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Title: The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases

Abstract

A non-bifurcating NADH-dependent, dimeric [FeFe]-hydrogenase (HydAB) from Syntrophus aciditrophicus was heterologously produced in Escherichia coli, purified and characterized herein. Purified recombinant HydAB catalyzed NAD+ reduction coupled to hydrogen oxidation and produced hydrogen from NADH without the involvement of ferredoxin. Hydrogen partial pressures (2.2 to 40.2 Pa) produced by the purified recombinant HydAB at NADH to NAD+ ratios of 1 to 5 were similar to the hydrogen partial pressures generated by pure and cocultures of S. aciditrophicus (5.9 to 36.6 Pa). As a result, the hydrogen partial pressures observed in metabolizing cultures and cocultures of S. aciditrophicus can be generated by HydAB if S. aciditrophicus maintains NADH to NAD+ ratios greater than one. The flavin-containing beta subunits from S. aciditrophicus HydAB and the non-bifurcating NADH-dependent S. wolfei Hyd1ABC share a number of conserved residues with the flavin-containing beta subunits from non-bifurcating NADH-dependent enzymes such as NADH:quinone oxidoreductases and formate dehydrogenases. A number of differences were observed between sequences of these non-bifurcating NADH-dependent enzymes and [FeFe]-hydrogenases and formate dehydrogenases known to catalyze electron bifurcation including differences in the number of [Fe-S] centers and in conserved residues near predicted cofactor binding sites. These differences can be used to distinguish members of these twomore » groups of enzymes and may be relevant to the differences in ferredoxin-dependence and ability to mediate electron-bifurcation. These findings show that two phylogenetically distinct syntrophic fatty acid-oxidizing bacteria, Syntrophomonas wolfei a member of the phylum Firmicutes, and S. aciditrophicus, a member of the class Deltaproteobacteria, possess functionally similar [FeFe]-hydrogenases that produce hydrogen from NADH during syntrophic fatty acid oxidation without the involvement of reduced ferredoxin. The reliance on a non-bifurcating NADH-dependent [FeFe]-hydrogenases may explain the obligate requirement that many syntrophic metabolizers have for a hydrogen-using partner microorganism when grown on fatty, aromatic and alicyclic acids.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Univ. of Oklahoma, Norman, OK (United States); Montana State Univ., Bozeman, MT (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division
OSTI Identifier:
1633663
Alternate Identifier(s):
OSTI ID: 1631530
Grant/Contract Number:  
FG02-96ER20214; SC0020246
Resource Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Name: Frontiers in Microbiology Journal Volume: 11; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
Switzerland
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 08 HYDROGEN; [FeFe]-Hydrogenase; Syntrophy; Interspecies Electron Transfer; NADH-Dependent Hydrogen Production; NADH:Quinone Oxidoreductase; Anaerobe Physiology; Electron-Bifurcating Enzymes

