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Craske MW, Wilson JS, Fogg PCM. Gene transfer agents: structural and functional properties of domesticated viruses. Trends Microbiol 2024:S0966-842X(24)00133-1. [PMID: 38806321 DOI: 10.1016/j.tim.2024.05.002] [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: 02/27/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.
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Affiliation(s)
| | - Jason S Wilson
- Biology Department, University of York, York YO10 5DD, UK; York Structural Biology Laboratory (YSBL), University of York, York YO10 5DD, UK
| | - Paul C M Fogg
- Biology Department, University of York, York YO10 5DD, UK; York Biomedical Research Institute (YBRI), University of York, York YO10 5NG, UK.
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2
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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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3
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Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae. mSphere 2023; 8:e0051722. [PMID: 36622251 PMCID: PMC9942592 DOI: 10.1128/msphere.00517-22] [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] [Indexed: 01/10/2023] Open
Abstract
In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.
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4
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Henriksen NNSE, Schostag MD, Balder SR, Bech PK, Strube ML, Sonnenschein EC, Gram L. The ability of Phaeobacter inhibens to produce tropodithietic acid influences the community dynamics of a microalgal microbiome. ISME COMMUNICATIONS 2022; 2:109. [PMID: 37938341 PMCID: PMC9723703 DOI: 10.1038/s43705-022-00193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
Microbial secondary metabolites facilitate microbial interactions and are crucial for understanding the complexity of microbial community dynamics. The purpose of the present study was to determine how a secondary metabolite producing marine bacteria or its metabolite deficient mutant affected the microbiome of the marine microalgae Tetraselmis suecica during a 70 day long co-evolution experiment. Using 16S rRNA gene amplicon sequencing, we found that neither the tropodithietic acid (TDA)-producing Phaeobacter inhibens wildtype nor the TDA-deficient mutant had major impacts on the community composition. However, a subset of strains, displayed temporally different relative abundance trajectories depending on the presence of P. inhibens. In particular, a Winogradskyella strain displayed temporal higher relative abundance when the TDA-producing wildtype was present. Numbers of the TDA-producing wildtype were reduced significantly more than those of the mutant over time indicating that TDA production was not an advantage. In communities without the P. inhibens wildtype strain, an indigenous population of Phaeobacter increased over time, indicating that indigenous Phaeobacter populations cannot co-exist with the TDA-producing wildtype. Despite that TDA was not detected chemically, we detected transcripts of the tdaC gene indicating that TDA could be produced in the microbial community associated with the algae. Our work highlights the importance of deciphering longitudinal strain dynamics when addressing the ecological effect of secondary metabolites in a relevant natural community.
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Affiliation(s)
| | - Morten Dencker Schostag
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Simone Rosen Balder
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Eva Christina Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
- Department of Biosciences, Swansea University, Singleton Park, SA2 8PP, Swansea, United Kingdom
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark.
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5
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Sherlock D, Fogg PCM. The archetypal gene transfer agent RcGTA is regulated via direct interaction with the enigmatic RNA polymerase omega subunit. Cell Rep 2022; 40:111183. [PMID: 35947951 PMCID: PMC9638019 DOI: 10.1016/j.celrep.2022.111183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/06/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022] Open
Abstract
Gene transfer agents (GTAs) are small virus-like particles that indiscriminately package and transfer any DNA present in their host cell, with clear implications for bacterial evolution. The first transcriptional regulator that directly controls GTA expression, GafA, was recently discovered, but its mechanism of action has remained elusive. Here, we demonstrate that GafA controls GTA gene expression via direct interaction with the RNA polymerase omega subunit (Rpo-ω) and also positively autoregulates its own expression by an Rpo-ω-independent mechanism. We show that GafA is a modular protein with distinct DNA and protein binding domains. The functional domains we observe in Rhodobacter GafA also correspond to two-gene operons in Hyphomicrobiales pathogens. These data allow us to produce the most complete regulatory model for a GTA and point toward an atypical mechanism for RNA polymerase recruitment and specific transcriptional activation in the Alphaproteobacteria.
