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Elg CA, Mack E, Rolfsmeier M, McLean TC, Kosterlitz O, Soderling E, Narum S, Rowley PA, Thomas CM, Top EM. Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579024. [PMID: 38370613 PMCID: PMC10871194 DOI: 10.1101/2024.02.05.579024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Plasmids play a major role in rapid adaptation of bacteria by facilitating horizontal transfer of diverse genes, most notably those conferring antibiotic resistance. While most plasmids that replicate in a broad range of bacteria also persist well in diverse hosts, there are exceptions that are poorly understood. We investigated why a broad-host range plasmid, pBP136, originally found in clinical Bordetella pertussis isolates, quickly became extinct in laboratory Escherichia coli populations. Through experimental evolution we found that inactivation of a previously uncharacterized plasmid gene, upf31, drastically improved plasmid maintenance in E. coli. This gene inactivation resulted in decreased transcription of the global plasmid regulators (korA, korB, and korC) and numerous genes in their regulons. It also caused transcriptional changes in many chromosomal genes primarily related to metabolism. In silico analyses suggested that the change in plasmid transcriptome may be initiated by Upf31 interacting with the plasmid regulator KorB. Expression of upf31 in trans negatively affected persistence of pBP136Δupf31 as well as the closely related archetypal IncP-1β plasmid R751, which is stable in E. coli and natively encodes a truncated upf31 allele. Our results demonstrate that while the upf31 allele in pBP136 might advantageously modulate gene expression in its original host, B. pertussis, it has harmful effects in E. coli. Thus, evolution of a single plasmid gene can change the range of hosts in which that plasmid persists, due to effects on the regulation of plasmid gene transcription.
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Affiliation(s)
- Clinton A. Elg
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Erin Mack
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Michael Rolfsmeier
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Thomas C. McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Olivia Kosterlitz
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
- Biology Department, University of Washington, Seattle, Washington, USA
| | | | - Solana Narum
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | | | - Eva M. Top
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, Idaho, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, Idaho, USA
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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Durand A, Maillard F, Foulon J, Chalot M. Interactions between Hg and soil microbes: microbial diversity and mechanisms, with an emphasis on fungal processes. Appl Microbiol Biotechnol 2020; 104:9855-9876. [PMID: 33043392 DOI: 10.1007/s00253-020-10795-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/06/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites. KEY POINTS: • The fungal communities are more resilient than bacterial communities to Hg exposure. • The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles. • Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments. • Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.
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Affiliation(s)
- Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine - INRAE, 2 avenue de la Forêt de Haye BP 20 163, 54505, Vandœuvre-lès-Nancy, France
| | - François Maillard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 Allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France.
- Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre-les-Nancy, France.
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Nielsen TK, Rasmussen M, Demanèche S, Cecillon S, Vogel TM, Hansen LH. Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH. Genome Biol Evol 2018; 9:2477-2490. [PMID: 28961970 PMCID: PMC5737581 DOI: 10.1093/gbe/evx185] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2017] [Indexed: 12/03/2022] Open
Abstract
Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH. The genome has an intricate organization of the chlorophenoxy-herbicide catabolic genes sdpA, rdpA, and cadABCD that encode the (R)- and (S)-enantiomer-specific 2,4-dichlorophenoxypropionate dioxygenases and four subunits of a Rieske non-heme iron oxygenase involved in 2-methyl-chlorophenoxyacetic acid degradation, respectively. Several major genomic rearrangements are proposed to help understand the evolution and mobility of these important genes and their genetic context. Single-strain mobilomic sequence analysis uncovered plasmids and insertion sequence-associated circular intermediates in this environmentally important bacterium and enabled the description of evolutionary models for pesticide degradation in strain MH and related organisms. The mobilome presented a complex mosaic of mobile genetic elements including four plasmids and several circular intermediate DNA molecules of insertion-sequence elements and transposons that are central to the evolution of xenobiotics degradation. Furthermore, two individual chromosomally integrated prophages were shown to excise and form free circular DNA molecules. This approach holds great potential for improving the understanding of genome plasticity, evolution, and microbial ecology.
