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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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Banks EJ, Le TBK. Co-opting bacterial viruses for DNA exchange: structure and regulation of gene transfer agents. Curr Opin Microbiol 2024; 78:102431. [PMID: 38309246 DOI: 10.1016/j.mib.2024.102431] [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: 11/23/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Horizontal gene transfer occurs via a range of mechanisms, including transformation, conjugation and bacteriophage transduction. Gene transfer agents (GTAs) are an alternative, less-studied route for interbacterial DNA exchange. Encoded within bacterial or archaeal genomes, GTAs assemble into phage-like particles that selflessly package and transmit host DNA to recipient bacteria. Several unique features distinguish GTAs from canonical phages such as an inability to self-replicate, thus producing non-infectious particles. GTAs are also deeply integrated into the physiology of the host cell and are maintained under tight host-regulatory control. Recent advances in understanding the structure and regulation of GTAs have provided further insights into a DNA transfer mechanism that is proving increasingly widespread across the bacterial tree of life.
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Affiliation(s)
- Emma J Banks
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
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3
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Kogay R, Zhaxybayeva O. Co-evolution of gene transfer agents and their alphaproteobacterial hosts. J Bacteriol 2024; 206:e0039823. [PMID: 38240570 PMCID: PMC10883770 DOI: 10.1128/jb.00398-23] [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: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 02/23/2024] Open
Abstract
Gene transfer agents (GTAs) are enigmatic elements that resemble small viruses and are known to be produced during nutritional stress by some bacteria and archaea. The production of GTAs is regulated by quorum sensing, under which a small fraction of the population acts as GTA producers, while the rest becomes GTA recipients. In contrast to canonical viruses, GTAs cannot propagate themselves because they package pieces of the producing cell's genome. In alphaproteobacteria, GTAs are mostly vertically inherited and reside in their hosts' genomes for hundreds of millions of years. While GTAs' ability to transfer genetic material within a population and their long-term preservation suggest an increased fitness of GTA-producing microbes, the associated benefits and type of selection that maintains GTAs are poorly understood. By comparing rates of evolutionary change in GTA genes to the rates in gene families abundantly present across 293 alphaproteobacterial genomes, we detected 59 gene families that likely co-evolve with GTA genes. These gene families are predominantly involved in stress response, DNA repair, and biofilm formation. We hypothesize that biofilm formation enables the physical proximity of GTA-producing cells, limiting GTA-derived benefits only to a group of closely related cells. We further conjecture that the population structure of biofilm-forming sub-populations ensures that the trait of GTA production is maintained despite the inevitable rise of "cheating" genotypes. Because release of GTA particles kills the producing cell, maintenance of GTAs is an exciting example of social evolution in a microbial population.IMPORTANCEGene transfer agents (GTAs) are viruses domesticated by some archaea and bacteria as vehicles for carrying pieces of the host genome. Produced under certain environmental conditions, GTA particles can deliver DNA to neighboring, closely related cells. The function of GTAs remains uncertain. While making GTAs is suicidal for a cell, GTA-encoding genes are widespread in genomes of alphaproteobacteria. Such GTA persistence implies functional benefits but raises questions about how selection maintains this lethal trait. By showing that GTA genes co-evolve with genes involved in stress response, DNA repair, and biofilm formation, we provide support for the hypothesis that GTAs facilitate DNA exchange during the stress conditions and present a model for how GTAs persist in biofilm-forming bacterial populations despite being lethal.
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Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
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4
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Langille E, Bottaro CS, Lang AS. Purification of Functional Gene Transfer Agents Using Two-Step Preparative Monolithic Chromatography. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:194-203. [PMID: 36793882 PMCID: PMC9917305 DOI: 10.1089/phage.2022.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Gene transfer agents (GTAs) are phage-like particles that transfer cellular genomic DNA between cells. A hurdle faced in studying GTA function and interactions with cells is the difficulty in obtaining pure and functional GTAs from cultures. Materials and Methods We used a novel two-step method for purification of GTAs from R. capsulatus by monolithic chromatography. Results Our efficient and simple process had advantages compared to previous approaches. The purified GTAs retained gene transfer activity and the packaged DNA could be used for further studies. Conclusions This method is applicable to GTAs produced by other species and small phages, and could be useful for therapeutic applications.
