala T, Dikici E, Zingg JM, Deo S, Daunert S. Engineered biosensors for the quorum sensing molecule 3,5-dimethyl-pyrazine-2-ol (DPO) reveal its presence in humans, animals, and bacterial species beyond Vibrio cholerae. Biosens Bioelectron 2023; 237:115494. [PMID: 37419073 DOI: 10.1016/j.bios.2023.115494] [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: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023]
Abstract
A biosensor was engineered to enable the study of the novel quorum sensing molecule (QSM), 3,5-dimethylpyrazin-2-ol (DPO), employed by Vibrio cholerae to regulate biofilm formation and virulence factor production. Investigations into bacterial quorum sensing (QS), a form of communication based on the production and detection of QSMs to coordinate gene expression in a population dependent manner, offer a unique window to study the molecular underpinnings of microbial behavior and host interactions. Herein, we report the construction of an engineered microbial whole-cell bioluminescent biosensing system that incorporates the recognition of the VqmA regulatory protein of Vibrio cholerae with the bioluminescent reporting signal of luciferase for the selective, sensitive, stable, and reproducible detection of DPO in a variety of samples. Importantly, using our newly developed biosensor our studies demonstrate the detection of DPO in rodent and human samples. Employing our developed biosensor should help enable elucidation of microbial behavior at the molecular level and its impact in health and disease.
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Affiliation(s)
- Michael Moraskie
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Teresa Artola Zavala
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA; Universidad Francisco de Vitoria, Madrid, Spain
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute-BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA; The Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33146, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33146, USA.
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27
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Yang J, Bowring JZ, Krusche J, Lehmann E, Bejder BS, Silva SF, Bojer MS, Grunert T, Peschel A, Ingmer H. Cross-species communication via agr controls phage susceptibility in Staphylococcus aureus. Cell Rep 2023; 42:113154. [PMID: 37725513 DOI: 10.1016/j.celrep.2023.113154] [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: 04/09/2023] [Revised: 08/06/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
Bacteria use quorum sensing (QS) to coordinate group behavior in response to cell density, and some bacterial viruses (phages) also respond to QS. In Staphylococcus aureus, the agr-encoded QS system relies on accumulation of auto-inducing cyclic peptides (AIPs). Other staphylococci also produce AIPs of which many inhibit S. aureus agr. We show that agr induction reduces expression of tarM, encoding a glycosyltransferase responsible for α-N-acetylglucosamine modification of the major S. aureus phage receptor, the wall teichoic acids. This allows lytic phage Stab20 and related phages to infect and kill S. aureus. However, in mixed communities, producers of inhibitory AIPs like S. haemolyticus, S. caprae, and S. pseudintermedius inhibit S. aureus agr, thereby impeding phage infection. Our results demonstrate that cross-species interactions dramatically impact phage susceptibility. These interactions likely influence microbial ecology and impact the efficacy of phages in medical and biotechnological applications such as phage therapy.
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Affiliation(s)
- Jingxian Yang
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Janine Zara Bowring
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Janes Krusche
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)," German Center for Infection Research (DZIF), Tübingen, Germany
| | - Esther Lehmann
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Benjamin Svejdal Bejder
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Stephanie Fulaz Silva
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Martin Saxtorph Bojer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark
| | - Tom Grunert
- Functional Microbiology, Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, 72076 Tübingen, Germany; Cluster of Excellence "Controlling Microbes to Fight Infections (CMFI)," German Center for Infection Research (DZIF), Tübingen, Germany
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Copenhagen, Denmark.
