151
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Artz JH, White SN, Zadvornyy OA, Fugate CJ, Hicks D, Gauss GH, Posewitz MC, Boyd ES, Peters JW. Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula. Front Bioeng Biotechnol 2015. [PMID: 26217660 PMCID: PMC4500099 DOI: 10.3389/fbioe.2015.00097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Mercuric ion reductase (MerA), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (Hg2+) and to catalyze their reduction to a more volatile, less toxic elemental form. Here, we present a biochemical and structural characterization of MerA from the thermophilic crenarchaeon Metallosphaera sedula. MerA from M. sedula is a thermostable enzyme, and remains active after extended incubation at 97°C. At 37°C, the NADPH oxidation-linked Hg2+ reduction specific activity was found to be 1.9 μmol/min⋅mg, increasing to 3.1 μmol/min⋅mg at 70°C. M. sedula MerA crystals were obtained and the structure was solved to 1.6 Å, representing the first solved crystal structure of a thermophilic MerA. Comparison of both the crystal structure and amino acid sequence of MerA from M. sedula to mesophillic counterparts provides new insights into the structural determinants that underpin the thermal stability of the enzyme.
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Affiliation(s)
- Jacob H Artz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Spencer N White
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Oleg A Zadvornyy
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Corey J Fugate
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Danny Hicks
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - George H Gauss
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines , Golden, CO , USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University , Bozeman, MT , USA ; Thermal Biology Institute, Montana State University , Bozeman, MT , USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
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152
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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153
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Microbial DNA records historical delivery of anthropogenic mercury. ISME JOURNAL 2015; 9:2541-50. [PMID: 26057844 PMCID: PMC4817628 DOI: 10.1038/ismej.2015.86] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 04/01/2015] [Accepted: 04/19/2015] [Indexed: 11/08/2022]
Abstract
Mercury (Hg) is an anthropogenic pollutant that is toxic to wildlife and humans, but the response of remote ecosystems to globally distributed Hg is elusive. Here, we use DNA extracted from a dated sediment core to infer the response of microbes to historical Hg delivery. We observe a significant association between the mercuric reductase gene (merA) phylogeny and the timing of Hg deposition. Using relaxed molecular clock models, we show a significant increase in the scaled effective population size of the merA gene beginning ~200 years ago, coinciding with the Industrial Revolution and a coincident strong signal for positive selection acting on residues in the terminal region of the mercuric reductase. This rapid evolutionary response of microbes to changes in the delivery of anthropogenic Hg indicates that microbial genomes record ecosystem response to pollutant deposition in remote regions.
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154
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Immunology, Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
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155
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Mathew DC, Ho YN, Gicana RG, Mathew GM, Chien MC, Huang CC. A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury. PLoS One 2015; 10:e0121178. [PMID: 25816328 PMCID: PMC4376707 DOI: 10.1371/journal.pone.0121178] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/28/2015] [Indexed: 11/24/2022] Open
Abstract
Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg x kg(-1) mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg x kg(-1), 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury.
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Affiliation(s)
- Dony Chacko Mathew
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, R. O. C
| | - Ying-Ning Ho
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, R. O. C
| | - Ronnie Gicaraya Gicana
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, R. O. C
| | - Gincy Marina Mathew
- School of Biosciences, Mar Athanasios College for Advanced Studies (MACFAST) BIOCAMPUS, Tiruvalla, Kerala, India
| | - Mei-Chieh Chien
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, R. O. C
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, R. O. C
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156
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Kaur G, Subramanian S. Repurposing TRASH: emergence of the enzyme organomercurial lyase from a non-catalytic zinc finger scaffold. J Struct Biol 2014; 188:16-21. [PMID: 25220669 DOI: 10.1016/j.jsb.2014.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/28/2014] [Accepted: 09/03/2014] [Indexed: 11/26/2022]
Abstract
The mercury resistance pathway enzyme organomercurial lyase (MerB) catalyzes the conversion of organomercurials to ionic mercury (Hg(2+)). Here, we provide evidence for the emergence of this enzyme from a TRASH-like, non-enzymatic, treble-clef zinc finger ancestor by domain duplication and fusion. Surprisingly, the structure-stabilizing metal-binding core of the treble-clef appears to have been repurposed in evolution to serve a catalytic role. Novel enzymatic functions are believed to have evolved from ancestral generalist catalytic scaffolds or from already specialized enzymes with catalytic promiscuity. The emergence of MerB from a zinc finger ancestor serves as a rare example of how a novel enzyme may emerge from a non-catalytic scaffold with a related binding function.
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Affiliation(s)
- Gurmeet Kaur
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India
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157
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Boyd ES, Thomas KM, Dai Y, Boyd JM, Outten FW. Interplay between oxygen and Fe-S cluster biogenesis: insights from the Suf pathway. Biochemistry 2014; 53:5834-47. [PMID: 25153801 PMCID: PMC4172210 DOI: 10.1021/bi500488r] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Iron–sulfur (Fe–S)
cluster metalloproteins conduct
essential functions in nearly all contemporary forms of life. The
nearly ubiquitous presence of Fe–S clusters and the fundamental
requirement for Fe–S clusters in both aerobic and anaerobic
Archaea, Bacteria, and Eukarya suggest that these clusters were likely
integrated into central metabolic pathways early in the evolution
of life prior to the widespread oxidation of Earth’s atmosphere.