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Affiliation(s)
- David Sherlock
- Biology Department, University of York, York YO10 5DD, UK
| | - Paul C M Fogg
- Biology Department, University of York, York YO10 5DD, UK; York Biomedical Research Institute (YBRI), University of York, York YO10 5NG, UK.
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The Roseobacter-Group Bacterium Phaeobacter as a Safe Probiotic Solution for Aquaculture. Appl Environ Microbiol 2021; 87:e0258120. [PMID: 33310713 DOI: 10.1128/aem.02581-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phaeobacter inhibens has been assessed as a probiotic bacterium for application in aquaculture. Studies addressing the efficacy and safety indicate that P. inhibens maintains its antagonistic activity against pathogenic vibrios in aquaculture live cultures (live feed and fish egg/larvae) while having no or a positive effect on the host organisms and a minor impact on the host microbiomes. While P. inhibens produces antibacterial and algicidal compounds, no study has so far found a virulent phenotype of P. inhibens cells against higher organisms. Additionally, an in silico search for antibiotic resistance genes using published genomes of representative strains did not raise concerns regarding the risk for antimicrobial resistance. P. inhibens occurs naturally in aquaculture systems, supporting its safe usage in this environment. In conclusion, at the current state of knowledge, P. inhibens is a "safe-to-use" organism.
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Birmes L, Freese HM, Petersen J. RepC_soli: a novel promiscuous plasmid type of Rhodobacteraceae mediates horizontal transfer of antibiotic resistances in the ocean. Environ Microbiol 2021; 23:5395-5411. [PMID: 33393148 DOI: 10.1111/1462-2920.15380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/28/2020] [Indexed: 11/29/2022]
Abstract
Alphaproteobacteria are typically characterized by a multipartite genome organization with a chromosome, stable chromids and accessory plasmids. Extrachromosomal elements determine the lifestyle of roseobacters and their horizontal transfer was previously correlated with rapid adaptations to novel ecological niches. We characterized the distribution and biology of a novel Rhodobacteraceae-specific plasmid type that was designated RepC_soli according to its diagnostic solitary replicase. This low copy number replicon exhibits an exceptional stability, which is likely ensured by non-canonical separate parA and parB partitioning genes. RepC_soli plasmids occur frequently in the surface-associated marine genus Phaeobacter and comparative genome analyses revealed the emergence of four compatibility groups. The universal presence of conserved type IV secretion systems in RepC_soli plasmids is indicative of their recurrent mobilization, a prediction that was experimentally validated by conjugation of the 57 kb Phaeobacter inhibens P72 plasmid (pP72_e) over genus borders. RepC_soli plasmids harbour a diverse collection of beneficial genes including transporters for heavy metal detoxification, prokaryotic defence systems and a conspicuous abundance of antibiotic resistance genes. The pP72_e-encoded efflux pump FloR conferred an about 50-fold increase of resistance against chloramphenicol. Its specific occurrence in Phaeobacter likely reflects a genetic footprint of (former) antimicrobial use in marine aquaculture.
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Affiliation(s)
- Lukas Birmes
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany
| | - Heike M Freese
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany
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Koch H, Germscheid N, Freese HM, Noriega-Ortega B, Lücking D, Berger M, Qiu G, Marzinelli EM, Campbell AH, Steinberg PD, Overmann J, Dittmar T, Simon M, Wietz M. Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Sci Rep 2020; 10:809. [PMID: 31964928 PMCID: PMC6972757 DOI: 10.1038/s41598-020-57526-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/23/2019] [Indexed: 01/28/2023] Open
Abstract
Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nora Germscheid
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dominik Lücking
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Galaxy Qiu
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Western Sydney University, Hawkesbury, Australia
| | - Ezequiel M Marzinelli
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
- University of Sydney, Camperdown, Australia
| | - Alexandra H Campbell
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- University of Sunshine Coast, Sunshine Coast, Australia
| | - Peter D Steinberg
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
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9
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Nappi J, Soldi E, Egan S. Diversity and Distribution of Bacteria Producing Known Secondary Metabolites. MICROBIAL ECOLOGY 2019; 78:885-894. [PMID: 31016338 DOI: 10.1007/s00248-019-01380-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.
