1
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Boyd CM, Seed KD. A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread. Nucleic Acids Res 2024:gkae675. [PMID: 39149900 DOI: 10.1093/nar/gkae675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/17/2024] Open
Abstract
ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery and virion components results in inhibition of ICP1's lifecycle. PLEs are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's pac site as a backup strategy to ensure genome packaging. PLE's pac site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
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Affiliation(s)
- Caroline M Boyd
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
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2
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Gomez JB, Waters CM. A Vibrio cholerae Type IV restriction system targets glucosylated 5-hydroxyl methyl cytosine to protect against phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588314. [PMID: 38617239 PMCID: PMC11014532 DOI: 10.1101/2024.04.05.588314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A major challenge faced by Vibrio cholerae is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, V. cholerae has evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized more were encoded in V. cholerae given the relative paucity of phage that have been isolated which infect this species. Using a V. cholerae genomic library, we identified a Type IV restriction system consisting of two genes within a 16kB region of the Vibrio pathogenicity island-2 that we name TgvA and TgvB (Type I-embedded gmrSD-like system of VPI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modification are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We show that additional phage defense genes are encoded in VPI-2 that protect against other phage like T3, secΦ18, secΦ27 and λ. Our study uncovers a novel Type IV restriction system in V. cholerae, increasing our understanding of the evolution and ecology of V. cholerae while highlighting the evolutionary interplay between restriction systems and phage genome modification.
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Affiliation(s)
- Jasper B Gomez
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Christopher M Waters
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
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3
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Boyd CM, Subramanian S, Dunham DT, Parent KN, Seed KD. A Vibrio cholerae viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids. eLife 2024; 12:RP87611. [PMID: 38206122 PMCID: PMC10945586 DOI: 10.7554/elife.87611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite from Vibrio cholerae, phage-inducible chromosomal island-like element (PLE), remodels the capsid it has been predicted to steal from the phage ICP1 (Netter et al., 2021). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like particle (PLP) assembly platform in Escherichia coli, we demonstrated that TcaP is a bona fide scaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (Kizziah et al., 2020). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes.
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Affiliation(s)
- Caroline M Boyd
- Department of Plant and Microbial Biology, Seed Lab, University of California, BerkeleyBerkeleyUnited States
| | - Sundharraman Subramanian
- Department of Biochemistry and Molecular Biology, Parent Lab, Michigan State UniversityEast LansingUnited States
| | - Drew T Dunham
- Department of Plant and Microbial Biology, Seed Lab, University of California, BerkeleyBerkeleyUnited States
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Parent Lab, Michigan State UniversityEast LansingUnited States
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, Seed Lab, University of California, BerkeleyBerkeleyUnited States
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4
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Woudstra C, Sørensen AN, Brøndsted L. Engineering of Salmonella Phages into Novel Antimicrobial Tailocins. Cells 2023; 12:2637. [PMID: 37998371 PMCID: PMC10670071 DOI: 10.3390/cells12222637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Due to the extensive use of antibiotics, the increase of infections caused by antibiotic-resistant bacteria is now a global health concern. Phages have proven useful for treating bacterial infections and represent a promising alternative or complement to antibiotic treatment. Yet, other alternatives exist, such as bacteria-produced non-replicative protein complexes that can kill their targeted bacteria by puncturing their membrane (Tailocins). To expand the repertoire of Tailocins available, we suggest a new approach that transforms phages into Tailocins. Here, we genetically engineered the virulent Ackermannviridae phage S117, as well as temperate phages Fels-1, -2 and Gifsy-1 and -2, targeting the food pathogen Salmonella, by deleting the portal vertex or major capsid gene using CRISPR-Cas9. We report the production of Tailocin particles from engineered virulent and temperate phages able to kill their native host. Our work represents a steppingstone that taps into the huge diversity of phages and transforms them into versatile puncturing new antimicrobials.
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Affiliation(s)
| | | | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (C.W.); (A.N.S.)
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5
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Barth ZK, Dunham DT, Seed KD. Nuclease genes occupy boundaries of genetic exchange between bacteriophages. NAR Genom Bioinform 2023; 5:lqad076. [PMID: 37636022 PMCID: PMC10448857 DOI: 10.1093/nargab/lqad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/13/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023] Open
Abstract
Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4's. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.
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Affiliation(s)
- Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Drew T Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA
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6
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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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7
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Barth ZK, Dunham DT, Seed KD. Nuclease genes occupy boundaries of genetic exchange between bacteriophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533998. [PMID: 36993569 PMCID: PMC10055350 DOI: 10.1101/2023.03.23.533998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4’s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.