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28
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Zurabov F, Glazunov E, Kochetova T, Uskevich V, Popova V. Bacteriophages with depolymerase activity in the control of antibiotic resistant Klebsiella pneumoniae biofilms. Sci Rep 2023; 13:15188. [PMID: 37704798 PMCID: PMC10499987 DOI: 10.1038/s41598-023-42505-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023] Open
Abstract
Klebsiella pneumoniae is associated with a variety of infections, such as pneumonia, urogenital infection, liver abscess, and bloodstream infection. It is especially dangerous for patients in medical facilities, where it can cause ventilator-associated pneumonia or intensive care unit-acquired pneumonia. The emergence of multidrug-resistant and hypervirulent strains as well as the ability to form biofilms on various medical devices complicates the treatment of such infections and makes the use of antibiotics ineffective. The application of bacteriophages is a promising alternative for combating Klebsiella pneumoniae biofilms. In the present study a cocktail of 3 bacteriophages with depolymerase activity was used to control antibiotic resistant Klebsiella pneumoniae biofilms in vitro. Biofilms were examined using optical and scanning electron microscopy. The obtained results demonstrate that the studied bacteriophage cocktail can effectively disrupt Klebsiella pneumoniae biofilms.
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Affiliation(s)
- Fedor Zurabov
- Research and Production Center "MicroMir", LLC, Moscow, Russia.
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia.
| | - Egor Glazunov
- Research and Production Center "MicroMir", LLC, Moscow, Russia
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29
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Attrill EL, Łapińska U, Westra ER, Harding SV, Pagliara S. Slow growing bacteria survive bacteriophage in isolation. ISME COMMUNICATIONS 2023; 3:95. [PMID: 37684358 PMCID: PMC10491631 DOI: 10.1038/s43705-023-00299-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
The interactions between bacteria and bacteriophage have important roles in the global ecosystem; in turn changes in environmental parameters affect the interactions between bacteria and phage. However, there is a lack of knowledge on whether clonal bacterial populations harbour different phenotypes that respond to phage in distinct ways and whether the abundance of such phenotypes within bacterial populations is affected by variations in environmental parameters. Here we study the impact of variations in nutrient availability, bacterial growth rate and phage abundance on the interactions between the phage T4 and individual Escherichia coli cells confined in spatial refuges. Surprisingly, we found that fast growing bacteria survive together with all of their clonal kin cells, whereas slow growing bacteria survive in isolation. We also discovered that the number of bacteria that survive in isolation decreases at increasing phage doses possibly due to lysis inhibition in the presence of secondary adsorptions. We further show that these changes in the phenotypic composition of the E. coli population have important consequences on the bacterial and phage population dynamics and should therefore be considered when investigating bacteria-phage interactions in ecological, health or food production settings in structured environments.
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Affiliation(s)
- Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Edze R Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK.
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30
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Xing J, Gumerov VM, Zhulin IB. Origin and functional diversification of PAS domain, a ubiquitous intracellular sensor. SCIENCE ADVANCES 2023; 9:eadi4517. [PMID: 37647406 PMCID: PMC10468136 DOI: 10.1126/sciadv.adi4517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Signal perception is a key function in regulating biological activities and adapting to changing environments. Per-Arnt-Sim (PAS) domains are ubiquitous sensors found in diverse receptors in bacteria, archaea, and eukaryotes, but their origins, distribution across the tree of life, and extent of their functional diversity are not fully characterized. Here, we show that using sequence conservation and structural information, it is possible to propose specific and potential functions for a large portion of nearly 3 million PAS domains. Our analysis suggests that PAS domains originated in bacteria and were horizontally transferred to archaea and eukaryotes. We reveal that gas sensing via a heme cofactor evolved independently in several lineages, whereas redox and light sensing via flavin adenine dinucleotide and flavin mononucleotide cofactors have the same origin. The close relatedness of human PAS domains to those in bacteria provides an opportunity for drug design by exploring potential natural ligands and cofactors for bacterial homologs.
