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The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics

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  • Authors: Gottfried Unden1, Philipp Aloysius Steinmetz2, and Pia Degreif-Dünnwald3
  • Editor: Valley Stewart4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany; 2: Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany; 3: Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany; 4: University of California—Davis, Davis, CA
  • Received 03 February 2014 Accepted 22 May 2014 Published 18 July 2014
  • Address correspondence to Gottfried Unden, unden@uni-mainz.de
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  • Abstract:

    contains a versatile respiratory chain that oxidizes 10 different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. is able to use two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. A large number of respiratory pathways can be established by combining different electron donors and acceptors. The respiratory dehydrogenases use quinones as the electron acceptors that are oxidized by the terminal reductase and oxidases. The enzymes vary largely with respect to their composition, architecture, membrane topology, and the mode of energy conservation. Most of the energy-conserving dehydrogenases (FdnGHI, HyaABC, HybCOAB, and others) and the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δ) by a redox-loop mechanism. Two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases and terminal reductases do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known or can be predicted. The H/2e ratios for most respiratory chains are in the range from 2 to 6 H/2e. The energetics of the individual redox reactions and the respiratory chains is described and related to the H/2e ratios.

  • Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013

Key Concept Ranking

Acetyl Coenzyme A
0.48635793
Bacteria and Archaea
0.45924175
Electron Transport System
0.4345776
Nitric Oxide Synthase
0.43005142
0.48635793

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303. journal-id:
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/content/journal/ecosalplus/10.1128/ecosalplus.ESP-0005-2013
2014-07-18
2017-02-19

Abstract:

contains a versatile respiratory chain that oxidizes 10 different electron donor substrates and transfers the electrons to terminal reductases or oxidases for the reduction of six different electron acceptors. is able to use two more electron acceptors. The variation is further increased by the presence of isoenzymes for some substrates. A large number of respiratory pathways can be established by combining different electron donors and acceptors. The respiratory dehydrogenases use quinones as the electron acceptors that are oxidized by the terminal reductase and oxidases. The enzymes vary largely with respect to their composition, architecture, membrane topology, and the mode of energy conservation. Most of the energy-conserving dehydrogenases (FdnGHI, HyaABC, HybCOAB, and others) and the terminal reductases (CydAB, NarGHI, and others) form a proton potential (Δ) by a redox-loop mechanism. Two enzymes (NuoA-N and CyoABCD) couple the redox energy to proton translocation by proton pumping. A large number of dehydrogenases and terminal reductases do not conserve the redox energy in a proton potential. For most of the respiratory enzymes, the mechanism of proton potential generation is known or can be predicted. The H/2e ratios for most respiratory chains are in the range from 2 to 6 H/2e. The energetics of the individual redox reactions and the respiratory chains is described and related to the H/2e ratios.

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Figures

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Figure 1

Hyd-1 (or HyaABC) is presented as an H-quinol oxidoreductase, but there is also evidence that the big subunit HyaA contains a site for direct O reduction without involving quinone or an electron transport chain (H2-oxidase) (see text for details). The figure shows the composition of the enzymes from their subunits and the topology of subunits and active sites. The names of enzymes for which the topology of the enzymes and of the active sites is supported by experimental evidence or other direct indications are printed in bold. For other enzymes, the topology and the orientation of the active sites are mainly derived from bioinformatic information. All membrane-integral subunits of composite enzymes that are shown with TM arrangement contain TM helices. GlpC is amphipathic without predicted TM helix. The membrane association of the simple (one-subunit) is diverse and presented in more detail in Fig. 2 and the text. Designation of the enzymes and their subunits is according to the genetic nomenclature and to databases. Q and QH stand for quinones (oxidized and reduced states) and might be ubiquinone (ubiquinol) or menaquinone (menaquinol). The site of proton uptake is assumed to occur from the quinone site when no other experimental evidence is available. The location of HybO in the HybCOAB complex is not known. FdnGHI and SdhABCD are symmetric trimers [(FdnGHI) and (SdhABCD)] of the trimeric or tetrameric subcomplexes; only one of the monomers is shown. For details, see text of the corresponding enzymes and databases (see “Useful Websites”). DadA, -amino acid dehydrogenase; Dld, -lactate dehydrogenase; LldD, -lactate dehydrogenase; FdnGHI, anaerobic nitrate-coupled formate reductase; Fdo, aerobic formate dehydrogenase; Gcd, glucose Q-reductase (glucose oxidase); GlpD, aerobic glycerol-3-P dehydrogenase; HyaABC, hydrogenase 1; HybCOAB, hydrogenase 2; Mqo, malate:Q reductase; Ndh, NADH dehydrogenase II; NuoA-N, NADH dehydrogenase I, or NADH:Q (oxido)reductase I; PoxB, pyruvate:Q reductase (pyruvate oxidase); SdhABCD, succinate dehydrogenase. (E) GlpABC (anaerobic glycerol-3-P dehydrogenase). The figure shows the composition of the enzyme from the subunits and the topology of subunits and active sites. The model is hypothetical and mostly derived from bioinformatic information. (For details, see text and “Useful Websites.”) doi:10.1128/ecosalplus.ESP-0005-2013.f1

