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Title: Comparative proteomic analysis of Desulfotomaculum reducens MI-1: Insights into the metabolic versatility of a gram-positive sulfate- and metal-reducing bacterium

Journal Article · · Frontiers in Microbiology
 [1];  [2];  [2];  [2];  [1]
  1. Cornell Univ., Ithaca, NY (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
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In this study, the proteomes of the metabolically versatile and poorly characterized Gram-positive bacterium Desulfotomaculum reducens MI-1 were compared across four cultivation conditions including sulfate reduction, soluble Fe(III) reduction, insoluble Fe(III) reduction, and pyruvate fermentation. Collectively across conditions, we observed at high confidence ~38% of genome-encoded proteins. Here, we focus on proteins that display significant differential abundance on conditions tested. To the best of our knowledge, this is the first full-proteome study focused on a Gram-positive organism cultivated either on sulfate or metal-reducing conditions. Several proteins with uncharacterized function encoded within heterodisulfide reductase (hdr)-containing loci were upregulated on either sulfate (Dred_0633-4, Dred_0689-90, and Dred_1325-30) or Fe(III)-citrate-reducing conditions (Dred_0432-3 and Dred_1778-84). Two of these hdr-containing loci display homology to recently described flavin-based electron bifurcation (FBEB) pathways (Dred_1325-30 and Dred_1778-84). Additionally, we propose that a cluster of proteins, which is homologous to a described FBEB lactate dehydrogenase (LDH) complex, is performing lactate oxidation in D. reducens (Dred_0367-9). Analysis of the putative sulfate reduction machinery in D. reducens revealed that most of these proteins are constitutively expressed across cultivation conditions tested. In addition, peptides from the single multiheme c-type cytochrome (MHC) in the genome were exclusively observed on the insoluble Fe(III) condition, suggesting that this MHC may play a role in reduction of insoluble metals.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Cornell Univ., Ithaca, NY (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
SC0006644; AC05-76RL01830
OSTI ID:
1249361
Alternate ID(s):
OSTI ID: 1239630
Report Number(s):
PNNL-SA-115268
Journal Information:
Frontiers in Microbiology, Vol. 7; ISSN 1664-302X
Publisher:
Frontiers Research FoundationCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science

References (55)

MicrobesOnline: an integrated portal for comparative and functional genomics journal November 2009
The biogeochemistry and bioremediation of uranium and other priority radionuclides journal January 2014
DAnTE: a statistical tool for quantitative analysis of -omics data journal May 2008
Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium journal March 2014
A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by G eobacter sulfurreducens  PCA : A trans-outer membrane electron transfer complex journal September 2014
Characterization of the surfaceome of the metal-reducing bacterium Desulfotomaculum reducens journal August 2014
A protein trisulfide couples dissimilatory sulfate reduction to energy conservation journal December 2015
A modification of the methylene blue method to measure bacterial sulfide production in feces journal April 1992
The Response of Desulfotomaculum reducens MI-1 to U(VI) Exposure: A Transcriptomic Study journal June 2011
Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium D esulfotomaculum reducens  MI-1 using an NADH-based activity assay : Metal reductases from Gram-positive metal reducer journal January 2015
The “bacterial heterodisulfide” DsrC is a key protein in dissimilatory sulfur metabolism journal July 2014
A systematic investigation of multiheme c-type cytochromes in prokaryotes journal January 2010
Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor journal December 2008
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags journal August 2002
Coupled Ferredoxin and Crotonyl Coenzyme A (CoA) Reduction with NADH Catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from Clostridium kluyveri journal November 2007
IMG 4 version of the integrated microbial genomes comparative analysis system journal October 2013
Changes in Protein Expression Across Laboratory and Field Experiments in Geobacter bemidjiensis journal February 2015
Measurement of protein using bicinchoninic acid journal October 1985
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans journal March 2014
Uranium Reduction journal October 2006
Microbial Reduction of Fe(III) under Alkaline Conditions Relevant to Geological Disposal journal March 2013
A Comparative Genomic Analysis of Energy Metabolism in Sulfate Reducing Bacteria and Archaea journal January 2011
The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in D esulfovibrio vulgaris  Hildenborough : Role of FlxABCD-HdrABC in journal January 2015
Molecular Underpinnings of Fe(III) Oxide Reduction by Shewanella Oneidensis MR-1 journal January 2012
Characterizing Microbial Community and Geochemical Dynamics at Hydrothermal Vents Using Osmotically Driven Continuous Fluid Samplers journal April 2013
Energy Conservation via Electron-Transferring Flavoprotein in Anaerobic Bacteria journal November 2007
A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics journal August 2011
Fe(III) reduction during pyruvate fermentation by Desulfotomaculum reducens strain MI-1 journal November 2013
The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1: The genome of Desulfotomaculum reducens journal June 2010
Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments journal January 2013
Desulfotomaculum hydrothermale sp. nov., a thermophilic sulfate-reducing bacterium isolated from a terrestrial Tunisian hot spring journal November 2008
Universal sample preparation method for proteome analysis journal April 2009
Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments journal May 2015
Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation journal February 2013
A novel mode of lactate metabolism in strictly anaerobic bacteria: A novel mode of lactate metabolism in anaerobes journal May 2014
Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach journal August 2010
The ‘porin-cytochrome’ model for microbe-to-mineral electron transfer: Microbe-to-mineral electron transfer journal May 2012
The roles of outer membrane cytochromes of Shewanella and Geobacter in extracellular electron transfer journal August 2009
Microbial Populations Stimulated for Hexavalent Uranium Reduction in Uranium Mine Sediment journal March 2003
Indirect and suboptimal control of gene expression is widespread in bacteria journal January 2013
Unifying concepts in anaerobic respiration: Insights from dissimilatory sulfur metabolism journal February 2013
Sulfate-reducing bacterium grows with Cr(VI), U(VI), Mn(IV), and Fe(III) as electron acceptors journal May 1998
Bioenergetic challenges of microbial iron metabolisms journal July 2011
Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes journal December 2006
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases journal August 2008
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes journal May 2010
Comparative Bacterial Proteomics: Analysis of the Core Genome Concept journal February 2008
Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells journal April 2011
Evaluating the effects of causes of death on postmortem interval estimation by ATR-FTIR spectroscopy journal March 2019
Proteomic Analysis of Stationary Phase in the Marine Bacterium "Candidatus Pelagibacter ubique" journal May 2008
Rapid Assay for Microbially Reducible Ferric Iron in Aquatic Sediments journal January 1987
Enumeration and Characterization of Iron(III)-Reducing Microbial Communities from Acidic Subsurface Sediments Contaminated with Uranium(VI) journal December 2003
Classic Spotlight: Electron Bifurcation, a Unifying Concept for Energy Conservation in Anaerobes journal April 2016
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes journal October 2001
Lateral Gene Transfer of Dissimilatory (Bi)Sulfite Reductase Revisited journal March 2005

Cited By (5)

Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions journal March 2020
Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review journal March 2018
Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis journal March 2018
Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes journal May 2018
A Ferredoxin- and F 420 H 2 -Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea journal February 2017

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Related Subjects

Fe(III) reduction
sulfate reduction
Desulfotomaculum reducens
gram-positive bacteria
comparative proteomic analysis
flavin-based electron bifurcation
heterodisulfide reductase
59 BASIC BIOLOGICAL SCIENCES