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Affiliation(s)
- Jiawei Xing
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH USA
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31
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Schwartzkopf CM, Taylor VL, Groleau MC, Faith DR, Schmidt AK, Lamma TL, Brooks DM, Déziel E, Maxwell KL, Secor PR. Inhibition of PQS signaling by the Pf bacteriophage protein PfsE enhances viral replication in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554831. [PMID: 37662248 PMCID: PMC10473763 DOI: 10.1101/2023.08.25.554831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Quorum sensing, a bacterial signaling system that coordinates group behaviors as a function of cell density, plays an important role in regulating viral (phage) defense mechanisms in bacteria. The opportunistic pathogen Pseudomonas aeruginosa is a model system for the study of quorum sensing. P. aeruginosa is also frequently infected by Pf prophages that integrate into the host chromosome. Upon induction, Pf phages suppress host quorum sensing systems; however, the physiological relevance and mechanism of suppression are unknown. Here, we identify the Pf phage protein PfsE as an inhibitor of Pseudomonas Quinolone Signal (PQS) quorum sensing. PfsE binds to the host protein PqsA, which is essential for the biosynthesis of the PQS signaling molecule. Inhibition of PqsA increases the replication efficiency of Pf virions when infecting a new host and when the Pf prophage switches from lysogenic replication to active virion replication. In addition to inhibiting PQS signaling, our prior work demonstrates that PfsE also binds to PilC and inhibits type IV pili extension, protecting P. aeruginosa from infection by type IV pili-dependent phages. Overall, this work suggests that the simultaneous inhibition of PQS signaling and type IV pili by PfsE may be a viral strategy to suppress host defenses to promote Pf replication while at the same time protecting the susceptible host from competing phages.
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Affiliation(s)
| | | | - Marie-Christine Groleau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Amelia K. Schmidt
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Tyrza L. Lamma
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Diane M. Brooks
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Laval, Québec, Canada
| | - Karen L. Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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32
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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping. Nat Commun 2023; 14:5156. [PMID: 37620325 PMCID: PMC10449902 DOI: 10.1038/s41467-023-40724-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Host-pathogen interactions are pivotal in regulating establishment, progression, and outcome of an infection. While affinity-purification mass spectrometry has become instrumental in characterizing such interactions, it suffers from limitations in scalability and biological authenticity. Here we present the use of co-fractionation mass spectrometry for high throughput analysis of host-pathogen interactions from native viral infections of two jumbophages (ϕKZ and ϕPA3) in Pseudomonas aeruginosa. This approach enabled the detection of > 6000 unique host-pathogen interactions for each phage, encompassing > 50% of their respective proteomes. This deep coverage provided evidence for interactions between KZ-like phage proteins and the host ribosome, and revealed protein complexes for previously undescribed phage ORFs, including a ϕPA3 complex showing strong structural and sequence similarity to ϕKZ non-virion RNA polymerase. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of host-pathogen interactomes and protein complex dynamics upon infection.
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Affiliation(s)
- Andrea Fossati
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Deepto Mozumdar
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Claire Kokontis
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Melissa Mèndez-Moran
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Eliza Nieweglowska
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Adrian Pelin
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Yuping Li
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Baron Guo
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA
| | - David A Agard
- Department of Biochemistry, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Joseph Bondy-Denomy
- Department of Immunology and Microbiology, University of California San Francisco, San Francisco, 94158, CA, USA.
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, 94158, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA.
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Luthe T, Kever L, Thormann K, Frunzke J. Bacterial multicellular behavior in antiviral defense. Curr Opin Microbiol 2023; 74:102314. [PMID: 37030144 DOI: 10.1016/j.mib.2023.102314] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 04/08/2023]
Abstract
Multicellular behavior benefits seemingly simple organisms such as bacteria, by improving nutrient uptake, resistance to stresses, or by providing advantages in predatory interactions. Several recent studies have shown that this also extends to the defense against bacteriophages, which are omnipresent in almost all habitats. In this review, we summarize strategies conferring protection against phage infection at the multicellular level, covering secretion of small antiphage molecules or membrane vesicles, the role of quorum sensing in phage defense, the development of transient phage resistance, and the impact of biofilm components and architecture. Recent studies focusing on these topics push the boundaries of our understanding of the bacterial immune system and set the ground for an appreciation of bacterial multicellular behavior in antiviral defense.
