Isolation of cytochrome bc 1 complexes from the photosynthetic bacteria Rhodopseudomonas viridis and Rhodospirillum rubrum

The role of subunit VIII in the structural stability of the bc1 complex from Saccharomyces cerevisiae studied using hybrid complexes

The QCR8 genes encoding subunit VIII of the bc1 complex from Kluyveromyces lactis and Schizosaccharomyces pombe partially complement the respiratory-deficient phenotype of a S. cerevisiae QCR8-null mutant. This implies that the heterologous Qcr8 subunits can be imported by S. cerevisiae mitochondria and that they assemble to form a hybrid bc1 complex that is sufficiently active to support growth. In contrast, the QCR8 gene from bovine heart, encoding the 9.5-kDa subunit, is not able to restore respiratory function to the S. cerevisiae null mutant. This lack of functional complementation is directly attributable to the inability of S. cerevisiae mitochondria to import this protein as shown by in vitro assays. However, a hybrid gene encoding the N-terminal 26 residues of S. cerevisiae subunit VIII and the rest of the 9.5-kDa bovine heart homologue, was able to functionally complement the QCR8-null mutant, albeit to a very low extent. Successful import into S. cerevisiae mitochondria was confirmed by in vitro import experiments. Surprisingly, although assembly of these hybrid complexes is reduced to an extent that is proportional to the evolutionary distance of the homologue to S. cerevisiae, the specific activities of the assembled complexes are the same as for the wild-type bc1 complex. After solubilisation of the mitochondrial membranes with the mild detergent dodecyl maltoside, the wild-type enzyme can be inactivated by incubation at increased temperature, independent of protease activity. The rate of inactivation can be significantly increased by the addition of o-phenanthroline [Boumans, H., Grivell, L. A. & Berden, J. A. (1997) J. Biol. Chem. 272, 16753-16760]. The hybrid complexes are much more sensitive to both types of treatment. We conclude that substitution of subunit VIII by a homologous counterpart results in a loosening of the structure of the bc1 complex on the intermembrane space side, resulting in a less stable insertion of the Rieske Fe-S protein in vivo and therefore a lower stability of the assembled enzyme under certain in vitro conditions, but without an effect on catalytic activity.

A point mutation in the mitochondrial cytochrome b gene obviates the requirement for the nuclear encoded core protein 2 subunit in the cytochrome bc1 complex in Saccharomyces cerevisiae

A yeast mutant (cor2-45) in which approximately half of the C terminus of core protein 2 of the cytochrome bc1 complex is lacking due to a frameshift mutation that introduces a stop at codon 197 in the COR2 gene fails to assemble the cytochrome bc1 complex and does not grow on non-fermentable carbon sources that require respiration. The loss of respiration is more severe with this frameshift mutation than with the complete deletion of the COR2 gene, suggesting deleterious effects of the truncated core 2 protein. A search for extragenic suppressors of the nuclear cor2-45 mutation resulted (in addition to the expected nuclear suppressors) in the isolation of a suppressor mutation in the mitochondrial DNA that replaces serine 223 by proline in cytochrome b. Assembly of the cytochrome bc1 complex and the respiratory deficient phenotype of the cor2-45 mutant are restored by the proline for serine replacement in cytochrome b. Surprisingly, this amino acid replacement in cytochrome b corrects not only the phenotype resulting from the cor2-45 frameshift mutation, but it also obviates the need for core protein 2 in the cytochrome bc1 complex since it alleviates the respiratory deficiency resulting from the complete deletion of the COR2 gene. This is the first report of a homoplasmic missense point mutation of the mitochondrial DNA acting as a functional suppressor of a mutation located in a nuclear gene and the first demonstration that the supernumerary core protein 2 subunit is not essential for the electron transfer and energy transducing functions of the mitochondrial cytochrome bc1 complex.