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Affiliation(s)
- Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Drew T Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley. 271 Koshland Hall, Berkeley, CA 94720, USA
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8
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Dunham DT, Angermeyer A, Seed KD. The RNA-RNA interactome between a phage and its satellite virus reveals a small RNA that differentially regulates gene expression across both genomes. Mol Microbiol 2023; 119:515-533. [PMID: 36786209 PMCID: PMC10392615 DOI: 10.1111/mmi.15046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Satellite viruses are present across all domains of life, defined as subviral parasites that require infection by another virus for satellite progeny production. Phage satellites exhibit various regulatory mechanisms to manipulate phage gene expression to the benefit of the satellite, redirecting resources from the phage to the satellite, and often inhibiting phage progeny production. While small RNAs (sRNAs) are well documented as regulators of prokaryotic gene expression, they have not been shown to play a regulatory role in satellite-phage conflicts. Vibrio cholerae encodes the phage inducible chromosomal island-like element (PLE), a phage satellite, to defend itself against the lytic phage ICP1. Here, we use Hi-GRIL-seq to identify a complex RNA-RNA interactome between PLE and ICP1. Both inter- and intragenome RNA interactions were detected, headlined by the PLE sRNA, SviR. SviR is involved in regulating both PLE and ICP1 gene expression uniquely, decreasing ICP1 target translation and affecting PLE transcripts. The striking conservation of SviR across all known PLEs suggests the sRNA is deeply rooted in the PLE-ICP1 conflict and implicates sRNAs as unidentified regulators of gene expression in phage-satellite interactions.
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Affiliation(s)
- Drew T Dunham
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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9
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Alqurainy N, Miguel-Romero L, Moura de Sousa J, Chen J, Rocha EPC, Fillol-Salom A, Penadés JR. A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature. Cell Host Microbe 2023; 31:69-82.e5. [PMID: 36596306 DOI: 10.1016/j.chom.2022.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/06/2022] [Accepted: 12/01/2022] [Indexed: 01/03/2023]
Abstract
Phage satellites are genetic elements that couple their life cycle to that of helper phages they parasitize, interfering with phage packaging through the production of small capsids, where only satellites are packaged. So far, in all analyzed systems, the satellite-sized capsids are composed of phage proteins. Here, we report that a family of phage-inducible chromosomal islands (PICIs), a type of satellites, encodes all the proteins required for both the production of small-sized capsids and the exclusive packaging of the PICIs into these capsids. Therefore, this new family, named capsid-forming PICIs (cf-PICIs), only requires phage tails to generate PICI particles. Remarkably, the representative cf-PICIs are produced with no cost from their helper phages, suggesting that the relationship between these elements is not parasitic. Finally, our phylogenomic studies indicate that cf-PICIs are present both in gram-positive and gram-negative bacteria and have evolved at least three times independently to spread in nature.
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Affiliation(s)
- Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia
| | - Laura Miguel-Romero
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Jorge Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - John Chen
- Department of Microbiology and Immunology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Universidad CEU Cardenal Herrera, CEU Universities, Valencia 46115, Spain.
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10
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Molina-Quiroz RC, Camilli A, Silva-Valenzuela CA. Role of Bacteriophages in the Evolution of Pathogenic Vibrios and Lessons for Phage Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:149-173. [PMID: 36792875 PMCID: PMC10587905 DOI: 10.1007/978-3-031-22997-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Viruses of bacteria, i.e., bacteriophages (or phages for short), were discovered over a century ago and have played a major role as a model system for the establishment of the fields of microbial genetics and molecular biology. Despite the relative simplicity of phages, microbiologists are continually discovering new aspects of their biology including mechanisms for battling host defenses. In turn, novel mechanisms of host defense against phages are being discovered at a rapid clip. A deeper understanding of the arms race between bacteria and phages will continue to reveal novel molecular mechanisms and will be important for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections, respectively. Here we delve into the molecular interactions of Vibrio species and phages.
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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
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, MA, USA
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11
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When bacteria are phage playgrounds: interactions between viruses, cells, and mobile genetic elements. Curr Opin Microbiol 2022; 70:102230. [PMID: 36335712 DOI: 10.1016/j.mib.2022.102230] [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: 09/23/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. We describe two key types of interactions - defense systems and genetic regulation - that allow the partners of the interaction to destroy or control the others. These interactions evolve rapidly by genetic exchanges, including among competing partners. They are sometimes followed by functional diversification. Gene exchanges also facilitate the emergence of cross-talk between elements in the same bacterium. In the end, these processes produce multilayered networks of interactions that shape the outcome of viral infections.