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Silpe JE, Duddy OP, Johnson GE, Beggs GA, Hussain FA, Forsberg KJ, Bassler BL. Small protein modules dictate prophage fates during polylysogeny. Nature 2023; 620:625-633. [PMID: 37495698 PMCID: PMC10432266 DOI: 10.1038/s41586-023-06376-y] [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: 09/16/2022] [Accepted: 06/27/2023] [Indexed: 07/28/2023]
Abstract
Most bacteria in the biosphere are predicted to be polylysogens harbouring multiple prophages1-5. In studied systems, prophage induction from lysogeny to lysis is near-universally driven by DNA-damaging agents6. Thus, how co-residing prophages compete for cell resources if they respond to an identical trigger is unknown. Here we discover regulatory modules that control prophage induction independently of the DNA-damage cue. The modules bear little resemblance at the sequence level but share a regulatory logic by having a transcription factor that activates the expression of a neighbouring gene that encodes a small protein. The small protein inactivates the master repressor of lysis, which leads to induction. Polylysogens that harbour two prophages exposed to DNA damage release mixed populations of phages. Single-cell analyses reveal that this blend is a consequence of discrete subsets of cells producing one, the other or both phages. By contrast, induction through the DNA-damage-independent module results in cells producing only the phage sensitive to that specific cue. Thus, in the polylysogens tested, the stimulus used to induce lysis determines phage productivity. Considering the lack of potent DNA-damaging agents in natural habitats, additional phage-encoded sensory pathways to lysis likely have fundamental roles in phage-host biology and inter-prophage competition.
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Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Grace E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Grace A Beggs
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Fatima A Hussain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin J Forsberg
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Duddy OP, Silpe JE, Fei C, Bassler BL. Natural silencing of quorum-sensing activity protects Vibrio parahaemolyticus from lysis by an autoinducer-detecting phage. PLoS Genet 2023; 19:e1010809. [PMID: 37523407 PMCID: PMC10426928 DOI: 10.1371/journal.pgen.1010809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/15/2023] [Accepted: 07/15/2023] [Indexed: 08/02/2023] Open
Abstract
Quorum sensing (QS) is a chemical communication process that bacteria use to track population density and orchestrate collective behaviors. QS relies on the production, accumulation, and group-wide detection of extracellular signal molecules called autoinducers. Vibriophage 882 (phage VP882), a bacterial virus, encodes a homolog of the Vibrio QS receptor-transcription factor, called VqmA, that monitors the Vibrio QS autoinducer DPO. Phage VqmA binds DPO at high host-cell density and activates transcription of the phage gene qtip. Qtip, an antirepressor, launches the phage lysis program. Phage-encoded VqmA when bound to DPO also manipulates host QS by activating transcription of the host gene vqmR. VqmR is a small RNA that controls downstream QS target genes. Here, we sequence Vibrio parahaemolyticus strain O3:K6 882, the strain from which phage VP882 was initially isolated. The chromosomal region normally encoding vqmR and vqmA harbors a deletion encompassing vqmR and a portion of the vqmA promoter, inactivating that QS system. We discover that V. parahaemolyticus strain O3:K6 882 is also defective in its other QS systems, due to a mutation in luxO, encoding the central QS transcriptional regulator LuxO. Both the vqmR-vqmA and luxO mutations lock V. parahaemolyticus strain O3:K6 882 into the low-cell density QS state. Reparation of the QS defects in V. parahaemolyticus strain O3:K6 882 promotes activation of phage VP882 lytic gene expression and LuxO is primarily responsible for this effect. Phage VP882-infected QS-competent V. parahaemolyticus strain O3:K6 882 cells lyse more rapidly and produce more viral particles than the QS-deficient parent strain. We propose that, in V. parahaemolyticus strain O3:K6 882, constitutive maintenance of the low-cell density QS state suppresses the launch of the phage VP882 lytic cascade, thereby protecting the bacterial host from phage-mediated lysis.