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Image of Figure 2
Figure 2

(Left) The membrane anchor of Gcd consists of five predicted transmembrane helices. The catalytic side is in the peripheral part of the enzyme with the active site PQQ, which is accessible for the hydrophilic substrate glucose. PQQH is reoxidized by UQ, which is able to access the PQQH from the membrane side. (Right) Dld is membrane associated by electrostatic interaction of basic amino acid residues with the phospholipid surface and interaction of hydrophobic amino acid residues in the upper layer of the membrane. FAD at the active site is reduced by -lactate accessing from the water space, and FADH is reoxidized directly by Q from the membrane side. doi:10.1128/ecosalplus.ESP-0005-2013.f2

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 3

The HycC and HycD proteins of FHL contain 12 to 14 and 8 TM helices, respectively; no TM helices are predicted for the other subunits. The catalytic subunit of hydrogenase (HycE) carries a NiFe cofactor, and that of the formate dehydrogenase (FDH-H or Hyd-3) carries a Mo-Se cofactor. HycB, HycF, and HycG are predicted to contain FeS cofactors and to transfer electrons from FDH-H to HycE. HycC is supposed to thrive H-translocation driven by the redox reaction of the enzyme (formate + H → H + CO); HycD might contribute to H-translocation (see text for details). In the RsxABCDGE complex, subunits RsxA, RsxD, and RsxE are predicted as membrane-integral proteins with 6, 9, and 6 to 7 TM helices, respectively. The Rsx complex ( 144 ) was later renamed RnfABCDGE in databases. RsxB and RsxG contain one TM helix each and are assumed to be membrane associated. RsxB contains a FeS cluster and is supposed to transfer electrons to the FeS cluster of SoxR. From the other subunits, RsxC is suggested to carry FMN and two [4Fe-4S] clusters, RsxG carries an FMN cofactor, and RsxD carries a FAD cofactor. The RseC protein is required for reaction of SoxR with RsxABCDGE. RnfD is homologous to the supposed Na-translocating subunit of Na-translocating Rnf complexes. For more information, see the text and references 7 , 131 , 140 , and 144 . doi:10.1128/ecosalplus.ESP-0005-2013.f3

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 4

Dihydroorotate dehydrogenase (PyrD) catalyzes the oxidation of dihydroorotate by quinones in pyrimidine biosynthesis. The enzyme is anchored in the membrane by an N-terminal TM helix. Active-site FMN is reduced by dihydroorotate and reoxidized by UQ or MK. The membrane-associated HemG (protoporphyrinogen IX oxidase; heme biosynthesis) abstracts six electrons from protoporphyrinogen IX and transfers them to quinones. DsbAB is a periplasmic protein thiol-disulfide oxidoreductase complex for the introduction of disulfides in periplasmic proteins. Reduced DsbA, with two Cys-SH, transfers 2[H] in a translocation process finally to Cys-SH of DsbB that becomes oxidized by a quinone from the membrane. DsbB is composed of four TM helices and a periplasmic loop with the active-site Cys residues. The sensor histidine kinase ArcB is a dimer that is fixed by two TM helices to the membrane. Each monomer contains two reactive Cys residues that become oxidized by UQ, forming two intermolecular Cys disulfides, when the quinone prevails in the oxidized state in the membrane (aerobic respiration). The intermolecular disulfide formation is supposed to affect the kinase activity of ArcB by conformational change. doi:10.1128/ecosalplus.ESP-0005-2013.f4

