BBA - Bioenergetics (v.1553, #1-2)

Succinate:quinone oxidoreductases: an overview by C.Roy D. Lancaster (1-6).
Keywords: Atomic model; Bioenergetics; Fumarate reductase; Membrane protein; Succinate dehydrogenase; X-Ray crystallography;

An attempt is made to retrace, from personal experience, the discovery of redox-reactive non-heme iron in living matter, which turned out to occur in the form of iron–sulfur (Fe–S) clusters, and then to recount the immediate application of this knowledge in exploring the composition of the mitochondrial respiratory chain, and in the rather detailed description of the workings of its components and, for the purposes of the present volume, of succinate dehydrogenase. The relationship of these events to the general status of technology and the available methodology and instrumentation is considered in some detail, with the conclusion that there scarcely was a way that these discoveries could have been made earlier. It is then shown how methods, techniques and interpretations of results were developed and evolved during the applications that were made to a complex problem such as that of the composition, structure and functioning of succinate dehydrogenase. A tabulation of the most significant events – concerning specifically spectroscopy and its interpretations – in this development is given up to the year 2000.
Keywords: Iron–sulfur cluster; Electron paramagnetic resonance spectroscopy; Magnetic circular dichroism spectroscopy; Resonance Raman spectroscopy; Mössbauer spectroscopy; EXAFS spectroscopy;

Fumarate respiration of Wolinella succinogenes: enzymology, energetics and coupling mechanism by Achim Kröger; Simone Biel; Jörg Simon; Roland Gross; Gottfried Unden; C.Roy D. Lancaster (23-38).
Wolinella succinogenes performs oxidative phosphorylation with fumarate instead of O2 as terminal electron acceptor and H2 or formate as electron donors. Fumarate reduction by these donors (‘fumarate respiration’) is catalyzed by an electron transport chain in the bacterial membrane, and is coupled to the generation of an electrochemical proton potential (Δp) across the bacterial membrane. The experimental evidence concerning the electron transport and its coupling to Δp generation is reviewed in this article. The electron transport chain consists of fumarate reductase, menaquinone (MK) and either hydrogenase or formate dehydrogenase. Measurements indicate that the Δp is generated exclusively by MK reduction with H2 or formate; MKH2 oxidation by fumarate appears to be an electroneutral process. However, evidence derived from the crystal structure of fumarate reductase suggests an electrogenic mechanism for the latter process.
Keywords: Fumarate respiration; Electron transport; Coupling mechanism; Hydrogenase; Formate dehydrogenase; Wolinella succinogenes;

C4-dicarboxylate carriers and sensors in bacteria by I.G Janausch; E Zientz; Q.H Tran; A Kröger; G Unden (39-56).
Bacteria contain secondary carriers for the uptake, exchange or efflux of C4-dicarboxylates. In aerobic bacteria, dicarboxylate transport (Dct)A carriers catalyze uptake of C4-dicarboxylates in a H+- or Na+-C4-dicarboxylate symport. Carriers of the dicarboxylate uptake (Dcu)AB family are used for electroneutral fumarate:succinate antiport which is required in anaerobic fumarate respiration. The DcuC carriers apparently function in succinate efflux during fermentation. The tripartite ATP-independent periplasmic (TRAP) transporter carriers are secondary uptake carriers requiring a periplasmic solute binding protein. For heterologous exchange of C4-dicarboxylates with other carboxylic acids (such as citrate:succinate by CitT) further types of carriers are used. The different families of C4-dicarboxylate carriers, the biochemistry of the transport reactions, and their metabolic functions are described. Many bacteria contain membraneous C4-dicarboxylate sensors which control the synthesis of enzymes for C4-dicarboxylate metabolism. The C4-dicarboxylate sensors DcuS, DctB, and DctS are histidine protein kinases and belong to different families of two-component systems. They contain periplasmic domains presumably involved in C4-dicarboxylate sensing. In DcuS the periplasmic domain seems to be essential for direct interaction with the C4-dicarboxylates. In signal perception by DctB, interaction of the C4-dicarboxylates with DctB and the DctA carrier plays an important role.
Keywords: Fumarate/succinate transport; Dicarboxylate uptake carrier; Dicarboxylate transport A carrier; Antiport; Fumarate (succinate) sensor; Dicarboxylate uptake S; Dicarboxylate transport B; Two-component system; Histidine protein kinase;