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Affiliation(s)
- Olivia P. Duddy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Justin E. Silpe
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Chenyi Fei
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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36
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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: 0] [Impact Index Per Article: 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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37
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Duddy OP, Silpe JE, Fei C, Bassler BL. Natural Silencing of Quorum-Sensing Activity Protects Vibrio parahaemolyticus from Lysis by an Autoinducer-Detecting Phage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543668. [PMID: 37333398 PMCID: PMC10274711 DOI: 10.1101/2023.06.05.543668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Quorum sensing (QS) is a chemical communication process that bacteria use to track population density and orchestrate collective behaviors. QS relies on the production, accumulation, and group-wide detection of extracellular signal molecules called autoinducers. Vibriophage 882 (phage VP882), a bacterial virus, encodes a homolog of the Vibrio QS receptor-transcription factor, called VqmA, that monitors the Vibrio QS autoinducer DPO. Phage VqmA binds DPO at high host-cell density and activates transcription of the phage gene qtip . Qtip, an antirepressor, launches the phage lysis program. Phage-encoded VqmA when bound to DPO also manipulates host QS by activating transcription of the host gene vqmR . VqmR is a small RNA that controls downstream QS target genes. Here, we sequence Vibrio parahaemolyticus strain O3:K6 882, the strain from which phage VP882 was initially isolated. The chromosomal region normally encoding vqmR and vqmA harbors a deletion encompassing vqmR and a portion of the vqmA promoter, inactivating that QS system. We discover that V. parahaemolyticus strain O3:K6 882 is also defective in its other QS systems, due to a mutation in luxO , encoding the central QS transcriptional regulator LuxO. Both the vqmR-vqmA and luxO mutations lock V. parahaemolyticus strain O3:K6 882 into the low-cell density QS state. Reparation of the QS defects in V. parahaemolyticus strain O3:K6 882 promotes activation of phage VP882 lytic gene expression and LuxO is primarily responsible for this effect. Phage VP882-infected QS-competent V. parahaemolyticus strain O3:K6 882 cells lyse more rapidly and produce more viral particles than the QS-deficient parent strain. We propose that, in V. parahaemolyticus strain O3:K6 882, constitutive maintenance of the low-cell density QS state suppresses the launch of the phage VP882 lytic cascade, thereby protecting the bacterial host from phage-mediated lysis.
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Affiliation(s)
- Olivia P. Duddy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Justin E. Silpe
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chenyi Fei
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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38
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Miller Conrad LC, Perez LJ. A Geneticist Transcribing the Chemical Language of Bacteria. Isr J Chem 2023; 63:e202200079. [PMID: 37469628 PMCID: PMC10353724 DOI: 10.1002/ijch.202200079] [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: 10/03/2022] [Indexed: 12/05/2022]
Abstract
The study of quorum sensing, bacterial cell-to-cell communication mediated by the production and detection of small molecule signals, has skyrocketed since its discovery in the last third of the 20th century. Building from early investigations of bacterial bioluminescence, the process has been characterized to control a numerous and growing number of group behaviors, including virulence and biofilm formation. Bonnie Bassler has made key contributions to the understanding of quorum sensing, leading interdisciplinary efforts to characterize key signaling pathway components and their respective signaling molecules across a range of gram-negative bacteria. This review highlights her work in the field, with a particular emphasis on the chemical contributions of her work.
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Affiliation(s)
- Laura C. Miller Conrad
- Department of Chemistry, San José State University, 1 Washington Sq, San Jose, CA 95192, USA
| | - Lark J. Perez
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
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39
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Silpe JE, Duddy OP, Bassler BL. Induction mechanisms and strategies underlying interprophage competition during polylysogeny. PLoS Pathog 2023; 19:e1011363. [PMID: 37200239 DOI: 10.1371/journal.ppat.1011363] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Justin E Silpe
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Olivia P Duddy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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40
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Liu X, Ye Y, Zhang Z, Rensing C, Zhou S, Nealson KH. Prophage Induction Causes Geobacter Electroactive Biofilm Decay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:6196-6204. [PMID: 36997849 DOI: 10.1021/acs.est.2c08443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sustaining a metabolically active electroactive biofilm (EAB) is essential for the high efficiency and durable operation of microbial fuel cells (MFCs). However, EABs usually decay during long-term operation, and, until now, the causes remain unknown. Here, we report that lysogenic phages can cause EAB decay in Geobacter sulfurreducens fuel cells. A cross-streak agar assay and bioinformatic analysis revealed the presence of prophages on the G. sulfurreducens genome, and a mitomycin C induction assay revealed the lysogenic to lytic transition of those prophages, resulting in a progressive decay in both current generation and the EAB. Furthermore, the addition of phages purified from decayed EAB resulted in accelerated decay of the EAB, thereafter contributing to a faster decline in current generation; otherwise, deleting prophage-related genes rescued the decay process. Our study provides the first evidence of an interaction between phages and electroactive bacteria and suggests that attack by phages is a primary cause of EAB decay, having significant implications in bioelectrochemical systems.