Intriguingly, Fe–S cluster-dependent metabolism is sensitive
to disruption by oxygen because of the decreased bioavailability of
ferric iron as well as direct oxidation of sulfur trafficking intermediates
and Fe–S clusters by reactive oxygen species. This fact, coupled
with the ubiquity of Fe–S clusters in aerobic organisms, suggests
that organisms evolved with mechanisms that facilitate the biogenesis
and use of these essential cofactors in the presence of oxygen, which
gradually began to accumulate around 2.5 billion years ago as oxygenic
photosynthesis proliferated and reduced minerals that buffered against
oxidation were depleted. This review highlights the most ancient of
the Fe–S cluster biogenesis pathways, the Suf system, which
likely was present in early anaerobic forms of life. Herein, we use
the evolution of the Suf pathway to assess the relationships between
the biochemical functions and physiological roles of Suf proteins,
with an emphasis on the selective pressure of oxygen toxicity. Our
analysis suggests that diversification into oxygen-containing environments
disrupted iron and sulfur metabolism and was a main driving force
in the acquisition of accessory Suf proteins (such as SufD, SufE,
and SufS) by the core SufB–SufC scaffold complex. This analysis
provides a new framework for the study of Fe–S cluster biogenesis
pathways and Fe–S cluster-containing metalloenzymes and their
complicated patterns of divergence in response to oxygen.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Immunology, Montana State University , 109 Lewis Hall, Bozeman, Montana 59717, United States
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158
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Nygren H, Dahlén G, Malmberg P. Analysis of As- and Hg-Species in Metal-Resistant Oral Bacteria, by Imaging ToF-SIMS. Basic Clin Pharmacol Toxicol 2014; 115:129-33. [DOI: 10.1111/bcpt.12205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/21/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Håkan Nygren
- Department of Cell Biology and Medical Chemistry; Institute of Biomedicine; University of Gothenburg; Gothenburg Sweden
| | - Gunnar Dahlén
- Department of Oral Microbiology; Institute of Odontology; University of Gothenburg; Gothenburg Sweden
| | - Per Malmberg
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
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159
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Brandt U, Hiessl S, Schuldes J, Thürmer A, Wübbeler JH, Daniel R, Steinbüchel A. Genome-guided insights into the versatile metabolic capabilities of the mercaptosuccinate-utilizing β-proteobacterium Variovorax paradoxus strain B4. Environ Microbiol 2013; 16:3370-86. [PMID: 24245581 DOI: 10.1111/1462-2920.12340] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022]
Abstract
Variovorax paradoxus B4 is able to utilize 2-mercaptosuccinate (MS) as sole carbon, sulfur and energy source. The whole genome of V. paradoxus B4 was sequenced, annotated and evaluated with special focus on genomic elements related to MS metabolism. The genome encodes two chromosomes harbouring 5 795 261 and 1 353 255 bp. A total of 6753 putative protein-coding sequences were identified. Based on the genome and in combination with results from previous studies, a putative pathway for the degradation of MS could be postulated. The putative molybdopterin oxidoreductase identified during transposon mutagenesis probably catalyses the conversion of MS first into sulfinosuccinate and then into sulfosuccinate by successive transfer of oxygen atoms. Subsequently, the cleavage of sulfosuccinate yields oxaloacetate and sulfite, while the latter is oxidized to sulfate. The expression of the putative molybdopterin oxidoreductase was induced by MS, but not by gluconate, as confirmed by reverse transcriptase polymerase chain reaction. Further, in silico studies combined with experiments and comparative genomics revealed high metabolic diversity of strain B4. It bears a high potential as plant growth-promoting bacterium and as candidate for degradation and detoxification of xenobiotics and other hardly degradable substances. Additionally, the strain is of special interest for production of polythioesters with sulfur-containing precursors as MS.
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Affiliation(s)
- Ulrike Brandt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Corrensstraße 3, Münster, D-48149, Germany
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160
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Sayed A, Ghazy MA, Ferreira AJS, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JAC, Bajic VB, Siam R, El-Dorry H. A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. J Biol Chem 2013; 289:1675-87. [PMID: 24280218 DOI: 10.1074/jbc.m113.493429] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A unique combination of physicochemical conditions prevails in the lower convective layer (LCL) of the brine pool at Atlantis II (ATII) Deep in the Red Sea. With a maximum depth of over 2000 m, the pool is characterized by acidic pH (5.3), high temperature (68 °C), salinity (26%), low light levels, anoxia, and high concentrations of heavy metals. We have established a metagenomic dataset derived from the microbial community in the LCL, and here we describe a gene for a novel mercuric reductase, a key component of the bacterial detoxification system for mercuric and organomercurial species. The metagenome-derived gene and an ortholog from an uncultured soil bacterium were synthesized and expressed in Escherichia coli. The properties of their products show that, in contrast to the soil enzyme, the ATII-LCL mercuric reductase is functional in high salt, stable at high temperatures, resistant to high concentrations of Hg(2+), and efficiently detoxifies Hg(2+) in vivo. Interestingly, despite the marked functional differences between the orthologs, their amino acid sequences differ by less than 10%. Site-directed mutagenesis and kinetic analysis of the mutant enzymes, in conjunction with three-dimensional modeling, have identified distinct structural features that contribute to extreme halophilicity, thermostability, and high detoxification capacity, suggesting that these were acquired independently during the evolution of this enzyme. Thus, our work provides fundamental structural insights into a novel protein that has undergone multiple biochemical and biophysical adaptations to promote the survival of microorganisms that reside in the extremely demanding environment of the ATII-LCL.
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Affiliation(s)
- Ahmed Sayed
- From the Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, AUC Avenue, P. O. Box 74, New Cairo 11835, Egypt
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161
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Baquero F, Tedim AP, Coque TM. Antibiotic resistance shaping multi-level population biology of bacteria. Front Microbiol 2013; 4:15. [PMID: 23508522 PMCID: PMC3589745 DOI: 10.3389/fmicb.2013.00015] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/22/2013] [Indexed: 12/21/2022] Open
Abstract
Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level population biology of bacteria.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Ana P. Tedim
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
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