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12
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Nguyen MHT, Netter Z, Angermeyer A, Seed KD. A phage weaponizes a satellite recombinase to subvert viral restriction. Nucleic Acids Res 2022; 50:11138-11153. [PMID: 36259649 DOI: 10.1093/nar/gkac845] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/14/2022] [Accepted: 10/10/2022] [Indexed: 11/14/2022] Open
Abstract
Bacteria can acquire mobile genetic elements (MGEs) to combat infection by viruses (phages). Satellite viruses, including the PLEs (phage-inducible chromosomal island-like elements) in epidemic Vibrio cholerae, are MGEs that restrict phage replication to the benefit of their host bacterium. PLEs parasitize the lytic phage ICP1, unleashing multiple mechanisms to restrict phage replication and promote their own spread. In the arms race against PLE, ICP1 uses nucleases, including CRISPR-Cas, to destroy PLE's genome during infection. However, through an unknown CRISPR-independent mechanism, specific ICP1 isolates subvert restriction by PLE. Here, we discover ICP1-encoded Adi that counteracts PLE by exploiting the PLE's large serine recombinase (LSR), which normally mobilizes PLE in response to ICP1 infection. Unlike previously characterized ICP1-encoded anti-PLE mechanisms, Adi is not a nuclease itself but instead appears to modulate the activity of the LSR to promote destructive nuclease activity at the LSR's specific attachment site, attP. The PLE LSR, its catalytic activity, and attP are additionally sufficient to sensitize a PLE encoding a resistant variant of the recombination module to Adi activity. This work highlights a unique type of adaptation arising from inter-genome conflicts, in which the intended activity of a protein can be weaponized to overcome the antagonizing genome.
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Affiliation(s)
- Maria H T Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Zoe Netter
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
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13
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Sulser S, Vucicevic A, Bellini V, Moritz R, Delavat F, Sentchilo V, Carraro N, van der Meer JR. A bistable prokaryotic differentiation system underlying development of conjugative transfer competence. PLoS Genet 2022; 18:e1010286. [PMID: 35763548 PMCID: PMC9286271 DOI: 10.1371/journal.pgen.1010286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/15/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022] Open
Abstract
The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7–4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements. Horizontal gene transfer processes among prokaryotes have raised wide interest, which is attested by broad public health concern of rapid spread of antibiotic resistances. However, we typically take for granted that horizontal transfer is the result of some underlying spontaneous low frequency event, but this is not necessarily the case. As we show here, mobile genetic elements from the class of integrative and conjugative elements (ICEs) impose a coordinated program on the host cell in order to transfer, leading to an exclusive differentiated set of transfer competent cells. We base our conclusions on single cell microscopy studies to compare the rare activation of ICE promoters in individual cells in bacterial populations, and on mutant and RNA-seq analysis to show their dependency on ICE factors. This is an important finding because it implies that conjugation itself is subject to natural selection, which would lead to selection of fitter elements that transfer better or become more widespread.
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Affiliation(s)
- Sandra Sulser
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Andrea Vucicevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Veronica Bellini
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Roxane Moritz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - François Delavat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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14
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LeGault KN, Barth ZK, DePaola P, Seed KD. A phage parasite deploys a nicking nuclease effector to inhibit viral host replication. Nucleic Acids Res 2022; 50:8401-8417. [PMID: 35066583 PMCID: PMC9410903 DOI: 10.1093/nar/gkac002] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/17/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
PLEs (phage-inducible chromosomal island-like elements) are phage parasites integrated into the chromosome of epidemic Vibrio cholerae. In response to infection by its viral host ICP1, PLE excises, replicates and hijacks ICP1 structural components for transduction. Through an unknown mechanism, PLE prevents ICP1 from transitioning to rolling circle replication (RCR), a prerequisite for efficient packaging of the viral genome. Here, we characterize a PLE-encoded nuclease, NixI, that blocks phage development likely by nicking ICP1’s genome as it transitions to RCR. NixI-dependent cleavage sites appear in ICP1’s genome during infection of PLE(+) V. cholerae. Purified NixI demonstrates in vitro nuclease activity specifically for sites in ICP1’s genome and we identify a motif that is necessary for NixI-mediated cleavage. Importantly, NixI is sufficient to limit ICP1 genome replication and eliminate progeny production, representing the most inhibitory PLE-encoded mechanism revealed to date. We identify distant NixI homologs in an expanded family of putative phage parasites in vibrios that lack nucleotide homology to PLEs but nonetheless share genomic synteny with PLEs. More generally, our results reveal a previously unknown mechanism deployed by phage parasites to limit packaging of their viral hosts’ genome and highlight the prominent role of nuclease effectors as weapons in the arms race between antagonizing genomes.
