Iron-sulphur clusters in fumarate reductase from Vibrio succinogenes

Modular structure of complex II: An evolutionary perspective

Succinate dehydrogenases (SDHs) and fumarate reductases (FRDs) catalyse the interconversion of succinate and fumarate, a reaction highly conserved in all domains of life. The current classification of SDH/FRDs is based on the structure of the membrane anchor subunits and their cofactors. It is, however, unknown whether this classification would hold in the context of evolution. In this work, a large-scale comparative genomic analysis of complex II addresses the questions of its taxonomic distribution and phylogeny. Our findings report that for types C, D, and F, structural classification and phylogeny go hand in hand, while for types A, B and E the situation is more complex, highlighting the possibility for their classification into subgroups. Based on these findings, we proposed a revised version of the evolutionary scenario for these enzymes in which a primordial soluble module, corresponding to the cytoplasmatic subunits, would give rise to the current diversity via several independent membrane anchor attachment events.

The fumarate reductase operon of Wolinella succinogenes. Sequence and expression of the frdA and frdB genes

The genes of the fumarate reductase of Wolinella succinogenes are organized in an operon. The three structural genes in the order frdC, frdA, frdB, are preceded by a common promoter (Körtner et al. 1990) and followed by a terminator of transcription. The proteins encoded by the genes are identical with the subunits present in the isolated enzyme. FrdA and FrdB are hydrophilic proteins consisting of 656 and 238 amino acids, respectively. The 12 cysteine residues present in FrdB form 3 ferredoxin-like clusters, whereas the 12 cysteines of FrdA are not clustered. Expression of FrdA and FrdB in Escherichia coli from a plasmid containing a DNA fragment with both genes in full length, gave rise to the EPR signals of the bi- and trinuclear iron-sulfur centers of the enzyme. Only the binuclear center was seen on the expression of FrdB together with a C-terminal fragment of FrdA (130 amino acid residues). Neither of the two centers was detected on the expression of FrdA together with a N-terminal fragment of FrdB including cysteine cluster I. Sequence comparison of FrdA and FrdB with the corresponding subunits of the fumarate reductases of E. coli or Proteus vulgaris or to those of the succinate dehydrogenases of E. coli or Bacillus subtilis revealed strong homologies (28-36% identical amino acid residues). Part of the homologous peptide stretches could be assigned to domains that are involved in the binding of the substrate of the FAD prosthetic group of the enzyme.

Ligands to the 2Fe iron-sulfur center in succinate dehydrogenase

Membrane-bound succinate oxidoreductases are flavoenzymes containing one each of a 2Fe, a 3Fe and a 4Fe iron-sulfur center. Amino acid sequence homologies indicate that all three centers are located in the Ip (B) subunit. From polypeptide and gene analysis of Bacillus subtilis succinate dehydrogenase-defective mutants combined with earlier EPR spectroscopic data, we show that four conserved cysteine residues in the first half of Ip are the ligands to the [2Fe-2S] center. These four residues have previously been predicted to be the ligands. Our results also suggest that the N-terminal part of B. subtilis Ip constitutes a domain which can incorporate separately the 2Fe center and interact with Fp, the flavin-containing subunit of the dehydrogenase.

Cloning and expression of the genes of two fumarate reductase subunits from Wolinella succinogenes

The fumarate reductase complex of the anaerobic bacterium Wolinella succinogenes catalyzes the electron transfer from menaquinol to fumarate. Two structural genes coding for subunits of the enzyme have been cloned in Escherichia coli. The genes were isolated from a lambda EMBL3 phage gene bank by immunological screening and subcloned in an expression vector. The genes frdA and frdB, which encode the FAD protein (Frd A, Mr 79,000) and the iron-sulfur protein (Frd B, Mr 31,000) of the fumarate reductase complex, were cloned together with a W. succinogenes promoter. The gene order was promoter-frdA-frdB. The FAD protein and the iron-sulfur protein were expressed in the correct molar mass in E. coli from the clones. The identity of the frdA gene and the suggested polarity were confirmed by comparing the amino-terminal sequence of the Frd A protein with that predicted from the 5'-terminal nucleotide sequence of frdA. The frdA and frdB genes are present only once in the genome. A region downstream of frdB, possibly a gene encoding cytochrome b of the fumarate reductase complex, hybridizes with a second site in the genome.