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Affiliation(s)
- Evan Langille
- Department of Chemistry and Memorial University of Newfoundland, St. John's, Canada
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Christina S. Bottaro
- Department of Chemistry and Memorial University of Newfoundland, St. John's, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
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5
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Koppenhöfer S, Tomasch J, Lang AS. Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria. Microb Genom 2022; 8:mgen000890. [PMID: 36350115 PMCID: PMC9836097 DOI: 10.1099/mgen.0.000890] [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: 11/11/2022] Open
Abstract
Gene transfer agents (GTAs) are phage-like particles that transfer pieces of cellular genomic DNA to other cells. Homologues of the Rhodobacter capsulatus GTA (RcGTA) structural genes are widely distributed in the Alphaproteobacteria and particularly well conserved in the order Rhodobacterales. Possible reasons for their widespread conservation are still being discussed. It has been suggested that these alphaproteobacterial elements originate from a prophage that was present in an ancestral bacterium and subsequently evolved into a GTA that is now widely maintained in extant descendant lineages. Here, we analysed genomic properties that might relate to the conservation of these alphaproteobacterial GTAs. This revealed that the chromosomal locations of the GTA gene clusters are biased. They primarily occur on the leading strand of DNA replication, at large distances from long repetitive elements, and thus are in regions of lower plasticity, and in areas of extreme GC skew, which also accumulate core genes. These extreme GC skew regions arise from the preferential use of codons with an excess of G over C, a distinct phenomenon from the elevated GC content that has previously been found to be associated with GTA genes. The observed properties, along with their high level of conservation, show that GTA genes share multiple features with core genes in the examined lineages of the Alphaproteobacteria.
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Affiliation(s)
- Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St John’s, Newfoundland and Labrador, Canada
| | - Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Science – Centre Algatech, Třeboň, Czech Republic
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St John’s, Newfoundland and Labrador, Canada,*Correspondence: Andrew S. Lang,
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DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus. Genes (Basel) 2022; 13:genes13112071. [DOI: 10.3390/genes13112071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.
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Lang AS. Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair. PLoS Biol 2022; 20:e3001874. [PMID: 36346786 PMCID: PMC9642860 DOI: 10.1371/journal.pbio.3001874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The potential benefits of producing gene transfer agents (GTAs) have long been speculated. A new study in PLOS Biology shows that DNA transfer by these phage-like elements allows cells with DNA damage to perform DNA repair and survive.
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Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
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8
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Kogay R, Koppenhöfer S, Beatty JT, Kuhn JH, Lang AS, Zhaxybayeva O. Formal recognition and classification of gene transfer agents as viriforms. Virus Evol 2022; 8:veac100. [PMID: 36381234 PMCID: PMC9662315 DOI: 10.1093/ve/veac100] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/10/2022] [Accepted: 10/14/2022] [Indexed: 06/19/2024] Open
Abstract
Morphological and genetic features strongly suggest that gene transfer agents (GTAs) are caudoviricete-derived entities that have evolved in concert with cellular genomes to such a degree that they should not be considered viruses. Indeed, GTA particles resemble caudoviricete virions, but, in contrast to caudoviricetes (or any viruses), GTAs can encapsidate at best only part of their own genomes, are induced solely in small subpopulations of prokaryotic host cells, and are transmitted vertically as part of cellular genomes during replication and division. Therefore, the lifecycles of GTAs are analogous to virus-derived entities found in the parasitoid wasps, which have recently been recognized as non-virus entities and therefore reclassified as viriforms. We evaluated three distinct, independently exapted GTA groups, for which the genetic basis for GTA particle production has been established. Based on the evidence, we outline a classification scheme for these viriforms.