The interaction between cytochrome c2 and the cytochrome bc1 complex in the photosynthetic purple bacteria Rhodobacter capsulatus and Rhodopseudomonas viridis

The rates of electron transfer from a ubiquinol analogue to cytochrome c2 catalyzed by the cytochrome bc1 complexes of Rhodobacter capsulatus and Rhodopseudomonas viridis were measured as a function of ionic strength. The effects of ionic strength on the kinetic parameters for the reactions are consistent with a role for electrostatic complex formation between cytochrome c2 and the cytochrome bc1 complex in the electron-transfer pathways in both photosynthetic purple non-sulfur bacteria. Additional support for a docking model in which positively charged lysines on cytochrome c2 interact with negatively charged groups on the Rb. capsulatus cytochrome bc1 complex was obtained from kinetic experiments using Rb. capsulatus cytochrome c2 and equine cytochrome c in which specific lysine residues were altered by site-directed mutagenesis and chemical modification, respectively. Equine cytochrome c, which is a poor electron donor to the reaction center of Rps. viridis, is an effective electron acceptor for the Rps. viridis cytochrome bc1 complex. Chemical modification of lysine residues on Rps. viridis cytochrome c2 has a substantially greater effect on the reduction of the Rps. viridis reaction center by ferrocytochrome c2 than on the oxidation of the Rps. viridis cytochrome bc1 complex by ferricytochrome c2. These data suggest that the docking site for Rps. viridis cytochrome c2 on the Rps. viridis reaction center tetraheme subunit differs in structure from the docking site for the cytochrome on the Rps. viridis cytochrome bc1 complex to a significant extent. In this respect, Rps. viridis differs from photosynthetic purple non-sulfur bacteria in which the reaction center does not contain a tetraheme subunit, where the binding sites for cytochrome c2 on the reaction center and the cytochrome bc1 complex appear to be quite similar.

Abundance, subunit composition, redox properties, and catalytic activity of the cytochrome bc1 complex from alkaliphilic and halophilic, photosynthetic members of the family Ectothiorhodospiraceae

Ubiquinol-cytochrome c oxidoreductase (cytochrome bc1) complexes were demonstrated to be present in the membranes of the alkaliphilic and halophilic purple sulfur bacteria Ectothiorhodospira halophila, Ectothiorhodospira mobilis, and Ectothiorhodospira shaposhnikovii by protoheme extraction, immunoblotting, and electron paramagnetic resonance spectroscopy. The gy values of the Rieske [2Fe-2S] clusters observed in membranes of E. mobilis and E. halophila were 1.895 and 1.910, respectively. In E. mobilis membranes, the cytochrome bc1 complex was present in a stoichiometry of approximately 0.2 per reaction center. This complex was isolated and characterized. It contained four prosthetic groups: low-potential cytochrome b (cytochrome bL; Em = -142 mV), high-potential cytochrome b (cytochrome bH; Em = 116 mV), cytochrome c1 (Em = 341 mV), and a Rieske iron-sulfur cluster. The absorbance spectrum of cytochrome bL displayed an asymmetric alpha-band with a maximum at 564 nm and a shoulder at 559 nm. The alpha bands of cytochrome bH and cytochrome c1 peaked at 559.5 and 553 nm, respectively. These prosthetic groups were associated with three different polypeptides: cytochrome b, cytochrome c1, and the Rieske iron-sulfur protein, with apparent molecular masses of 43, 30, and 21 kDa, respectively. No evidence for the presence of a fourth subunit was obtained. Maximal ubiquinol-cytochrome c oxidoreductase activity of the purified complex was observed at pH 8; the turnover rate was 57 mol of cytochrome c reduced.(mol of cytochrome c1)-1.s-1. The complex showed a strikingly low sensitivity towards typical inhibitors of cytochrome bc1 complexes.

Hydroubiquinone-cytochrome c2 oxidoreductase from Rhodobacter capsulatus: definition of a minimal, functional isolated preparation