Phorphorylative electron transport chains lacking a cytochrome bc1 complex

Electron transport-coupled phosphorylation with fumarate as terminal acceptor in Wolinella succinogenes yields less than 1 ATP/2 electrons. The delta mu H generated by the electron transport is 0.18 V and the H+/electron ratio is 1. The electron transport chain is made up of two dehydrogenases (hydrogenase and formate dehydrogenase) that catalyze the reduction of menaquinone, and fumarate reductase which catalyzes the oxidation of menaquinol. C-type cytochromes are not involved. The phosphorylative electron transport with sulfur as terminal acceptor in W. succinogenes or Desulfuromonas acetoxidans does not involve known quinones. The ATP yields should be even smaller than those with fumarate. Succinate oxidation by sulfur, which is a catabolic reaction in D. acetoxidans, is accomplished by reversed electron transport.

Evidence that centre 2 in Escherichia coli fumarate reductase is a [4Fe-4S]cluster

Redox titrations of the iron-sulphur clusters in fumarate reductase purified from Escherichia coli, monitored by ESR spectroscopy, identified three redox events, similar to those observed in other fumarate reductases and succinate dehydrogenases: Centre 1, a [2Fe-2S] cluster, at g = 2.03, 1.93, appeared on reduction with Em = -20 mV. Centre 3, probably a [3Fe-xS] cluster, at g = 2.02 appeared in the oxidized state with Em = -70 mV. Centre 2 has been observed as an increase in the electron-spin relaxation of Centre 1. It titrates as an n = 1 species with Em = -320 mV, but in our hands did not appear to contribute significant intensity to the g = 2.03, 1.93 signal. It therefore appears to be an additional centre which undergoes spin-spin interaction with Centre 1. The reduction of Centre 2 coincided with the appearance of an extremely broad ESR spectrum, observed at temperatures below 20 K, with features at g = 2.17, 1.9, 1.68. The broad signal was observed in both soluble and membrane-bound preparations. Its midpoint potential was -320 mV. Its integrated intensity was approximately equal to that of Centre 1, if its broad outer wings were taken into account. Consideration of the ESR properties of this signal, together with the amino acid sequence of the frdB subunit of the enzyme, indicates that Centre 2 is a [4Fe-4S] cluster which, in its reduced state, enhances the spin relaxation of the [2Fe-2S] Centre 1.

Isolation of fumarate reductase from Desulfovibrio multispirans, a sulfate reducing bacterium

Fumarate reductase was isolated and purified 100-fold to homogeneity from Desulfovibrio multispirans, a new species of sulfate-reducing bacteria. The enzyme contained 1 mol of non-covalently bound FAD and four subunits with Mr 45,000, 32,000, 30,000 and 27,000. EPR spectroscopy showed the existence of two iron-sulfur clusters. The absorption spectrum showed a broad region of high absorbance from 450 nm to 300 nm with a protein peak at 278 nm. The ratio of A278:A400 was 2.60. The specific activity was 110 mumoles H2/mg of protein. The Km for fumarate was 2.5 mM. The activation energy was 8.7 kcal/mol. Electron transport from H2 to fumarate in intact cells was inhibited by 2-heptyl-4-hydroxy-quinoline-N-oxide, a quinone inhibitor, indicating the participation of quinone (probably menaquinone) in fumarate reduction.