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Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, USA
| | | | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s, NL A1C 5S7, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, USA
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s, NL A1C 5S7, Canada
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9
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The Sixth Element: a 102-kb RepABC Plasmid of Xenologous Origin Modulates Chromosomal Gene Expression in Dinoroseobacter shibae. mSystems 2022; 7:e0026422. [PMID: 35920548 PMCID: PMC9426580 DOI: 10.1128/msystems.00264-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The model organism Dinoroseobacter shibae and many other marine Rhodobacterales (Roseobacteraceae, Alphaproteobacteria) are characterized by a multipartite genome organization. Here, we show that the original isolate (Dshi-6) contained six extrachromosomal replicons (ECRs), whereas the strain deposited at the DSMZ (Dshi-5) lacked a 102-kb plasmid. To determine the role of the sixth plasmid, we investigated the genomic and physiological differences between the two strains. Therefore, both genomes were (re)sequenced, and gene expression, growth, and substrate utilization were examined. For comparison, we included additional plasmid-cured strains in the analysis. In the Dshi-6 population, the conjugative 102-kb RepABC-9 plasmid was present in only about 50% of the cells, irrespective of its experimentally validated stability. In the presence of the sixth plasmid, copy number changes of other ECRs, in particular, a decrease of the 86-kb plasmid, were observed. The most conspicuous finding was the strong influence of plasmids on chromosomal gene expression, especially the repression of the CtrA regulon and the activation of the denitrification gene cluster. Expression is inversely controlled by either the presence of the 102-kb plasmid or the absence of the 86-kb plasmid. We identified regulatory genes on both plasmids, i.e., a sigma 70 factor and a quorum sensing synthase, that might be responsible for these major changes. The tremendous effects that were probably even underestimated challenge the current understanding of the relevance of volatile plasmids not only for the original host but also for new recipients after conjugation. IMPORTANCE Plasmids are small DNA molecules that replicate independently of the bacterial chromosome. The common view of the role of plasmids is dominated by the accumulation of resistance genes, which is responsible for the antibiotic crisis in health care and livestock breeding. Beyond rapid adaptations to a changing environment, no general relevance for the host cell’s regulome was attributed to these volatile ECRs. The current study shows for the model organism D. shibae that its chromosomal gene expression is strongly influenced by two plasmids. We provide evidence that the gain or loss of plasmids not only results in minor alterations of the genetic repertoire but also can have tremendous effects on bacterial physiology. The central role of some plasmids in the regulatory network of the host could also explain their persistence despite fitness costs, which has been described as the “plasmid paradox.”
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10
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George EE, Tashyreva D, Kwong WK, Okamoto N, Horák A, Husnik F, Lukeš J, Keeling PJ. Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes. Genome Biol Evol 2022; 14:6615375. [PMID: 35738252 PMCID: PMC9254644 DOI: 10.1093/gbe/evac099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/14/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.
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Affiliation(s)
- Emma E George
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
| | - Daria Tashyreva
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Waldan K Kwong
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Instituto Gulbenkian de Ciência, 6, 2780-156 Oeiras, Portugal
| | - Noriko Okamoto
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | - Aleš Horák
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Filip Husnik
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada.,Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic.,University of South Bohemia, Faculty of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
| | - Patrick J Keeling
- University of British Columbia, Department of Botany, Vancouver, V6T 1Z4, Canada
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11
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Bordenstein SR, Bordenstein SR. Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae. PLoS Genet 2022; 18:e1010227. [PMID: 35666732 PMCID: PMC9203015 DOI: 10.1371/journal.pgen.1010227] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/16/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia’s mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO’s relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the putative origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to distinguish the four variants. We identify a novel, putative lytic cassette and WO’s association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages, including non-Wolbachia phages from aquatic environments, that includes a new family and two new genera to capture the collective relatedness of these viruses.