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 5

The figure shows the composition of the enzymes from their subunits and the topology of the subunits. The names of enzymes for which the topology of the enzymes and of the active sites is supported by experimental evidence or other direct indications are printed in bold. Enzyme names for which the information is mainly derived from bioinformatic information and without direct experimental proof are printed in regular type. Designation of the enzymes and their subunits is according to the genetic nomenclature. NarGHI and FrdABCD are symmetric dimers [Nar(GHI) and (FrdABCD)] of the trimer or tetramer; only one half of the dimer is shown. Q and QH2 stand for quinones (oxidized and reduced states) and might be ubiquinone (ubiquinol) or menaquinone (menaquinol). The release of protons from QH is assumed to occur at the quinone site when no other experimental evidence is available. For details, see the text regarding the corresponding enzymes and databases (see “Useful Websites”). AppBC, quinol oxidase II; CydAB, quinol oxidase ; CyoABCD, quinol oxidase ; DmsABC, DMSO reductase; FrdABCD, fumarate reductase; NarGHI, (anaerobic) nitrate reductase; NarZYV, (“aerobic” or constitutive) nitrate reductase Z. NapABCGH, periplasmic nitrate reductase; NrfABCD, respiratory nitrite reductase; TorAC, TMAO reductase. Other details are as described for Fig. 1 . doi:10.1128/ecosalplus.ESP-0005-2013.f5

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 6

TtrABC and PhsABC show periplasmic orientation of the tetrathionate and thiosulfate sites and a predicted overall structure similar to that of FdnGHI or DmsABC. The sequence of the membrane anchor PhsC suggests five TM helices with four conserved His residues for the binding of two heme molecules. The heme molecules have predicted positions close to the periplasmic and the cytoplasmic side of the membrane, suggesting that the QH site is close to the cytoplasmic face of the membrane. According to the scheme, 2H from the quinol are released to the cytoplasm, followed by the transfer of 2e to the thiosulfate site and consumption of 2H in the periplasm. By this architecture, the enzyme performs a reverse redox half-loop reaction. The reaction is electrogenic and consumes a proton potential according to the scheme to drive the endergonic redox reaction (see text for details). doi:10.1128/ecosalplus.ESP-0005-2013.f6

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 7

The use of the quinols by the terminal reductases was determined by the use of mutants deficient in the synthesis of UQ ( mutant), of the naphthoquinones (MK + DMK) ( mutant), and of MK ( mutant). Broken arrows indicate use of the respective quinone in the respiratory pathway (or growth on the respective acceptor) with reduced rate. NarGHI and DmsABC use MK as the only or preferred naphthoquinone and are indicated by an asterisk. doi:10.1128/ecosalplus.ESP-0005-2013.f7

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 8

FdnGHI and NarGHI each perform redox half-loop reactions with opposite orientation. The redox half-loop of FdnGHI is characterized by the location of the active sites for the hydrophilic substrate (formate) and of the quinone site on the opposite side of the membrane, resulting in the release of 2H on the periplasmic side (formate site) and the consumption of 2H on the cytoplasmic side (quinone site). The heme groups of the transmembrane domains FdnI and NarI and their approximate topology are indicated. The reactions results in a H/2e ratio of 2 by the consumption and release of (scalar) protons on opposite sides that becomes electrogenic by the transfer of negative charge of the electron in the opposite direction (periplasmic to cytoplasmic side). By combination of the redox half-loops in FdnGHI and NarGHI an overall H/2e ratio of 4 is achieved ( 39 ). doi:10.1128/ecosalplus.ESP-0005-2013.f8

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 9

The heme groups of the transmembrane domain FdnI of formate dehydrogenase and their approximate topology are indicated. Reaction of FdnGHI generates 2H/2e. FrdABCD and DmsABC each release and consume protons on the same side of the membrane, and the reaction is electroneutral for each enzyme. FrdABCD consumes and releases protons on the cytoplasmic, and DmsABC at the periplasmic, face of the membrane. The terminal reductases function as electron sink without contributing to proton potential Δ. Overall H/e is the same (2H/2e) for formate-fumarate and formate-DMSO respiration. doi:10.1128/ecosalplus.ESP-0005-2013.f9

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Figure 10

The figure shows the orientation of the active sites for the substrates and the release and consumption of (scalar) protons. The H/e ratios are 0 for each individual enzyme and also for the overall reaction of Ndh with FrdABCD or DmsABC. doi:10.1128/ecosalplus.ESP-0005-2013.f10

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Tables

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Table 1

Energetic parameters for the respiratory dehydrogenases of and serovar Typhimurium

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Table 2

Energetic parameters for the terminal reductases and oxidases of and serovar Typhimurium

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013
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Table 3

Some typical respiratory chains of : composition from enzymes and resulting H/2e ratios

Citation: Unden G, Steinmetz P, Degreif-Dünnwald P. 2014. The Aerobic and Anaerobic Respiratory Chain of and : Enzymes and Energetics, EcoSal Plus 2014; doi:10.1128/ecosalplus.ESP-0005-2013

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