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Affiliation(s)
- Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yin Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhishuai Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, California 90089, United States
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41
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Molina-Quiroz RC, Silva-Valenzuela CA. Interactions of Vibrio phages and their hosts in aquatic environments. Curr Opin Microbiol 2023; 74:102308. [PMID: 37062175 DOI: 10.1016/j.mib.2023.102308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 04/18/2023]
Abstract
Bacteriophages (phages) are viruses that specifically infect bacteria. These viruses were discovered a century ago and have been used as a model system in microbial genetics and molecular biology. In order to survive, bacteria have to quickly adapt to phage challenges in their natural settings. In turn, phages continuously develop/evolve mechanisms for battling host defenses. A deeper understanding of the arms race between bacteria and phages is essential for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections. Vibrio species and their phages (vibriophages) are a suitable model to study these interactions. Phages are highly ubiquitous in aquatic environments and Vibrio are waterborne bacteria that must survive the constant attack by phages for successful transmission to their hosts. Here, we review relevant literature from the past two years to delve into the molecular interactions of Vibrio species and their phages in aquatic niches.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts Medical Center and Tufts University, Boston, MA, USA
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42
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Shan X, Szabo RE, Cordero OX. Mutation-induced infections of phage-plasmids. Nat Commun 2023; 14:2049. [PMID: 37041135 PMCID: PMC10090143 DOI: 10.1038/s41467-023-37512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Phage-plasmids are extra-chromosomal elements that act both as plasmids and as phages, whose eco-evolutionary dynamics remain poorly constrained. Here, we show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in a population of marine Roseobacter. Recurrent loss-of-function mutations in the phage repressor that controls prophage induction leads to constitutively lytic phage-plasmids that spread rapidly throughout the population. The entire phage-plasmid genome is packaged into virions, which were horizontally transferred by re-infecting lysogenized cells, leading to an increase in phage-plasmid copy number and to heterozygosity in a phage repressor locus in re-infected cells. However, the uneven distribution of phage-plasmids after cell division (i.e., segregational drift) leads to the production of offspring carrying only the constitutively lytic phage-plasmid, thus restarting the lysis-reinfection-segregation life cycle. Mathematical models and experiments show that these dynamics lead to a continuous productive infection of the bacterial population, in which lytic and lysogenic phage-plasmids coexist. Furthermore, analyses of marine bacterial genome sequences indicate that the plasmid backbone here can carry different phages and disseminates trans-continentally. Our study highlights how the interplay between phage infection and plasmid genetics provides a unique eco-evolutionary strategy for phage-plasmids.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel E Szabo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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43
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Wang M, Lian Y, Wang Y, Zhu L. The role and mechanism of quorum sensing on environmental antimicrobial resistance. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 322:121238. [PMID: 36758922 DOI: 10.1016/j.envpol.2023.121238] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
As more environmental contaminants emerging, antibiotics and antibiotic resistance genes (ARGs) have caused a substantial increase of antimicrobial resistance (AMR) in environment. Quorum sensing (QS) is a bacterial cell-to-cell communication process that regulates many traits and gene expression, including ARGs and the related genes that contribute to AMR development. Herein, we summarize the role, physiology, and genetic mechanisms of bacterial QS in AMR development in the environment. First, the effect of QS on AMR is introduced. Next, the role of QS in bacterial physiological behaviors that promote AMR development, including membrane permeability, tactic movement, biofilm formation, persister formation, and small colony variants (SCVs), is systematically analyzed. Furthermore, the regulation of QS on the expression of ARGs, generation of reactive oxygen species (ROS), which affects ARGs formation, and horizontal gene transfer (HGT), which accelerates the transmission of ARGs, are discussed to reveal the molecular mechanism for AMR development. This review provides a reference for a better understanding of AMR evolution and novel insights into AMR prevention.