Reversible succinate dehydrogenase (SDH) activities have been ubiquitously detected in organisms from the three domains of life. They represent constituents either of respiratory complexes II in aerobes, or of fumarate dehydrogenase complexes in anaerobes. The present review gives a survey on archaeal succinate:quinone oxidoreductases (SQRs) analyzed so far. Though some of these could be studied in detail enzymologically and spectroscopically, the existence of others has been deduced only from published genome sequences. Interestingly, two groups of enzyme complexes can be distinguished in Archaea. One group resembles the properties of SDHs known from bacteria and mitochondria. The other represents a novel class with an unusual iron–sulfur cluster in subunit B and atypical sequence motifs in subunit C which may influence electron transport mechanisms and pathways. This novel class of SQRs is discussed in comparison to the so-called ‘classical’ complexes. A phylogenetic analysis is presented suggesting a co-evolution of the flavoprotein-binding subunit A and subunit B containing the three iron–sulfur clusters.
Keywords: Archaeon; Succinate:acceptor oxidoreductase; Complex II; Evolution; Succinate dehydrogenase;

An overview of the present knowledge about succinate:quinone oxidoreductase in Paracoccus denitrificans and Bacillus subtilis is presented. P. denitrificans contains a monoheme succinate:ubiquinone oxidoreductase that is similar to that of mammalian mitochondria with respect to composition and sensitivity to carboxin. Results obtained with carboxin-resistant P. denitrificans mutants provide information about quinone-binding sites on the enzyme and the molecular basis for the resistance. B. subtilis contains a diheme succinate:menaquinone oxidoreductase whose activity is dependent on the electrochemical gradient across the cytoplasmic membrane. Data from studies of mutant variants of the B. subtilis enzyme combined with available crystal structures of a similar enzyme, Wolinella succinogenes fumarate reductase, substantiate a proposed explanation for the mechanism of coupling between quinone reductase activity and transmembrane potential.
Keywords: Cytochrome structure; Carboxin resistance; Succinate dehydrogenase; Heme protein;

The ϵ-proteobacteria form a subdivision of the Proteobacteria including the genera Wolinella, Campylobacter, Helicobacter, Sulfurospirillum, Arcobacter and Dehalospirillum. The majority of these bacteria are oxidase-positive microaerophiles indicating an electron transport chain with molecular oxygen as terminal electron acceptor. However, numerous members of the ϵ-proteobacteria also grow in the absence of oxygen. The common presence of menaquinone and fumarate reduction activity suggests anaerobic fumarate respiration which was demonstrated for the rumen bacterium Wolinella succinogenes as well as for Sulfurospirillum deleyianum, Campylobacter fetus, Campylobacter rectus and Dehalospirillum multivorans. To date, complete genome sequences of Helicobacter pylori and Campylobacter jejuni are available. These bacteria and W. succinogenes contain the genes frdC, A and B encoding highly similar heterotrimeric enzyme complexes belonging to the family of succinate:quinone oxidoreductases. The crystal structure of the W. succinogenes quinol:fumarate reductase complex (FrdCAB) was solved recently, thus providing a model of succinate:quinone oxidoreductases from ϵ-proteobacteria. Succinate:quinone oxidoreductases are being discussed as possible therapeutic targets in the treatment of several pathogenic ϵ-proteobacteria.
Keywords: Fumarate reductase; Fumarate respiration; Succinate dehydrogenase; Wolinella succinogenes; Helicobacter pylori; Campylobacter jejuni;

The Saccharomyces cerevisiae mitochondrial succinate:ubiquinone oxidoreductase by Bernard D. Lemire; Kayode S. Oyedotun (102-116).
The Saccharomyces cerevisiae succinate dehydrogenase (SDH) provides an excellent model system for studying the assembly, structure, and function of a mitochondrial succinate:quinone oxidoreductase. The powerful combination of genetic and biochemical approaches is better developed in yeast than in other eukaryotes. The yeast protein is strikingly similar to other family members in the structural and catalytic properties of its subunits. However, the membrane domain and particularly the role of the single heme in combination with two ubiquinone-binding sites need further investigation. The assembly of subunits and cofactors that occurs to produce new holoenzyme molecules is a complex process that relies on molecular chaperones. The yeast SDH provides the best opportunity for understanding the biogenesis of this family of iron–sulfur flavoproteins.
Keywords: Mitochondrion; Quinone; Chaperone; Membrane protein; Assembly; Heme;

The succinate dehydrogenase consists of only four subunits, all nuclearly encoded, and is part of both the respiratory chain and the Krebs cycle. Mutations in the four genes encoding the subunits of the mitochondrial respiratory chain succinate dehydrogenase have been recently reported in human and shown to be associated with a wide spectrum of clinical presentations. Although a comparatively rare deficiency in human, molecularly defined succinate dehydrogenase deficiency has already been found to cause encephalomyopathy in childhood, optic atrophy or tumor in adulthood. Because none of the typical housekeeping genes encoding this respiratory chain complex is known to present tissue-specific isoforms, the tissue-specific involvement represents a quite intriguing question, which is mostly addressed in this review. A differential impairment of electron flow through the respiratory chain, handling of oxygen, and/or metabolic blockade possibly associated with defects in the different subunits that can be advocated to account for tissue-specific involvement is discussed.
Keywords: Succinate dehydrogenase; Human; Encephalomyopathy; Paraganglioma;