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Affiliation(s)
- Kristen N LeGault
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Peter DePaola
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, 271 Koshland Hall, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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15
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Ibarra-Chávez R, Hansen MF, Pinilla-Redondo R, Seed KD, Trivedi U. Phage satellites and their emerging applications in biotechnology. FEMS Microbiol Rev 2021; 45:fuab031. [PMID: 34104956 PMCID: PMC8632786 DOI: 10.1093/femsre/fuab031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
The arms race between (bacterio)phages and their hosts is a recognised hot spot for genome evolution. Indeed, phages and their components have historically paved the way for many molecular biology techniques and biotech applications. Further exploration into their complex lifestyles has revealed that phages are often parasitised by distinct types of hyperparasitic mobile genetic elements. These so-called phage satellites exploit phages to ensure their own propagation and horizontal transfer into new bacterial hosts, and their prevalence and peculiar lifestyle has caught the attention of many researchers. Here, we review the parasite-host dynamics of the known phage satellites, their genomic organisation and their hijacking mechanisms. Finally, we discuss how these elements can be repurposed for diverse biotech applications, kindling a new catalogue of exciting tools for microbiology and synthetic biology.
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Affiliation(s)
- Rodrigo Ibarra-Chávez
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Rafael Pinilla-Redondo
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
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16
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LeGault KN, Hays SG, Angermeyer A, McKitterick AC, Johura FT, Sultana M, Ahmed T, Alam M, Seed KD. Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts. Science 2021; 373:eabg2166. [PMID: 34326207 PMCID: PMC9064180 DOI: 10.1126/science.abg2166] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
Bacteriophage predation selects for diverse antiphage systems that frequently cluster on mobilizable defense islands in bacterial genomes. However, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts where there is need to inform phage therapy efforts and to understand how phages drive pathogen evolution. Using time-shift experiments, we uncovered fluctuations in Vibrio cholerae's resistance to phages in clinical samples. We mapped phage resistance determinants to SXT integrative and conjugative elements (ICEs), which notoriously also confer antibiotic resistance. We found that SXT ICEs, which are widespread in γ-proteobacteria, invariably encode phage defense systems localized to a single hotspot of genetic exchange. We identified mechanisms that allow phage to counter SXT-mediated defense in clinical samples, and document the selection of a novel phage-encoded defense inhibitor. Phage infection stimulates high-frequency SXT ICE conjugation, leading to the concurrent dissemination of phage and antibiotic resistances.
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Affiliation(s)
- Kristen N LeGault
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Stephanie G Hays
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Amelia C McKitterick
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Fatema-Tuz Johura
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Marzia Sultana
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Munirul Alam
- icddr,b, formerly International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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17
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Boyd CM, Angermeyer A, Hays SG, Barth ZK, Patel KM, Seed KD. Bacteriophage ICP1: A Persistent Predator of Vibrio cholerae. Annu Rev Virol 2021; 8:285-304. [PMID: 34314595 PMCID: PMC9040626 DOI: 10.1146/annurev-virology-091919-072020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteriophages or phages—viruses of bacteria—are abundant and considered to be highly diverse. Interestingly, a particular group of lytic Vibrio cholerae–specific phages (vibriophages) of the International Centre for Diarrheal Disease Research, Bangladesh cholera phage 1 (ICP1) lineage show high levels of genome conservation over large spans of time and geography, despite a constant coevolutionary arms race with their host. From a collection of 67 sequenced ICP1 isolates, mostly from clinical samples, we find these phages have mosaic genomes consisting of large, conserved modules disrupted by variable sequences that likely evolve mostly through mobile endonuclease-mediated recombination during coinfection. Several variable regions have been associated with adaptations against antiphage elements in V. cholerae; notably, this includes ICP1’s CRISPR-Cas system. The ongoing association of ICP1 and V. cholerae in cholera-endemic regions makes this system a rich source for discovery of novel defense and counterdefense strategies in bacteria-phage conflicts in nature.