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Affiliation(s)
- Sarah R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
| | - Seth R. Bordenstein
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, United States of America
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12
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Fallon AM. Muramidase, nuclease, or hypothetical protein genes intervene between paired genes encoding DNA packaging terminase and portal proteins in Wolbachia phages and prophages. Virus Genes 2022; 58:327-349. [PMID: 35538383 DOI: 10.1007/s11262-022-01907-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/11/2022] [Indexed: 12/25/2022]
Abstract
Genomes of the obligate intracellular alpha proteobacterium Wolbachia pipientis often encode prophage-like regions, and in a few cases, purified particles have been recovered. Because the structure of a conserved WO phage genome has been difficult to establish, we examined paired terminase and portal genes in Wolbachia phages and prophages, relative to those encoded by the gene transfer agent RcGTA from the free-living alpha proteobacterium Rhodobacter capsulatus. Terminase and portal proteins from Wolbachia have higher similarity to orthologs encoded by RcGTA than to orthologs encoded by bacteriophage lambda. In lambdoid phages, these proteins play key roles in assembly of mature phage particles, while in less well-studied gene transfer agents, terminase and portal proteins package random fragments of bacterial DNA, which could confound elucidation of WO phage genomes. In WO phages and prophages, terminase genes followed by a short gpW gene may be separated from the downstream portal gene by open-reading frames encoding a GH_25 hydrolase/muramidase, a PD-(D/E)XK nuclease, a hypothetical protein and/or a RelE/ParE toxin-antitoxin module. These aspects of gene organization, coupled with evidence for a low, non-inducible yield of WO phages, and the small size of WO phage particles described in the literature raise the possibility that Wolbachia prophage regions participate in processes that extend beyond conventional bacteriophage lysogeny and lytic replication. These intervening genes, and their possible relation to functions associated with GTAs, may contribute to variability among WO phage genomes recovered from physical particles and impact the ability of WO phages to act as transducing agents.
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Affiliation(s)
- Ann M Fallon
- Department of Entomology, University of Minnesota, 1980 Folwell Ave, St. Paul, MN, 55108, USA.
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13
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Khare T, Anand U, Dey A, Assaraf YG, Chen ZS, Liu Z, Kumar V. Exploring Phytochemicals for Combating Antibiotic Resistance in Microbial Pathogens. Front Pharmacol 2021; 12:720726. [PMID: 34366872 PMCID: PMC8334005 DOI: 10.3389/fphar.2021.720726] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 06/28/2021] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance or microbial drug resistance is emerging as a serious threat to human healthcare globally, and the multidrug-resistant (MDR) strains are imposing major hurdles to the progression of drug discovery programs. Newer antibiotic-resistance mechanisms in microbes contribute to the inefficacy of the existing drugs along with the prolonged illness and escalating expenditures. The injudicious usage of the conventional and commonly available antibiotics in human health, hygiene, veterinary and agricultural practices is proving to be a major driver for evolution, persistence and spread of antibiotic-resistance at a frightening rate. The drying pipeline of new and potent antibiotics is adding to the severity. Therefore, novel and effective new drugs and innovative therapies to treat MDR infections are urgently needed. Apart from the different natural and synthetic drugs being tested, plant secondary metabolites or phytochemicals are proving efficient in combating the drug-resistant strains. Various phytochemicals from classes including alkaloids, phenols, coumarins, terpenes have been successfully demonstrated their inhibitory potential against the drug-resistant pathogens. Several phytochemicals have proved effective against the molecular determinants responsible for attaining the drug resistance in pathogens like membrane proteins, biofilms, efflux pumps and bacterial cell communications. However, translational success rate needs to be improved, but the trends are encouraging. This review highlights current knowledge and developments associated challenges and future prospects for the successful application of phytochemicals in combating antibiotic resistance and the resistant microbial pathogens.
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Affiliation(s)
- Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India.,Department of Environmental Science, Savitribai Phule Pune University, Pune, India
| | - Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Abhijit Dey
- Ethnopharmacology and Natural Product Research Laboratory, Department of Life Sciences, Presidency University, Kolkata, India
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Zhijun Liu
- Department of Microbiology, Weifang Medical University, Weifang, China
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India.,Department of Environmental Science, Savitribai Phule Pune University, Pune, India
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14
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Esterman ES, Wolf YI, Kogay R, Koonin EV, Zhaxybayeva O. Evolution of DNA packaging in gene transfer agents. Virus Evol 2021; 7:veab015. [PMID: 33732503 PMCID: PMC7947584 DOI: 10.1093/ve/veab015] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.