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Affiliation(s)
- Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yulu Lian
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
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44
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Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL. Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523954. [PMID: 36711836 PMCID: PMC9882154 DOI: 10.1101/2023.01.13.523954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Host-pathogen interactions (HPIs) are pivotal in regulating establishment, progression, and outcome of an infection. Affinity-purification mass spectrometry has become instrumental for the characterization of HPIs, however the targeted nature of exogenously expressing individual viral proteins has limited its utility to the analysis of relatively small pathogens. Here we present the use of co-fractionation mass spectrometry (SEC-MS) for the high-throughput analysis of HPIs from native viral infections of two jumbophages ( ϕ KZ and ϕ PA3) in Pseudomonas aeruginosa . This enabled the detection > 6000 unique host-pathogen and > 200 pathogen-pathogen interactions for each phage, encompassing > 50% of the phage proteome. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. Prediction of novel ORFs revealed a ϕ PA3 complex showing strong structural and sequence similarity to ϕ KZ nvRNAp, suggesting ϕ PA3 also possesses two RNA polymerases acting at different stages of the infection cycle. We further expanded our understanding on the molecular organization of the virion packaged and injected proteome by identifying 23 novel virion components and 5 novel injected proteins, as well as providing the first evidence for interactions between KZ-like phage proteins and the host ribosome. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of hostpathogen interactomes and protein complex dynamics upon infection.
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45
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Unveil the Secret of the Bacteria and Phage Arms Race. Int J Mol Sci 2023; 24:ijms24054363. [PMID: 36901793 PMCID: PMC10002423 DOI: 10.3390/ijms24054363] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage's nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and other defense systems to interfere with the replication of phage genes in the host; through the quorum sensing (QS) enhancement of phage's resistant effect. At the same time, phages have also evolved a variety of counter-defense strategies, such as degrading extracellular polymeric substances (EPS) that mask receptors or recognize new receptors, thereby regaining the ability to adsorb host cells; modifying its own genes to prevent the R-M systems from recognizing phage genes or evolving proteins that can inhibit the R-M complex; through the gene mutation itself, building nucleus-like compartments or evolving anti-CRISPR (Acr) proteins to resist CRISPR-Cas systems; and by producing antirepressors or blocking the combination of autoinducers (AIs) and its receptors to suppress the QS. The arms race between bacteria and phages is conducive to the coevolution between bacteria and phages. This review details bacterial anti-phage strategies and anti-defense strategies of phages and will provide basic theoretical support for phage therapy while deeply understanding the interaction mechanism between bacteria and phages.
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46
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Sanchez S, Ng WL. Motility Control as a Possible Link Between Quorum Sensing to Surface Attachment in Vibrio Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:65-75. [PMID: 36792871 DOI: 10.1007/978-3-031-22997-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
In this chapter, we discuss motility control as a possible link between quorum sensing (QS) to surface attachment in Vibrio species. QS regulates a variety of behaviors that are important for the life cycle of many bacterial species, including virulence factor production, biofilm formation, or metabolic homeostasis. Therefore, without QS, many species of bacteria cannot survive in their natural environments. Here, we summarize several QS systems in different Vibrio species and discuss some of emerging features that suggest QS is intimately connected to motility control. Finally, we speculate the connection between motility and QS is critical for Vibrio species to detect solid surfaces for surface attachment.
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Affiliation(s)
- Sandra Sanchez
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, USA.
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Staying below the Radar: Unraveling a New Family of Ubiquitous "Cryptic" Non-Tailed Temperate Vibriophages and Implications for Their Bacterial Hosts. Int J Mol Sci 2023; 24:ijms24043937. [PMID: 36835353 PMCID: PMC9966536 DOI: 10.3390/ijms24043937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name "Asemoviridae" with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage-host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution.