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Affiliation(s)
- Caroline M Boyd
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Angus Angermeyer
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Stephanie G Hays
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Kishen M Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; .,Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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18
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Barth ZK, Nguyen MH, Seed KD. A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence-specific immunity against subviral parasites. eLife 2021; 10:68339. [PMID: 34232860 PMCID: PMC8263062 DOI: 10.7554/elife.68339] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/27/2021] [Indexed: 02/06/2023] Open
Abstract
Mobile genetic elements, elements that can move horizontally between genomes, have profound effects on their host's fitness. The phage-inducible chromosomal island-like element (PLE) is a mobile element that integrates into the chromosome of Vibrio cholerae and parasitizes the bacteriophage ICP1 to move between cells. This parasitism by PLE is such that it abolishes the production of ICP1 progeny and provides a defensive boon to the host cell population. In response to the severe parasitism imposed by PLE, ICP1 has acquired an adaptive CRISPR-Cas system that targets the PLE genome during infection. However, ICP1 isolates that naturally lack CRISPR-Cas are still able to overcome certain PLE variants, and the mechanism of this immunity against PLE has thus far remained unknown. Here, we show that ICP1 isolates that lack CRISPR-Cas encode an endonuclease in the same locus, and that the endonuclease provides ICP1 with immunity to a subset of PLEs. Further analysis shows that this endonuclease is of chimeric origin, incorporating a DNA-binding domain that is highly similar to some PLE replication origin-binding proteins. This similarity allows the endonuclease to bind and cleave PLE origins of replication. The endonuclease appears to exert considerable selective pressure on PLEs and may drive PLE replication module swapping and origin restructuring as mechanisms of escape. This work demonstrates that new genome defense systems can arise through domain shuffling and provides a greater understanding of the evolutionary forces driving genome modularity and temporal succession in mobile elements.
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Affiliation(s)
- Zachary K Barth
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Maria Ht Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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19
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Evolutionary Sweeps of Subviral Parasites and Their Phage Host Bring Unique Parasite Variants and Disappearance of a Phage CRISPR-Cas System. mBio 2021; 13:e0308821. [PMID: 35164562 PMCID: PMC8844924 DOI: 10.1128/mbio.03088-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio cholerae is a significant threat to global public health in part due to its propensity for large-scale evolutionary sweeps where lineages emerge and are replaced. These sweeps may originate from the Bay of Bengal, where bacteriophage predation and the evolution of antiphage counterdefenses is a recurring theme. The bacteriophage ICP1 is a key predator of epidemic V. cholerae and is notable for acquiring a CRISPR-Cas system to combat PLE, a defensive subviral parasite encoded by its V. cholerae host. Here, we describe the discovery of four previously unknown PLE variants through a retrospective analysis of >3,000 publicly available sequences as well as one additional variant (PLE10) from recent surveillance of cholera patients in Bangladesh. In recent sampling we also observed a lineage sweep of PLE-negative V. cholerae occurring within the patient population in under a year. This shift coincided with a loss of ICP1's CRISPR-Cas system in favor of a previously prevalent PLE-targeting endonuclease called Odn. Interestingly, PLE10 was resistant to ICP1-encoded Odn, yet it was not found in any recent V. cholerae strains. We also identified isolates from within individual patient samples that revealed both mixed PLE(+)/PLE(-) V. cholerae populations and ICP1 strains possessing CRISPR-Cas or Odn with evidence of in situ recombination. These findings reinforce our understanding of the successive nature of V. cholerae evolution and suggest that ongoing surveillance of V. cholerae, ICP1, and PLE in Bangladesh is important for tracking genetic developments relevant to pandemic cholera that can occur over relatively short timescales. IMPORTANCE With 1 to 4 million estimated cases annually, cholera is a disease of serious global concern in regions where access to safe drinking water is limited by inadequate infrastructure, inequity, or natural disaster. The Global Task Force on Cholera Control (GTFCC.org) considers outbreak surveillance to be a primary pillar in the strategy to reduce mortality from cholera worldwide. Therefore, developing a better understanding of temporal evolutionary changes in the causative agent of cholera, Vibrio cholerae, could help in those efforts. The significance of our research is in tracking the genomic shifts that distinguish V. cholerae outbreaks, with specific attention paid to current and historical trends in the arms race between V. cholerae and a cooccurring viral (bacteriophage) predator. Here, we discover additional diversity of a specific phage defense system in epidemic V. cholerae and document the loss of a phage-encoded CRISPR-Cas system, underscoring the dynamic nature of microbial populations across cholera outbreaks.
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