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Affiliation(s)
| | | | - Sandrine Demanèche
- Environmental Microbial Genomics, Laboratoire Ampère (CNRS UMR5005), École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Sébastien Cecillon
- Environmental Microbial Genomics, Laboratoire Ampère (CNRS UMR5005), École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère (CNRS UMR5005), École Centrale de Lyon, Université de Lyon, Ecully, France
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Broaders E, O'Brien C, Gahan CGM, Marchesi JR. Evidence for plasmid-mediated salt tolerance in the human gut microbiome and potential mechanisms. FEMS Microbiol Ecol 2016; 92:fiw019. [PMID: 26850157 PMCID: PMC5831011 DOI: 10.1093/femsec/fiw019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/31/2016] [Indexed: 11/25/2022] Open
Abstract
The human gut microbiome is critical to health and wellbeing. It hosts a complex ecosystem comprising a multitude of bacterial species, which contributes functionality that would otherwise be absent from the host. Transient and commensal bacteria in the gut must withstand many stresses. The influence of mobile genetic elements such as plasmids in stress adaptation within the ecosystem is poorly understood. Using a mobilomic approach we found evidence for plasmid-mediated osmotolerance as a phenotype amongst the Proteobacteria in healthy faecal slurries. A transconjugant carrying multiple plasmids acquired from healthy faecal slurry demonstrated increased osmotolerance in the presence of metal salts, particularly potassium chloride, which was not evident in the recipient. Pyrosequencing and analysis of the total plasmid DNA demonstrated the presence of plasmid-borne osmotolerance systems (including KdpD and H-NS) which may be linked to the observed phenotype. This is the first report of a transferable osmotolerance phenotype in gut commensals and may have implications for the transfer of osmotolerance in other niches. There is evidence of a transferable osmotolerance phenotype in gut commensals which may have implications for the transfer of osmotolerance in other niches.
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Affiliation(s)
- Eileen Broaders
- Alimentary Pharmabiotic Centre, University College Cork, College Road, Cork, T12 YT20, Ireland Department of Microbiology, University College Cork, College Road, Cork, T12 YT20, Ireland
| | - Ciarán O'Brien
- Department of Microbiology, University College Cork, College Road, Cork, T12 YT20, Ireland
| | - Cormac G M Gahan
- Alimentary Pharmabiotic Centre, University College Cork, College Road, Cork, T12 YT20, Ireland Department of Microbiology, University College Cork, College Road, Cork, T12 YT20, Ireland School of Pharmacy, University College Cork, Cork, T12 YT20, Ireland
| | - Julian R Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, College Road, Cork, T12 YT20, Ireland School of Biosciences, Cardiff University, Cardiff CF103AX, UK Centre for Digestive and Gut Health, Imperial College London, London W2 1NY, UK
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Heuer H, Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 2012; 36:1083-104. [DOI: 10.1111/j.1574-6976.2012.00337.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 10/15/2011] [Accepted: 02/24/2012] [Indexed: 11/26/2022] Open
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Schlüter A, Szczepanowski R, Pühler A, Top EM. Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 2007; 31:449-77. [PMID: 17553065 DOI: 10.1111/j.1574-6976.2007.00074.x] [Citation(s) in RCA: 286] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The dramatic spread of antibiotic resistance is a crisis in the treatment of infectious diseases that affect humans. Several studies suggest that wastewater treatment plants (WWTP) are reservoirs for diverse mobile antibiotic resistance elements. This review summarizes findings derived from genomic analysis of IncP-1 resistance plasmids isolated from WWTP bacteria. Plasmids that belong to the IncP-1 group are self-transmissible, and transfer to and replicate in a wide range of hosts. Their backbone functions are described with respect to their impact on vegetative replication, stable maintenance and inheritance, mobility and plasmid control. Accessory genetic modules, mainly representing mobile genetic elements, are integrated in-between functional plasmid backbone modules. These elements carry determinants conferring resistance to nearly all clinically relevant antimicrobial drug classes, to heavy metals, and quaternary ammonium compounds used as disinfectants. All plasmids analysed here contain integrons that potentially facilitate integration, exchange and dissemination of resistance gene cassettes. Comparative genomics of accessory modules located on plasmids from WWTP and corresponding modules previously identified in other bacterial genomes revealed that animal, human and plant pathogens and other bacteria isolated from different habitats share a common pool of resistance determinants.