Role of complex II in anaerobic respiration of the parasite mitochondria from Ascaris suum and Plasmodium falciparum by Kiyoshi Kita; Hiroko Hirawake; Hiroko Miyadera; Hisako Amino; Satoru Takeo (123-139).
Parasites have developed a variety of physiological functions necessary for existence within the specialized environment of the host. Regarding energy metabolism, which is an essential factor for survival, parasites adapt to low oxygen tension in host mammals using metabolic systems that are very different from that of the host. The majority of parasites do not use the oxygen available within the host, but employ systems other than oxidative phosphorylation for ATP synthesis. In addition, all parasites have a life cycle. In many cases, the parasite employs aerobic metabolism during their free-living stage outside the host. In such systems, parasite mitochondria play diverse roles. In particular, marked changes in the morphology and components of the mitochondria during the life cycle are very interesting elements of biological processes such as developmental control and environmental adaptation. Recent research has shown that the mitochondrial complex II plays an important role in the anaerobic energy metabolism of parasites inhabiting hosts, by acting as quinol–fumarate reductase.
Keywords: Complex II; Quinol–fumarate reductase; Anaerobic respiration; Parasite mitochondria; Plasmodium falciparum; Ascaris suum;

Succinate dehydrogenase and fumarate reductase from Escherichia coli by Gary Cecchini; Imke Schröder; Robert P Gunsalus; Elena Maklashina (140-157).
Succinate-ubiquinone oxidoreductase (SQR) as part of the trichloroacetic acid cycle and menaquinol-fumarate oxidoreductase (QFR) used for anaerobic respiration by Escherichia coli are structurally and functionally related membrane-bound enzyme complexes. Each enzyme complex is composed of four distinct subunits. The recent solution of the X-ray structure of QFR has provided new insights into the function of these enzymes. Both enzyme complexes contain a catalytic domain composed of a subunit with a covalently bound flavin cofactor, the dicarboxylate binding site, and an iron–sulfur subunit which contains three distinct iron–sulfur clusters. The catalytic domain is bound to the cytoplasmic membrane by two hydrophobic membrane anchor subunits that also form the site(s) for interaction with quinones. The membrane domain of E. coli SQR is also the site where the heme b 556 is located. The structure and function of SQR and QFR are briefly summarized in this communication and the similarities and differences in the membrane domain of the two enzymes are discussed.
Keywords: Succinate dehydrogenase; Fumarate reductase; Ubiquinone reductase; Menaquinol oxidase; Flavoprotein; Iron–sulfur protein;

Quinol:fumarate oxidoreductases and succinate:quinone oxidoreductases: phylogenetic relationships, metal centres and membrane attachment by Rita S Lemos; Andreia S Fernandes; Manuela M Pereira; Cláudio M Gomes; Miguel Teixeira (158-170).
A comprehensive phylogenetic analysis of the core subunits of succinate:quinone oxidoreductases and quinol:fumarate oxidoreductases is performed, showing that the classification of the enzymes as type A to E based on the type of the membrane anchor fully correlates with the specific characteristics of the two core subunits. A special emphasis is given to the type E enzymes, which have an atypical association to the membrane, possibly involving anchor subunits with amphipathic helices. Furthermore, the redox properties of the SQR/QFR proteins are also reviewed, stressing out the recent observation of redox-Bohr effect upon haem reduction, observed for the Desulfovibrio gigas and Rhodothermus marinus enzymes, which indicates a direct protonation event at the haems or at a nearby residue. Finally, the possible contribution of these enzymes to the formation/dissipation of a transmembrane proton gradient is discussed, considering recent experimental and structural data.
Keywords: Succinate:quinone oxidoreductase; Quinol:fumarate oxidoreductase; Redox-Bohr; Phylogeny; Amphipathic helix;

A membrane protein complex, succinate dehydrogenase (SQR) from Escherichia coli has been purified and crystallised. This enzyme is composed of four subunits containing FAD, three iron–sulphur clusters and one haem b as prosthetic groups. The obtained crystals belong to the hexagonal space group P63 with the unit-cell dimensions of a=b=123.8 Å and c=214.6 Å. An asymmetric unit of the crystals contains one SQR monomer (M r 120 kDa). A data set is now available at 4.0 Å resolution with 88.1% completeness and 0.106 R merge. We have obtained a molecular replacement solution that shows sensible molecular packing, using the soluble domain of E. coli QFR (fumarate reductase) as a search model. The packing suggests that E. coli SQR is a crystallographic trimer rather than a dimer as observed for the E. coli QFR.
Keywords: Succinate dehydrogenase; Membrane protein; X-ray crystallography;