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Affiliation(s)
- Emma S Esterman
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
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15
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Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013 addresses these very questions. This paper comprises a summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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16
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Benler S, Koonin EV. Phage lysis‐lysogeny switches and programmed cell death: Danse macabre. Bioessays 2020; 42:e2000114. [DOI: 10.1002/bies.202000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/25/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
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17
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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18
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Colombet J, Fuster M, Billard H, Sime-Ngando T. Femtoplankton: What's New? Viruses 2020; 12:E881. [PMID: 32806713 PMCID: PMC7472349 DOI: 10.3390/v12080881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 01/01/2023] Open
Abstract
Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010-2020) of high abundances of biomimetic mineral-organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.
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Affiliation(s)
- Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (M.F.); (H.B.); (T.S.-N.)
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19
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White RA, Visscher PT, Burns BP. Between a Rock and a Soft Place: The Role of Viruses in Lithification of Modern Microbial Mats. Trends Microbiol 2020; 29:204-213. [PMID: 32654857 DOI: 10.1016/j.tim.2020.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/07/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022]
Abstract
Stromatolites are geobiological systems formed by complex microbial communities, and fossilized stromatolites provide a record of some of the oldest life on Earth. Microbial mats are precursors of extant stromatolites; however, the mechanisms of transition from mat to stromatolite are controversial and are still not well understood. To fully recognize the profound impact that these ecosystems have had on the evolution of the biosphere requires an understanding of modern lithification mechanisms and how they relate to the geological record. We propose here viral mechanisms in carbonate precipitation, leading to stromatolite formation, whereby viruses directly or indirectly impact microbial metabolisms that govern the transition from microbial mat to stromatolite. Finding a tangible link between host-virus interactions and changes in biogeochemical processes will provide tools to interpret mineral biosignatures through geologic time, including those on Earth and beyond.
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Affiliation(s)
- Richard Allen White
- Plant Pathology, Washington State University, Pullman, WA, USA; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; RAW Molecular Systems (RMS) LLC, Spokane, WA, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; Departments of Marine Sciences and Geosciences, University of Connecticut, CT, USA; Biogeosciences, the Université de Bourgogne Franche-Comté, Dijon, France
| | - Brendan P Burns
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.
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20
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Bárdy P, Füzik T, Hrebík D, Pantůček R, Thomas Beatty J, Plevka P. Structure and mechanism of DNA delivery of a gene transfer agent. Nat Commun 2020; 11:3034. [PMID: 32541663 PMCID: PMC7296036 DOI: 10.1038/s41467-020-16669-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/17/2020] [Indexed: 11/09/2022] Open
Abstract
Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
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Affiliation(s)
- Pavol Bárdy
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Dominik Hrebík
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.
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21
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Molecules to Microbes. SCI 2020. [DOI: 10.3390/sci2020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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22
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Abstract
Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.
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Affiliation(s)
- Steen Christensen
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Laura R Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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23
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Ding H, Grüll MP, Mulligan ME, Lang AS, Beatty JT. Induction of Rhodobacter capsulatus Gene Transfer Agent Gene Expression Is a Bistable Stochastic Process Repressed by an Extracellular Calcium-Binding RTX Protein Homologue. J Bacteriol 2019; 201:e00430-19. [PMID: 31501287 PMCID: PMC6832060 DOI: 10.1128/jb.00430-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/06/2019] [Indexed: 01/28/2023] Open
Abstract
Bacteriophage-like gene transfer agents (GTAs) have been discovered in both of the prokaryotic branches of the three-domain phylogenetic tree of life. The production of a GTA (RcGTA) by the phototrophic alphaproteobacterium Rhodobacter capsulatus is regulated by quorum sensing and a phosphorelay homologous to systems in other species that control essential functions such as the initiation of chromosome replication and cell division. In wild-type strains, RcGTA is produced in <3% of cells in laboratory cultures. Mutants of R. capsulatus that exhibit greatly elevated production of RcGTA were created decades ago by chemical mutagenesis, but the nature and molecular consequences of the mutation were unknown. We show that the number of cells in a population that go on to express RcGTA genes is controlled by a stochastic process, in contrast to a genetic process. We used transposon mutagenesis along with a fluorescent protein reporter system and genome sequence data to identify a gene, rcc00280, that encodes an RTX family calcium-binding protein homologue. The Rc280 protein acts as an extracellular repressor of RcGTA gene expression by decreasing the percentage of cells that induce the production of RcGTA.IMPORTANCE GTAs catalyze horizontal gene transfer (HGT), which is important for genomic evolution because the majority of genes found in bacterial genomes have undergone HGT at some point in their evolution. Therefore, it is important to determine how the production of GTAs is regulated to understand the factors that modulate the frequency of gene transfer and thereby specify the tempo of evolution. This work describes a new type of genetic regulation in which an extracellular calcium-binding protein homologue represses the induction of the Rhodobacter capsulatus GTA, RcGTA.