Nucleotide sequence encoding the iron-sulphur protein subunit of the succinate dehydrogenase of Escherichia coli

The nucleotide sequence of a 961 base-pair segment of DNA containing the sdhB gene, which encodes the iron-sulphur protein subunit of the E. coli succinate dehydrogenase, has been determined. The sdhB structural gene comprises 711 base pairs (237 codons, excluding the translational initiator and terminator). It is separated by a 15 base-pair intergenic region from the preceding flavoprotein gene (sdhA) and is the distal gene of an operon that also includes genes (sdhC and D) encoding two hydrophobic subunits, sdhCDAB. The distal end of the sdh operon is linked to the 2-oxoglutarate dehydrogenase gene (sucA) by a complex region of dyad symmetry that is homologous with several potential intercistronic regulatory elements or transcriptional attenuators. The sdhB structural gene encodes a polypeptide of Mr26637 that is strikingly homologous with the iron-sulphur protein subunit of fumarate reductase (38% identity, increasing to 58% when conservative changes are included). Both subunits contain 11 cysteine residues, 10 being conserved in three clusters resembling those found in ferredoxins. This work completes the sequence of a 9897 base-pair segment of DNA containing seven tricarboxylic acid cycle genes encoding three enzymes or enzyme complexes, citrate synthase (gltA), succinate dehydrogenase (sdh), and the 2-oxoglutarate dehydrogenase complex (suc), that are organized thus: gltA-sdhCDAB-sucAB.

Three-iron clusters in iron-sulfur proteins

Contents. 1. Introduction and history. 2. Characteristic spectroscopic features of 3Fe clusters. 1. General considerations. 2. Mössbauer spectroscopy. 3. Magnetic circular dichroism (MCD) spectroscopy. 4. Electron paramagnetic resonance (EPR) spectroscopy. 5. Resonance Raman (RR) spectroscopy. 6. Extended X-ray fine-structure (EXAFS) spectroscopy. 3. Results of X-Ray diffraction studies. 4. Proteins containing or showing features characteristic of 3Fe clusters 1. Overview. 2. Ferredoxin I of Azotobacter vinelandii. 3. Ferredoxin II of Desulfovibrio gigas. 4. Aconitase from beef heart. 5. Other observations and considerations relevant to 3Fe clusters or cluster interconversions 1. Oxidative degradation of [4Fe-4S] clusters to 3Fe clusters. 2. Extrusion studies on 3Fe clusters. 3. Reconstitution of 3Fe clusters. 4. Disposition of iron ligands in cluster interconversions. 6. Do all 3Fe clusters have the same structure? Evidence for [3Fe-4S] clusters. 7. Are 3Fe clusters artifacts or biologically significant structures?

The function of the subunits of the fumarate reductase complex of Vibrio succinogenes

The membrane-bound fumarate reductase complex of Vibrio succinogenes catalyzes the reduction of fumarate by 2,3-dimethyl-1,4-naphthohydroquinone (dimethylnaphthohydroquinone) and consists of three different peptides (Mr 79,000, Mr 31,000 and Mr 25,000), the smallest of which is cytochrome b [Unden, G., Hackenberg, H. and Kröger A. (1980) Biochem. Biophys. Acta 591, 275-288]. The complex was cleaved with guanidinium chloride, the resulting subunits characterized and their functions within the complex investigated by reconstitutional experiments. 1. The Mr-79,000 subunits catalyzed the reduction of fumarate by benzylviologen radicals as well as the oxidation of succinate by methylene blue, but not fumarate reduction by dimethylnaphthohydroquinone. 2. The spectral and the redox properties of the isolated cytochrome b (Mr 25,000) were equivalent to those of the high-potential cytochrome b of the bacteria. The isolated cytochrome b had a midpoint potential of -15 mV and was reducible by dimethylnaphthohydroquinone in the absence of the other subunits. 3. The Mr-31,000 subunit did not catalyze any of the reactions mentioned above. For the reduction of cytochrome b by succinate in the presence of the Mr-79,000 subunit, an amount of the Mr-31,000 subunit was required which was equimolar to cytochrome b. 4. The activity of fumarate reduction by dimethylnaphthohydroquinone could be restored by coprecipitation of the three subunits. It is concluded that the fumarate reductase complex has two different sites, which are essential for its function in the phosphorylative electron transport of the bacterium. The site reacting with the substrates fumarate and succinate is situated on the Mr-79,000 subunit, and that reacting with dimethylnaphthohydroquinone is cytochrome b. The Mr-31,000 subunit mediates the electron transport between cytochrome b and the Mr-79,000 subunit.