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Affiliation(s)
- Jadranka Nappi
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Erika Soldi
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia.
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10
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Kopejtka K, Lin Y, Jakubovičová M, Koblížek M, Tomasch J. Clustered Core- and Pan-Genome Content on Rhodobacteraceae Chromosomes. Genome Biol Evol 2019; 11:2208-2217. [PMID: 31273387 PMCID: PMC6699656 DOI: 10.1093/gbe/evz138] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2019] [Indexed: 12/18/2022] Open
Abstract
In Bacteria, chromosome replication starts at a single origin of replication and proceeds on both replichores. Due to its asymmetric nature, replication influences chromosome structure and gene organization, mutation rate, and expression. To date, little is known about the distribution of highly conserved genes over the bacterial chromosome. Here, we used a set of 101 fully sequenced Rhodobacteraceae representatives to analyze the relationship between conservation of genes within this family and their distance from the origin of replication. Twenty-two of the analyzed species had core genes clustered significantly closer to the origin of replication with representatives of the genus Celeribacter being the most apparent example. Interestingly, there were also eight species with the opposite organization. In particular, Rhodobaca barguzinensis and Loktanella vestfoldensis showed a significant increase of core genes with distance from the origin of replication. The uneven distribution of low-conserved regions is in particular pronounced for genomes in which the halves of one replichore differ in their conserved gene content. Phage integration and horizontal gene transfer partially explain the scattered nature of Rhodobacteraceae genomes. Our findings lay the foundation for a better understanding of bacterial genome evolution and the role of replication therein.
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Affiliation(s)
- Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Yan Lin
- Department of Physics, School of Science, Tianjin University, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Markéta Jakubovičová
- Faculty of Information Technology, Czech Technical University in Prague, Czech Republic
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Center Algatech, Institute of Microbiology CAS, Třeboň, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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11
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Tomasch J, Wang H, Hall ATK, Patzelt D, Preusse M, Petersen J, Brinkmann H, Bunk B, Bhuju S, Jarek M, Geffers R, Lang AS, Wagner-Döbler I. Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random. Genome Biol Evol 2018; 10:359-369. [PMID: 29325123 PMCID: PMC5786225 DOI: 10.1093/gbe/evy005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 02/07/2023] Open
Abstract
Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world’s oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a “headful” type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated.
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Affiliation(s)
- Jürgen Tomasch
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany.,Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Hui Wang
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - April T K Hall
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Diana Patzelt
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Jörn Petersen
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Henner Brinkmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabin Bhuju
- Group Genome Analytics, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Michael Jarek
- Group Genome Analytics, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Robert Geffers
- Group Genome Analytics, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Irene Wagner-Döbler
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany
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12
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Overmann J, Huang S, Nübel U, Hahnke RL, Tindall BJ. Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms. Syst Appl Microbiol 2018; 42:22-29. [PMID: 30197212 DOI: 10.1016/j.syapm.2018.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 12/12/2022]
Abstract
To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.
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Affiliation(s)
- Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Braunschweig-Hannover, Braunschweig, Germany; German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Sixing Huang
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Braunschweig-Hannover, Braunschweig, Germany
| | - Richard L Hahnke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Brian J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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Sonnenschein EC, Phippen CBW, Bentzon-Tilia M, Rasmussen SA, Nielsen KF, Gram L. Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:383-393. [PMID: 29624899 DOI: 10.1111/1758-2229.12649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter, 27-4, did not produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina, Thalassiosira pseudonana and Emiliania huxleyi, while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.
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Affiliation(s)
- Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Silas Anselm Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
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