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Affiliation(s)
- Hao Ding
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc P Grüll
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Martin E Mulligan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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24
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Grüll MP, Mulligan ME, Lang AS. Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. FEMS Microbiol Lett 2019; 365:5067299. [PMID: 30085064 DOI: 10.1093/femsle/fny192] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/04/2018] [Indexed: 12/18/2022] Open
Abstract
Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.
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Affiliation(s)
| | - M E Mulligan
- Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
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25
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Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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26
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Québatte M, Dehio C. Bartonella gene transfer agent: Evolution, function, and proposed role in host adaptation. Cell Microbiol 2019; 21:e13068. [PMID: 31231937 PMCID: PMC6899734 DOI: 10.1111/cmi.13068] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/09/2019] [Accepted: 06/13/2019] [Indexed: 01/05/2023]
Abstract
The processes underlying host adaptation by bacterial pathogens remain a fundamental question with relevant clinical, ecological, and evolutionary implications. Zoonotic pathogens of the genus Bartonella constitute an exceptional model to study these aspects. Bartonellae have undergone a spectacular diversification into multiple species resulting from adaptive radiation. Specific adaptations of a complex facultative intracellular lifestyle have enabled the colonisation of distinct mammalian reservoir hosts. This remarkable host adaptability has a multifactorial basis and is thought to be driven by horizontal gene transfer (HGT) and recombination among a limited genus‐specific pan genome. Recent functional and evolutionary studies revealed that the conserved Bartonella gene transfer agent (BaGTA) mediates highly efficient HGT and could thus drive this evolution. Here, we review the recent progress made towards understanding BaGTA evolution, function, and its role in the evolution and pathogenesis of Bartonella spp. We notably discuss how BaGTA could have contributed to genome diversification through recombination of beneficial traits that underlie host adaptability. We further address how BaGTA may counter the accumulation of deleterious mutations in clonal populations (Muller's ratchet), which are expected to occur through the recurrent transmission bottlenecks during the complex infection cycle of these pathogens in their mammalian reservoir hosts and arthropod vectors.
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27
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Koppenhöfer S, Wang H, Scharfe M, Kaever V, Wagner-Döbler I, Tomasch J. Integrated Transcriptional Regulatory Network of Quorum Sensing, Replication Control, and SOS Response in Dinoroseobacter shibae. Front Microbiol 2019; 10:803. [PMID: 31031742 PMCID: PMC6473078 DOI: 10.3389/fmicb.2019.00803] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022] Open
Abstract
Quorum sensing (QS) coordinates population wide gene expression of bacterial species. Highly adaptive traits like gene transfer agents (GTA), morphological heterogeneity, type 4 secretion systems (T4SS), and flagella are QS controlled in Dinoroseobacter shibae, a Roseobacter model organism. Its QS regulatory network is integrated with the CtrA phosphorelay that controls cell division in alphaproteobacteria. To elucidate the network topology, we analyzed the transcriptional response of the QS-negative D. shibae strain ΔluxI1 toward externally added autoinducer (AI) over a time period of 3 h. The signaling cascade is initiated by the CtrA phosphorelay, followed by the QS genes and other target genes, including the second messenger c-di-GMP, competence, flagella and pili. Identification of transcription factor binding sites in promoters of QS induced genes revealed the integration of QS, CtrA phosphorelay and the SOS stress response mediated by LexA. The concentration of regulatory genes located close to the origin or terminus of replication suggests that gene regulation and replication are tightly coupled. Indeed, addition of AI first stimulates and then represses replication. The restart of replication comes along with increased c-di-GMP levels. We propose a model in which QS induces replication followed by differentiation into GTA producing and non-producing cells. CtrA-activity is controlled by the c-di-GMP level, allowing some of the daughter cells to replicate again. The size of the GTA producing subpopulation is tightly controlled by QS via the AI Synthase LuxI2. Finally, induction of the SOS response allows for integration of GTA DNA into the host chromosome.