Citation Formats

Losey, Nathaniel A., Poudel, Saroj, Boyd, Eric S., and McInerney, Michael J. The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases. Switzerland: N. p., 2020. Web. doi:10.3389/fmicb.2020.01109.
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Losey, Nathaniel A., Poudel, Saroj, Boyd, Eric S., & McInerney, Michael J. The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases. Switzerland. https://doi.org/10.3389/fmicb.2020.01109
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Losey, Nathaniel A., Poudel, Saroj, Boyd, Eric S., and McInerney, Michael J. Wed . "The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases". Switzerland. https://doi.org/10.3389/fmicb.2020.01109.
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@article{osti_1633663,
title = {The Beta Subunit of Non-bifurcating NADH-Dependent [FeFe]-Hydrogenases Differs From Those of Multimeric Electron-Bifurcating [FeFe]-Hydrogenases},
author = {Losey, Nathaniel A. and Poudel, Saroj and Boyd, Eric S. and McInerney, Michael J.},
abstractNote = {A non-bifurcating NADH-dependent, dimeric [FeFe]-hydrogenase (HydAB) from Syntrophus aciditrophicus was heterologously produced in Escherichia coli, purified and characterized herein. Purified recombinant HydAB catalyzed NAD+ reduction coupled to hydrogen oxidation and produced hydrogen from NADH without the involvement of ferredoxin. Hydrogen partial pressures (2.2 to 40.2 Pa) produced by the purified recombinant HydAB at NADH to NAD+ ratios of 1 to 5 were similar to the hydrogen partial pressures generated by pure and cocultures of S. aciditrophicus (5.9 to 36.6 Pa). As a result, the hydrogen partial pressures observed in metabolizing cultures and cocultures of S. aciditrophicus can be generated by HydAB if S. aciditrophicus maintains NADH to NAD+ ratios greater than one. The flavin-containing beta subunits from S. aciditrophicus HydAB and the non-bifurcating NADH-dependent S. wolfei Hyd1ABC share a number of conserved residues with the flavin-containing beta subunits from non-bifurcating NADH-dependent enzymes such as NADH:quinone oxidoreductases and formate dehydrogenases. A number of differences were observed between sequences of these non-bifurcating NADH-dependent enzymes and [FeFe]-hydrogenases and formate dehydrogenases known to catalyze electron bifurcation including differences in the number of [Fe-S] centers and in conserved residues near predicted cofactor binding sites. These differences can be used to distinguish members of these two groups of enzymes and may be relevant to the differences in ferredoxin-dependence and ability to mediate electron-bifurcation. These findings show that two phylogenetically distinct syntrophic fatty acid-oxidizing bacteria, Syntrophomonas wolfei a member of the phylum Firmicutes, and S. aciditrophicus, a member of the class Deltaproteobacteria, possess functionally similar [FeFe]-hydrogenases that produce hydrogen from NADH during syntrophic fatty acid oxidation without the involvement of reduced ferredoxin. The reliance on a non-bifurcating NADH-dependent [FeFe]-hydrogenases may explain the obligate requirement that many syntrophic metabolizers have for a hydrogen-using partner microorganism when grown on fatty, aromatic and alicyclic acids.},
doi = {10.3389/fmicb.2020.01109},
journal = {Frontiers in Microbiology},
number = ,
volume = 11,
place = {Switzerland},
year = {Wed Jun 17 00:00:00 EDT 2020},
month = {Wed Jun 17 00:00:00 EDT 2020}
}
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Journal Article:
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https://doi.org/10.3389/fmicb.2020.01109
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Cited by: 13 works
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Figures / Tables:

Table 1 Table 1: Specific Activities of Purified Recombinant HydAB.
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Works referenced in this record:

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
journal, May 2018

  • Kumar, Sudhir; Stecher, Glen; Li, Michael
  • Molecular Biology and Evolution, Vol. 35, Issue 6
  • DOI: 10.1093/molbev/msy096

F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification
journal, August 2004

  • Seedorf, Henning; Dreisbach, Annette; Hedderich, Reiner
  • Archives of Microbiology, Vol. 182, Issue 2-3
  • DOI: 10.1007/s00203-004-0675-3

Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus , a New Twist on ATP Formation
journal, August 2016

  • James, Kimberly L.; Ríos-Hernández, Luis A.; Wofford, Neil Q.
  • mBio, Vol. 7, Issue 4
  • DOI: 10.1128/mBio.01208-16

Flavin-Based Electron Bifurcation, A New Mechanism of Biological Energy Coupling
journal, February 2018

Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum strain SIT.
journal, April 2013

  • Visser, Michael; Worm, Petra; Muyzer, Gerard
  • Standards in Genomic Sciences, Vol. 8, Issue 1
  • DOI: 10.4056/sigs.3627141

The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth
journal, April 2007

  • McInerney, M. J.; Rohlin, L.; Mouttaki, H.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 18
  • DOI: 10.1073/pnas.0610456104

A Reversible Electron-Bifurcating Ferredoxin- and NAD-Dependent [FeFe]-Hydrogenase (HydABC) in Moorella thermoacetica
journal, January 2013

  • Wang, S.; Huang, H.; Kahnt, J.
  • Journal of Bacteriology, Vol. 195, Issue 6
  • DOI: 10.1128/JB.02158-12

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii
journal, November 2016

The tungsten-containing formate dehydrogenase from Methylobacterium extorquens AM1: Purification and properties
journal, January 2003

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994

  • Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
  • Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
  • DOI: 10.1093/nar/22.22.4673

The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features
journal, January 2008

  • Seedorf, H.; Fricke, W. F.; Veith, B.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 6
  • DOI: 10.1073/pnas.0711093105

Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway
journal, December 1998

Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation
journal, October 2012

The Mononuclear Molybdenum Enzymes
journal, January 2014

  • Hille, Russ; Hall, James; Basu, Partha
  • Chemical Reviews, Vol. 114, Issue 7
  • DOI: 10.1021/cr400443z

Molar Extinction Coefficient and Iron and Sulfide Content of Clostridial Ferredoxin
journal, October 1970

Structure of the Hydrophilic Domain of Respiratory Complex I from Thermus thermophilus
journal, March 2006

Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy
journal, December 2018

  • Schuchmann, Kai; Chowdhury, Nilanjan Pal; Müller, Volker
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.02911

Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase
journal, October 2010

  • Biegel, E.; Muller, V.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 42
  • DOI: 10.1073/pnas.1010318107

Benzoate Fermentation by the Anaerobic Bacterium Syntrophus aciditrophicus in the Absence of Hydrogen-Using Microorganisms
journal, December 2001

Spectroscopic and biochemical insight into an electron-bifurcating [FeFe] hydrogenase
journal, December 2019

  • Chongdar, Nipa; Pawlak, Krzysztof; Rüdiger, Olaf
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 25, Issue 1
  • DOI: 10.1007/s00775-019-01747-1

The multitude of iron–sulfur clusters in respiratory complex I
journal, August 2016

  • Gnandt, Emmanuel; Dörner, Katerina; Strampraad, Marc F. J.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1857, Issue 8
  • DOI: 10.1016/j.bbabio.2016.02.018

Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms
journal, January 1999

  • Jackson, Bradley E.; Bhupathiraju, V. K.; Tanner, Ralph S.
  • Archives of Microbiology, Vol. 171, Issue 2
  • DOI: 10.1007/s002030050685

Unification of [FeFe]-hydrogenases into three structural and functional groups
journal, September 2016

  • Poudel, Saroj; Tokmina-Lukaszewska, Monika; Colman, Daniel R.
  • Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1860, Issue 9
  • DOI: 10.1016/j.bbagen.2016.05.034

A Proteomic View at the Biochemistry of Syntrophic Butyrate Oxidation in Syntrophomonas wolfei
journal, February 2013

Physiology, Ecology, Phylogeny, and Genomics of Microorganisms Capable of Syntrophic Metabolism
journal, March 2008

  • McInerney, Michael J.; Struchtemeyer, Christopher G.; Sieber, Jessica
  • Annals of the New York Academy of Sciences, Vol. 1125, Issue 1
  • DOI: 10.1196/annals.1419.005

Syntrophy in anaerobic global carbon cycles
journal, December 2009

  • McInerney, Michael J.; Sieber, Jessica R.; Gunsalus, Robert P.
  • Current Opinion in Biotechnology, Vol. 20, Issue 6
  • DOI: 10.1016/j.copbio.2009.10.001

Methanogenic bacteria as endosymbionts of the ciliate Nyctotherus ovalis in the cockroach hindgut.
journal, January 1991

The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization1GenBank accession number AF044577.1
journal, August 1999

  • Verhagen, Marc F. J. M.; O’Rourke, Thomas; Adams, Michael W. W.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1412, Issue 3
  • DOI: 10.1016/S0005-2728(99)00062-6

Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism
journal, September 2018

On the Natural History of Flavin-Based Electron Bifurcation
journal, July 2018

  • Baymann, Frauke; Schoepp-Cothenet, Barbara; Duval, Simon
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.01357

H2 Production by Selenomonas ruminantium in the Absence and Presence of Methanogenic Bacteria
journal, January 1975

The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains
journal, August 1992

Microbial degradation of aromatic compounds — from one strategy to four
journal, October 2011

  • Fuchs, Georg; Boll, Matthias; Heider, Johann
  • Nature Reviews Microbiology, Vol. 9, Issue 11, p. 803-816
  • DOI: 10.1038/nrmicro2652

A hydrogenosome with a genome
journal, December 1998

  • Akhmanova, Anna; Voncken, Frank; van Alen, Theo
  • Nature, Vol. 396, Issue 6711
  • DOI: 10.1038/25023

Activity and properties of fumarate reductase in ruminal bacteria.
journal, January 2000

  • Asanuma, Narito; Hino, Tsuneo
  • The Journal of General and Applied Microbiology, Vol. 46, Issue 3
  • DOI: 10.2323/jgam.46.119