The hydroubiquinone-cytochrome c2 oxidoreductase (cyt bc1) from Rhodobacter capsulatus has been solubilized according to the dodecyl maltoside method and isolated, and its minimal functional composition has been characterized. We find the complex to be composed of three protein subunits corresponding to polypeptides of cyt b (44 kDa), cyt c1 (33 kDa), and 2Fe2S cluster (24 kDa). A fourth band sometimes discernable at 22 kDa appears to be an artifact of the polyacrylamide gel electrophoresis procedure. Its appearance is shown to be derived from the 2Fe2S cluster subunit by the similarity of the binding of subunit-specific monoclonal antibodies and the identical N-terminal sequence of the 24- and 22-kDa bands. The cofactors of cyt bc1, namely, cyt bH, cyt bL, cyt c1, and the 2Fe2S center, the Qos and Qow domains of the Qo site, and the Qi site appear intact as indicated by their optical and EPR spectral signatures, redox properties, and inhibitor binding. The electron paramagnetic resonance spectrum of the cyt bH heme is altered by antimycin, consistent with a change in the dihedral angle between the ligating histidine imidazoles, while the spectrum of the cyt bL heme is broadened by stigmatellin. The ubiquinone-10 content is variable, ranging from 0.8 to 3 molecules/cyt bc1. Activity studies define this three-subunit cyt bc1 complex as a minimal structure, equipped as the enzyme in the native state and capable of full catalytic activity.

The cytochrome bc 1 complexes of photosynthetic purple bacteria

Complete nucleotide sequences are now available for the pet (fbc) operons coding for the three electron carrying protein subunits of the cytochrome bc 1 complexes of four photosynthetic purple non-sulfur bacteria. It has been demonstrated that, although the complex from one of these bacteria may contain a fourth subunit, three subunit complexes appear to be fully functional. The ligands to the three hemes and the one [2Fe-2S] cluster in the complex have been identified and considerable progress has been made in mapping the two quinone-binding sites present in the complex, as well as the binding sites for quinone analog inhibitors. Hydropathy analyses and alkaline phosphatase fusion experiments have provided considerable insight into the likely folding pattern of the cytochrome b peptide of the complex and identification of the electrogenic steps associated with electron transport through the complex has allowed the orientation within the membrane of the electron-carrying groups of the complex to be modeled.

Characterization of the pet operon of Rhodospirillum rubrum

The three genes of the pet operon, coding, respectively, for the Rieske iron-sulfur protein, cytochrome b and cytochrome c 1 components of the cytochrome bc 1 complex in the photosynthetic bacterium Rhodospirillum rubrum have been sequenced. The amino acid sequences deduced for these three peptides from the nucleotide sequences of the genes have been confirmed, in part, by direct sequencing of portions of the three peptides separated from a sample of the purified, detergent-solubilized complex. These sequences show considerable homology with those previously obtained for the pet operons of other photosynthetic bacteria. Northern blots of R. rubrum mRNA have established that the operon is transcribed as a single polycistronic message, the start site of which has been determined by both primer extension and nuclease protection. Photosynthetic growth of R. rubrum was shown to be inhibited by antimycin A, a specific inhibitor of cytochrome bc 1 complexes, and antimycin A-resistant mutants of R. rubrum have been isolated. Preliminary results suggest that it may be possible to express the R. rubrum pet operon in a strain of the photosynthetic bacterium Rhodobacter capsulatus from which the native pet operon has been deleted.

The Rhodospirillum rubrum cytochrome bc1 complex: redox properties, inhibitor sensitivity and proton pumping

A detergent-solubilized, three-subunit-containing cytochrome bc1 complex, isolated from the photosynthetic bacterium R. rubrum, has been shown to be highly sensitive to stigmatellin, myxothiazol, antimycin A and UHDBT, four specific inhibitors of these complexes. Oxidation-reduction titrations have allowed the determination of Em values for all the electron-carrying prosthetic groups in the complex. Antimycin A has been shown to produce a red shift in the alpha-band absorbance maximum of one of the cytochrome b hemes in the complex and stigmatellin has been shown to alter both the Em and EPR g-values of the Rieske iron-sulfur protein in the complex. Western blots have revealed antigenic similarities between the cytochrome subunits of the R. rubrum complex and those of the related photosynthetic bacteria, Rb. capsulatus and Rb. sphaeroides. The R. rubrum complex has been incorporated into liposomes. These liposomes exhibit respiratory control and are able to couple electron transfer from quinol to cytochrome c to proton translocation across the liposome membrane in a manner consistent with a Q-cycle mechanism. It can thus be concluded that neither electron transport nor coupled proton translocation by the cytochrome bc1 complex requires more than three subunits in R. rubrum.