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Affiliation(s)
- Sonja Koppenhöfer
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hui Wang
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Maren Scharfe
- Group Genomic Analytics, Helmholtz Centre for Infection Research, Helmholtz Association of German Research Centers, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Hanover, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
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28
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Redfield RJ, Soucy SM. Evolution of Bacterial Gene Transfer Agents. Front Microbiol 2018; 9:2527. [PMID: 30410473 PMCID: PMC6209664 DOI: 10.3389/fmicb.2018.02527] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 01/30/2023] Open
Abstract
Bacterial gene transfer agents (GTAs) are small virus-like particles that package DNA fragments and inject them into cells. They are encoded by gene clusters resembling defective prophages, with genes for capsid head and tail components. These gene clusters are usually assumed to be maintained by selection for the benefits of GTA-mediated recombination, but this has never been tested. We rigorously examined the potential benefits of GTA-mediated recombination, considering separately transmission of GTA-encoding genes and recombination of all chromosomal genes. In principle GTA genes could be directly maintained if GTA particles spread them to GTA- cells often enough to compensate for the loss of GTA-producing cells. However, careful bookkeeping showed that losses inevitably exceed gains for two reasons. First, cells must lyse to release particles to the environment. Second, GTA genes are not preferentially replicated before DNA is packaged. A simulation model was then used to search for conditions where recombination of chromosomal genes makes GTA+ populations fitter than GTA- populations. Although the model showed that both synergistic epistasis and some modes of regulation could generate fitness benefits large enough to overcome the cost of lysis, these benefits neither allowed GTA+ cells to invade GTA- populations, nor allowed GTA+ populations to resist invasion by GTA- cells. Importantly, the benefits depended on highly improbable assumptions about the efficiencies of GTA production and recombination. Thus, the selective benefits that maintain GTA gene clusters over many millions of years must arise from consequences other than transfer of GTA genes or recombination of chromosomal genes.
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Affiliation(s)
- Rosemary J Redfield
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Shannon M Soucy
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
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29
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The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production in Rhodobacter capsulatus. Appl Environ Microbiol 2018; 84:AEM.00275-18. [PMID: 29625982 DOI: 10.1128/aem.00275-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/29/2018] [Indexed: 01/01/2023] Open
Abstract
Several members of the Rhodobacterales (Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is the Rhodobacter capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production in R. capsulatus We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels in R. capsulatus and identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in the RhodobacteralesIMPORTANCE Members of the Rhodobacterales are abundant in ocean and freshwater environments. The conserved GTA produced by many Rhodobacterales may have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA in R. capsulatus extends the model of CtrA regulation from Caulobacter crescentus to a member of the Rhodobacterales We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.
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30
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Braga LPP, Soucy SM, Amgarten DE, da Silva AM, Setubal JC. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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31
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Lang AS, Westbye AB, Beatty JT. The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange. Annu Rev Virol 2017; 4:87-104. [DOI: 10.1146/annurev-virology-101416-041624] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, A1B 3X9, Canada
| | - Alexander B. Westbye
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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32
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Westbye AB, O'Neill Z, Schellenberg-Beaver T, Beatty JT. The Rhodobacter capsulatus gene transfer agent is induced by nutrient depletion and the RNAP omega subunit. Microbiology (Reading) 2017; 163:1355-1363. [DOI: 10.1099/mic.0.000519] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander B. Westbye
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
- Present address: Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 't Horntje (Texel), Netherlands
| | - Zoe O'Neill
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Tegan Schellenberg-Beaver
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
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