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Chen C, Zhang Y, Yao X, Li S, Wang G, Huang Y, Yang Y, Zhang A, Liu C, Zhu D, Li H, Yan Q, Ma W. Characterizations of the Gut Bacteriome, Mycobiome, and Virome in Patients with Osteoarthritis. Microbiol Spectr 2023; 11:e0171122. [PMID: 36515546 PMCID: PMC9927108 DOI: 10.1128/spectrum.01711-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/13/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here, we explored the gut microbiotas of 44 OA patients and 46 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 6,567 nonredundant viral operational taxonomic units (vOTUs). We revealed that the gut microbiome (including bacteriome, mycobiome, and virome) of OA patients is fundamentally altered, characterized by a panel of 279 differentially abundant bacterial species, 10 fungal species, and 627 vOTUs. The representative OA-enriched bacteria included Anaerostipes hadrus (GENOME147149), Prevotella sp900313215 (GENOME08259), Eubacterium_E hallii (GENOME000299), and Blautia A (GENOME001004), while Bacteroides plebeius A (GENOME239725), Roseburia inulinivorans (GENOME 001770), Dialister sp900343095 (GENOME075103), Phascolarctobacterium faecium (GENOME233517), and several members of Faecalibacterium and Prevotella were depleted in OA patients. Fungi such as Debaryomyces fabryi (GenBank accession no. GCA_003708665), Candida parapsilosis (GCA_000182765), and Apophysomyces trapeziformis (GCA_000696975) were enriched in the OA gut microbiota, and Malassezia restricta (GCA_003290485), Aspergillus fumigatus (GCA_003069565), and Mucor circinelloides (GCA_010203745) were depleted. The OA-depleted viruses spanned Siphoviridae (95 vOTUs), Myoviridae (70 vOTUs), and Microviridae (5 vOTUs), while 30 Siphoviridae vOTUs were enriched in OA patients. Functional analysis of the gut bacteriome and virome also uncovered their functional signatures in relation to OA. Moreover, we demonstrated that the OA-associated gut bacterial and viral signatures are tightly interconnected, suggesting that they may impact disease together. Finally, we showed that the multikingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota for the prediction of OA and related diseases. Our results delineated the fecal bacteriome, mycobiome, and virome landscapes of the OA microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies. IMPORTANCE The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. We found that OA-associated gut bacterial and viral signatures were tightly interconnected, indicating that they may affect the disease together. The OA patients can be discriminated effectively from healthy controls using the multikingdom signatures, suggesting the potential of gut microbiota for the prediction of OA and related diseases.
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Affiliation(s)
- Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Xueming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Ying Huang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yutao Yang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Can Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dan Zhu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hufan Li
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Wukai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
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Misson P, Bruder E, Cornuault JK, De Paepe M, Nicolas P, Demarre G, Lakisic G, Petit MA, Espeli O, Lecointe F. Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection. PLoS Pathog 2023; 19:e1011127. [PMID: 36730457 PMCID: PMC9928086 DOI: 10.1371/journal.ppat.1011127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/14/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than other E. coli in macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohn's disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, both in vitro and inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108 viral particles per mL of culture supernatants in vitro, more than 100-fold higher than the other phages. Gally is also over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, a genotoxic environment, this over-induction is not observed. Analysis of the transcriptome and key steps of its lytic cycle in macrophages suggests that the excision of the Gally prophage continues to be repressed in macrophages. We conclude that strain LF82 has evolved an efficient way to block the lytic cycle of its most active prophage upon macrophage infection, which may participate to its good survival in macrophages.
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Affiliation(s)
- Pauline Misson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Emma Bruder
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Jeffrey K. Cornuault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marianne De Paepe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Gaëlle Demarre
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - François Lecointe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- * E-mail:
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Disarm The Bacteria: What Temperate Phages Can Do. Curr Issues Mol Biol 2023; 45:1149-1167. [PMID: 36826021 PMCID: PMC9955262 DOI: 10.3390/cimb45020076] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.
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