Formate Dehydrogenase from Pseudomonas oxalaticus
journal, February 1978

The rapid generation of mutation data matrices from protein sequences
journal, January 1992

Colorimetric ferrozine-based assay for the quantitation of iron in cultured cells
journal, August 2004

  • Riemer, Jan; Hoepken, Hans Hermann; Czerwinska, Hania
  • Analytical Biochemistry, Vol. 331, Issue 2
  • DOI: 10.1016/j.ab.2004.03.049

COBALT: constraint-based alignment tool for multiple protein sequences
journal, March 2007

Formate dehydrogenase from Methylosinus trichosporium OB3b. Purification and spectroscopic characterization of the cofactors.
journal, November 1991

A Bacterial Electron-bifurcating Hydrogenase
journal, July 2012

  • Schuchmann, Kai; Müller, Volker
  • Journal of Biological Chemistry, Vol. 287, Issue 37
  • DOI: 10.1074/jbc.M112.395038

Integrated thermodynamic analysis of electron bifurcating [FeFe]-hydrogenase to inform anaerobic metabolism and H2 production
journal, January 2020

  • Jay, Zackary J.; Hunt, Kristopher A.; Chou, Katherine J.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1861, Issue 1
  • DOI: 10.1016/j.bbabio.2019.148087

Syntrophomonas wolfei Uses an NADH-Dependent, Ferredoxin-Independent [FeFe]-Hydrogenase To Reoxidize NADH
journal, August 2017

  • Losey, Nathaniel A.; Mus, Florence; Peters, John W.
  • Applied and Environmental Microbiology, Vol. 83, Issue 20
  • DOI: 10.1128/AEM.01335-17

Sequence, assembly and evolution of a primordial ferredoxin from Thermotoga maritima.
journal, April 1994

Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option
journal, January 2020

The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
journal, January 2007

  • Boxma, Brigitte; Ricard, Guenola; van Hoek, Angela HAM
  • BMC Evolutionary Biology, Vol. 7, Issue 1
  • DOI: 10.1186/1471-2148-7-230

The Organellar Genome and Metabolic Potential of the Hydrogen-Producing Mitochondrion of Nyctotherus ovalis
journal, March 2011

  • de Graaf, Rob M.; Ricard, Guenola; van Alen, Theo A.
  • Molecular Biology and Evolution, Vol. 28, Issue 8
  • DOI: 10.1093/molbev/msr059

A new mechanistic model for an O2-protected electron-bifurcating hydrogenase, Hnd from Desulfovibrio fructosovorans
journal, December 2018

  • Kpebe, Arlette; Benvenuti, Martino; Guendon, Chloé
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1859, Issue 12
  • DOI: 10.1016/j.bbabio.2018.09.364

Membrane Complexes of Syntrophomonas wolfei Involved in Syntrophic Butyrate Degradation and Hydrogen Formation
journal, November 2016

Heterologous overproduction of 2[4Fe4S]- and [2Fe2S]-type clostridial ferredoxins and [2Fe2S]-type agrobacterial ferredoxin
journal, May 2016

Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit
journal, July 2014

  • Mansfeldt, Cresten B.; Rowe, Annette R.; Heavner, Gretchen L. W.
  • Applied and Environmental Microbiology, Vol. 80, Issue 19
  • DOI: 10.1128/aem.02130-14

CO2 Reduction to Formate by NADH Catalysed by Formate Dehydrogenase from Pseudomonas oxalaticus
journal, November 1976

The importance of hydrogen and formate transfer for syntrophic fatty, aromatic and alicyclic metabolism: Importance of interspecies hydrogen and formate transfer
journal, October 2013

  • Sieber, Jessica R.; Le, Huynh M.; McInerney, Michael J.
  • Environmental Microbiology, Vol. 16, Issue 1
  • DOI: 10.1111/1462-2920.12269

Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids
journal, March 2019

  • James, Kimberly L.; Kung, Johannes W.; Crable, Bryan R.
  • Environmental Microbiology, Vol. 21, Issue 5
  • DOI: 10.1111/1462-2920.14601

Proteomic analysis reveals metabolic and regulatory systems involved in the syntrophic and axenic lifestyle of Syntrophomonas wolfei
journal, February 2015

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