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Affiliation(s)
- Andreas Schlüter
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Bielefeld, Germany
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Johnsen AR, Kroer N. Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events. FEMS Microbiol Ecol 2006; 59:718-28. [PMID: 17100984 DOI: 10.1111/j.1574-6941.2006.00230.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Selection pressure may affect the horizontal transfer of plasmids. The inability to distinguish between gene transfer and the growth of transconjugants complicates testing. We have developed a method that enables the quantification of discrete transfer events. It uses large numbers of replicate matings (192 or 384) in microtiter wells and the counting of transfer-positive and transfer-negative wells. We applied the method to study the transfer of the IncP1 plasmid pRO103 between Escherichia coli and Pseudomonas putida strains. pRO103 encodes resistance to mercury and tetracycline and partial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D). The results showed positive correlation between transfer and donor metabolic activity, and an optimal temperature for transfer of 29 degrees C. On stimulation of donor activity, the optimal temperature was decreased to 24.5 degrees C. HgCl(2) above 1.0 microg L(-1) negatively affected transfer, whereas 2,4-D up to 0.3 mM had no effect. The negative effect of mercury was shown to be a result of stressing of the recipient. No effects of mercury on transfer could be detected by traditional filter mating. Thus, the method is superior to filter mating and, as the experimental design allows the manipulation of individual parameters, it is ideal for the assessment and comparison of effects of environmental factors on plasmid transfer.
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Affiliation(s)
- Anders R Johnsen
- National Environmental Research Institute, Department of Environmental Chemistry and Microbiology, Roskilde, Denmark
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Smalla K, Haines AS, Jones K, Krögerrecklenfort E, Heuer H, Schloter M, Thomas CM. Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory element. Appl Environ Microbiol 2006; 72:7253-9. [PMID: 16980416 PMCID: PMC1636140 DOI: 10.1128/aem.00922-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although it is generally assumed that mobile genetic elements facilitate the adaptation of microbial communities to environmental stresses, environmental data supporting this assumption are rare. In this study, river sediment samples taken from two mercury-polluted (A and B) and two nonpolluted or less-polluted (C and D) areas of the river Nura (Kazakhstan) were analyzed by PCR for the presence and abundance of mercury resistance genes and of broad-host-range plasmids. PCR-based detection revealed that mercury pollution corresponded to an increased abundance of mercury resistance genes and of IncP-1beta replicon-specific sequences detected in total community DNA. The isolation of IncP-1beta plasmids from contaminated sediments was attempted in order to determine whether they carry mercury resistance genes and thus contribute to an adaptation of bacterial populations to Hg pollution. We failed to detect IncP-1beta plasmids in the genomic DNA of the cultured Hg-resistant bacterial isolates. However, without selection for mercury resistance, three different IncP-1beta plasmids (pTP6, pTP7, and pTP8) were captured directly from contaminated sediment slurry in Cupriavidus necator JMP228 based on their ability to mobilize the IncQ plasmid pIE723. These plasmids hybridized with the merRTDeltaP probe and conferred Hg resistance to their host. A broad host range and high stability under conditions of nonselective growth were observed for pTP6 and pTP7. The full sequence of plasmid pTP6 was determined and revealed a backbone almost identical to that of the IncP-1beta plasmids R751 and pB8. However, this is the first example of an IncP-1beta plasmid which had acquired only a mercury resistance transposon but no antibiotic resistance or biodegradation genes. This transposon carries a rather complex set of mer genes and is inserted between Tra1 and Tra2.
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Affiliation(s)
- Kornelia Smalla
- Federal Biological Research Centre for Agriculture and Forestry (BBA), Messeweg 11-12, 38104 Braunschweig, Germany.
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Smalla K, Sobecky PA. The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches. FEMS Microbiol Ecol 2002; 42:165-75. [DOI: 10.1111/j.1574-6941.2002.tb01006.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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