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The Organisation of Proton Motive and Non-Proton Motive Redox Loops in Prokaryotic Respiratory Systems

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The Organisation of Proton Motive and Non-Proton Motive Redox Loops in Prokaryotic Respiratory Systems Biochimica et Biophysica Acta 1777 (2008) 1480–1490 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Review The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems Jörg Simon a,b,⁎, Rob J.M. van Spanning c, David J. Richardson d,⁎ a Institute of Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany b Department of Microbiology and Genetics, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany c Department of Molecular Cell Physiology, VU University Amsterdam, NL-1081 HV Amsterdam, The Netherlands d School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK article info abstract Article history: Respiration is fundamental to the aerobic and anaerobic energy metabolism of many prokaryotic and most Received 1 July 2008 eukaryotic organisms. In principle, the free energy of a redox reaction catalysed by a membrane-bound Received in revised form 8 September 2008 electron transport chain is transduced via the generation of an electrochemical ion (usually proton) gradient Accepted 9 September 2008 across a coupling membrane that drives ATP synthesis. The proton motive force (pmf) can be built up by Available online 30 September 2008 different mechanisms like proton pumping, quinone/quinol cycling or by a redox loop. The latter couples electron transport to a net proton transfer across the membrane without proton pumping. Instead, charge Keywords: Aerobic and anaerobic respiration separation is achieved by quinone-reactive enzymes or enzyme complexes whose active sites for substrates Proton motive force and quinones are situated on different sides of the coupling membrane. The necessary transmembrane Redox (half) loop electron transport is usually accomplished by the presence of two haem groups that face opposite sides of the Electron transport chain membrane. There are many different enzyme complexes that are part of redox loops and their catalysed Quinone reductase redox reactions can be either electrogenic, electroneutral (non-proton motive) or even pmf-consuming. This Quinol dehydrogenase article gives conceptual classification of different operational organisations of redox loops and uses this as a platform from which to explore the biodiversity of quinone/quinol-cycling redox systems. © 2008 Elsevier B.V. All rights reserved. 1. Introduction tricarboxylic acid cycle. The electrons are then passed via freely diffusible carriers, such as NADH, or protein-bound carriers, such as Respiration is a catabolic process that is fundamental to all FADH2, into a multi-protein electron transport pathway associated kingdoms of life [1]. In human mitochondria, the ATP factories of with the inner mitochondrial membrane (Fig. 1A). Here the electrons our cells, electrons are extracted from organic carbon as it is migrate through a range of electron transferring redox cofactors, such catabolised through metabolic pathways such as glycolysis and the as flavins, iron sulfur clusters, haem and copper centres, that are bound to integral membrane or membrane-associated protein com- plexes, and ultimately reduce oxygen to water. Electrons that enter the fl Abbreviations: DMSO, dimethylsulfoxide; FAD/FADH2, oxidised/reduced avin electron transport pathway have a low electrochemical potential. For adenine dinucleotide; Fe/S, iron sulfur cluster; H+/e−, ratio between the number of example, the midpoint redox potential (termed E0′ at pH 7.0) of the protons translocated across the coupling membrane and the amount of electrons + − transported in the accompanying redox reaction; MK/MKH , menaquinone/menaqui- NAD /NADH redox couple is around 320 mV, thus making NADH a 2 ′ nol; MKK, methyl-menaquinone; MP/MPH2, methanophenazine/dihydro-methanophe- strong reductant. By contrast, the E0 of the O2/H2O couple is around nazine; Mo-bis-MGD, molybdenum-bis-molybdopterin guanine dinucleotide; N, +820 mV, making it strongly oxidizing. Electrons thus flow ‘downhill’ + negatively charged side of the coupling membrane; NAD /NADH, oxidised/reduced in energy terms from NADH to oxygen and the free energy (ΔG) nicotinamide adenine dinucleotide; Nap, periplasmic nitrate reductase system; Ni/Fe, released during this electron transfer process is used to drive the catalytic Ni/Fe centre of hydrogenase; Nrf, cytochrome c nitrite reductase system; P, positively charged side of the coupling membrane; pmf, proton motive force; PQQ, translocation of protons across the inner mitochondrial membrane to pyrroloquinoline quinone; Q/QH2, (ubi- or mena-) quinone/(ubi- or mena-) quinol; generate a