The pet genes of Rhodospirillum rubrum: cloning and sequencing of the genes for the cytochrome bc1-complex

A cytochrome bc1-complex of Rs. rubrum was isolated and the three subunits were purified to homogeneity. The N-terminal amino acid sequence of the purified subunits was determined by automatic Edman degradation. The pet genes of Rhodospirillum rubrum coding for the three subunits of the cytochrome bc1-complex were isolated from a genomic library of Rs. rubrum using oligonucleotides specific for conserved regions of the subunits from other organisms and a heterologous probe derived from the genes for the complex of Rb. capsulatus. The complete nucleotide sequence of a 5500 bp SalI/SphI fragment is described which includes the pet genes and three additional unidentified open reading frames. The N-terminal amino acid sequence of the isolated subunits was used for the identification of the three genes. The genes encoding the subunits are organized as follows: Rieske protein, cytochrome b, cytochrome c1. Comparison of the N-terminal protein sequences with the protein sequences deduced from the nucleotide sequence showed that only cytochrome c1 is processed during transport and assembly of the three subunits of the complex. Only the N-terminal methionine of the Rieske protein is cleaved off. The similarity of the deduced amino acid sequence of the three subunits to the corresponding subunits of other organisms is described and implications for structural features of the subunits are discussed.

Resonance Raman spectroscopy of cytochrome bc1 complexes from Rhodospirillum rubrum: initial characterization and reductive titrations

Resonance Raman spectra of bc1 complexes from Rhodospirillum rubrum have been obtained. Various resonance conditions and the stoichiometric redox titration of the complex were used to isolate and identify the contributions of the heme c1 and heme b active sites to the observed spectra. The complex was found to partially photoreduce when exposed to laser excitation.

Cytochrome bc1 complexes of microorganisms

The cytochrome bc1 complex is the most widely occurring electron transfer complex capable of energy transduction. Cytochrome bc1 complexes are found in the plasma membranes of phylogenetically diverse photosynthetic and respiring bacteria, and in the inner mitochondrial membrane of all eucaryotic cells. In all of these species the bc1 complex transfers electrons from a low-potential quinol to a higher-potential c-type cytochrome and links this electron transfer to proton translocation. Most bacteria also possess alternative pathways of quinol oxidation capable of circumventing the bc1 complex, but these pathways generally lack the energy-transducing, protontranslocating activity of the bc1 complex. All cytochrome bc1 complexes contain three electron transfer proteins which contain four redox prosthetic groups. These are cytochrome b, which contains two b heme groups that differ in their optical and thermodynamic properties; cytochrome c1, which contains a covalently bound c-type heme; and a 2Fe-2S iron-sulfur protein. The mechanism which links proton translocation to electron transfer through these proteins is the proton motive Q cycle, and this mechanism appears to be universal to all bc1 complexes. Experimentation is currently focused on understanding selected structure-function relationships prerequisite for these redox proteins to participate in the Q-cycle mechanism. The cytochrome bc1 complexes of mitochondria differ from those of bacteria, in that the former contain six to eight supernumerary polypeptides, in addition to the three redox proteins common to bacteria and mitochondria. These extra polypeptides are encoded in the nucleus and do not contain redox prosthetic groups. The functions of the supernumerary polypeptides of the mitochondrial bc1 complexes are generally not known and are being actively explored by genetically manipulating these proteins in Saccharomyces cerevisiae.

Cloning and sequencing of the fbcF, B and C genes encoding the cytochrome b/c1 complex from Rhodopseudomonas viridis

The complete nucleotide sequence of the genes encoding the Rieske FeS, the cytochrome b and the cytochrome c1 subunits of the ubiquinol-cytochrome c2 oxidoreductase from the photosynthetic purple bacterium Rhodopseudomonas viridis, and the derived amino acid sequences are presented. These three genes, fbcF, fbcB and fbcC, are located at contiguous sites of the genome. The DNA-deduced amino acid sequences are compared with known primary structures of corresponding proteins from other purple photosynthetic bacteria, as well as mitochondria, cyanobacteria and chloroplasts.