transmembrane electrochemical proton gradient or proton SQO, succinate:quinone oxidoreductase; TMAO, trimethylamine-N-oxide; TMS, trans- motive force (pmf)(Fig. 1A) [2–4]. The pmf has both a chemical (ΔpH, α membrane ( -helical protein) segment dimensionless) and an electrical (Δψ, dimension: mV) component. ⁎ Corresponding authors. J. Simon is to be contacted at the Institute of Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Eq. 1 shows the corresponding formula in its simplest form. Germany. Tel.: +49 69 798 29516; fax: +49 69 798 29527. D.J. Richardson, School of ðÞΔψ− Δ ð Þ Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK. Tel.: +44 1603 pmf mV = 59 pH 1 593250; fax: +44 1603 592250. Δψ fi E-mail addresses: [email protected] (J. Simon), [email protected] Here, is de ned as the electrical potential difference between (D.J. Richardson). the positively and the negatively charged (P and N) side of the 0005-2728/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.bbabio.2008.09.008 J. Simon et al. / Biochimica et Biophysica Acta 1777 (2008) 1480–1490 1481 Fig. 1. Different mechanisms of pmf generation. (A) Schematic architecture of selected protein complexes involved in aerobic respiration, e.g. in mitochondria or in the bacterium P. denitrificans. (B) Dissection of principle mechanisms of pmf generation by intra- and interenzymic electron transport. Boxes represent electron transport enzymes or enzyme complexes in the membrane. Left, coupling ion pumping. Middle, proton translocation coupled to quinone redox chemistry. Right, pmf generation arising from divergent substrate site location without actual proton translocation. (C) The electron transport chain of anaerobic nitrate respiration with formate as electron donor in E. coli as a prototype of a two-enzyme full proton motive redox loop. The redox loop is a result of a combination of the proton translocation modes shown in the middle and on the right of (B). The structural models were prepared using PyMol and pdb files 1KQG and 1Q16. See Section 3 for details on enzyme architecture. P and N refer to the positively and negatively charged side of the membrane, respectively. 1482 J. Simon et al. / Biochimica et Biophysica Acta 1777 (2008) 1480–1490 membrane and is usually positive. The ΔpH is defined as the pH respiratory systems where the ΔG value of the redox reaction is difference between the P and the N side and is usually negative. Since smaller than in aerobic respiration and where, consequently, shorter the pmf has a value in the range of ∼150–200 mV, a potential change respiratory chains and less ion pumping enzymes are employed. The (ΔE) of at least this magnitude during transfer from donor to acceptor purpose of this article is to survey the possible mechanisms by which a is required if that step is to be coupled to pmf generation (H+/e− =ΔE/ pmf may conceptually be maintained by quinone-dependent respira- pmf at 100% thermodynamic efficiency). Overall, the transfer of 2 tory systems and to assess how many such ‘conceptual systems’ have electrons from NADH to oxygen results in 10 positive charges being been identified or can be inferred from data currently available in the translocated across the membrane and there are three key proton literature. The review focuses on the topological organisation of motive steps that contribute to this: (I) the NADH dehydrogenase different quinone-reducing and quinol-oxidising systems in biological complex (NADH:ubiquinone oxidoreductase) which is a proton pump, membranes of Bacteria and Archaea and discusses the consequences (II) the cytochrome bc1 complex (ubiquinone:cytochrome c oxidor- of this organisation for bioenergetics in terms of energy transduction eductase) that moves positive charge across the membrane via the so- or dissipation. Note that components of typical ‘mitochondrial-like’ called Q-cycle and (III) the cytochrome c oxidase (aa3-type), which aerobic respiratory chains will not be dealt with apart from succinate: combines proton pumping with opposite electron and proton move- quinone dehydrogenases. Likewise, established proton-pumping ments (Fig. 1A). This basic description of respiration is also enzymes or systems using Na+ as coupling ion are not within the fundamental to the bacterial and archaeal kingdoms of life, with one scope of this article. key difference. In Bacteria and Archaea, a diverse range of organic and inorganic substrates can be used to donate or accept electrons at 2. Configurations of quinone reducing and quinol oxidizing various electrochemical potentials in order to drive aerobic or enzyme systems involved in redox loops anaerobic respiratory electron transport systems [5]. In many mitochondrial and bacterial respiratory systems the link Conceptually, we propose that
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