The Rhodospirillum rubrum cytochrome bc1 complex: peptide composition, prosthetic group content and quinone binding

A cytochrome bc1 complex, essentially free of bacteriochlorophyll, has been purified from the photosynthetic purple non-sulfur bacterium Rhodospirillum rubrum. The complex catalyzes electron flow from quinol to cytochrome c (turnover number = 75 s-1) that is inhibited by low concentrations of antimycin A and myxothiazol. The complex contains only three peptide subunits: cytochrome b (Mr = 35,000); cytochrome c1 (Mr = 31,000) and the Rieske iron-sulfur protein (Mr = 22,400). Em values (pH 7.4) were measured for cytochrome c1 (+320 mV) and the two hemes of cytochrome b (-33 and -90 mV). Electron flow from quinol to cytochrome c is inhibited when the complex is pre-illuminated in the presence of a ubiquinone photoaffinity analog (azido-Q). During illumination, the azido-Q becomes covalently attached to the cytochrome b peptide and, to a lesser extent, to cytochrome c1.

Organization and structure of the genes for the cytochrome b/c1 complex in purple photosynthetic bacteria. A phylogenetic study describing the homology of the b/c1 subunits between prokaryotes, mitochondria, and chloroplasts

The cytochrome b/c1 complex is an ubiquitous energy transducing enzyme, part of the electron transport chain of prokaryotes, mitochondria, and chloroplasts (b6/f). In the ancient purple photosynthetic bacteria, the b/c1 complex occupies a central metabolic role, being part of their photosynthetic and respiratory electron transport chain. In Rhodobacter the three subunits of the b/c1 complex are FeS protein, cytochrome b, and cytochrome c1, and they are encoded by a constitutively expressed operon named fbc. The organization of the genes for the cytochrome b/c1 complex, the modality of transcription, and the biogenesis of the encoded polypeptides will be described. The Rhodobacter species used to isolate the fbc genes, previously reported as R. sphaeroides was identified as R. capsulatus. Further biochemical characterization of the prokaryotic b/c1 complex indicated that the three polypeptides encoded by the fbc operon comprise the entire catalytic structure: ubiquinol-cytochrome-c reductase. The amino acid sequences of the three b/c1 subunits from the photosynthetic bacterium Rhodobacter capsulatus were compared with the corresponding sequences from yeast mitochondria and spinach chloroplasts. The high homology found between the sequences of all three redox polypeptides from R. capsulatus and yeast mitochondria (cytochrome b 41%, FeS protein 46%, cytochrome c1 31%) provided further evidence that mitochondria arose from the phylogenetic line of purple bacteria. The structure of cytochrome b also exhibited considerable homology to chloroplast cytochrome b6 plus subunit IV (26%). The amino acid sequence of the Rieske FeS protein from R. capsulatus and chloroplasts were found to be conserved only in the C-terminal part (14% total identity), whereas the homology between cytochrome c1 and cytochrome f is very weak (12%), despite similar topology of the two polypeptides. Analysis of the homology suggested that the catalytic sites quinol oxidase (Q0) and quinone reductase (Qi) arose monophonetically, whereas cytochrome c and plastocyanin reductase sites are not homologous and could derive from diverse ancestral genes by convergent evolution.

Oxidation-reduction potentials and absorption spectra of two b-type cytochromes from the halophilic archaebacterium, Halobacterium halobium

The oxidation-reduction midpoint potentials were determined for two b-type cytochromes, which had been solubilized from the membrane of Halobacterium halobium and partially purified. The two b-type cytochromes have oxidation-reduction midpoint potentials of 175 and 7 mV, respectively. These b-type cytochromes could also be resolved by difference absorption spectroscopy, which revealed one b-type cytochrome with absorption maximum (alpha-peak) at 558 nm, reducible by ascorbate-tetramethyl-p-phenylenediamine, and the other with absorption maximum (alpha-peak) at 560 nm, reducible by dithionite. Different substrates such as succinate, NADH, and alpha-glycerophosphate were used to study the b-type cytochromes in situ when bound to the membrane in a functional state. Reducing equivalents from succinate and alpha-glycerophosphate appear to enter the respiratory chain at the 175 mV b-type cytochrome. Cytochrome a3 is spectrophotometrically shown to be present in the membrane of H. halobium.