Redox chain and energy transduction in chromatophores from Rhodopseudomonas capsulata cells grown anaerobically in the dark on glucose and dimethyl sulfoxide

Hydrogenases and H(+)-reduction in primary energy conservation

Hydrogenases are metalloenzymes subdivided into two classes that contain iron-sulfur clusters and catalyze the reversible oxidation of hydrogen gas (H(2)[Symbol: see text]left arrow over right arrow[Symbol: see text]2H(+)[Symbol: see text]+[Symbol: see text]2e(-)). Two metal atoms are present at their active center: either a Ni and an Fe atom in the [NiFe]hydrogenases, or two Fe atoms in the [FeFe]hydrogenases. They are phylogenetically distinct classes of proteins. The catalytic core of [NiFe]hydrogenases is a heterodimeric protein associated with additional subunits in many of these enzymes. The catalytic core of [FeFe]hydrogenases is a domain of about 350 residues that accommodates the active site (H cluster). Many [FeFe]hydrogenases are monomeric but possess additional domains that contain redox centers, mostly Fe-S clusters. A third class of hydrogenase, characterized by a specific iron-containing cofactor and by the absence of Fe-S cluster, is found in some methanogenic archaea; this Hmd hydrogenase has catalytic properties different from those of [NiFe]- and [FeFe]hydrogenases. The [NiFe]hydrogenases can be subdivided into four subgroups: (1) the H(2) uptake [NiFe]hydrogenases (group 1); (2) the cyanobacterial uptake hydrogenases and the cytoplasmic H(2) sensors (group 2); (3) the bidirectional cytoplasmic hydrogenases able to bind soluble cofactors (group 3); and (4) the membrane-associated, energy-converting, H(2) evolving hydrogenases (group 4). Unlike the [NiFe]hydrogenases, the [FeFe]hydrogenases form a homogeneous group and are primarily involved in H(2) evolution. This review recapitulates the classification of hydrogenases based on phylogenetic analysis and the correlation with hydrogenase function of the different phylogenetic groupings, discusses the possible role of the [FeFe]hydrogenases in the genesis of the eukaryotic cell, and emphasizes the structural and functional relationships of hydrogenase subunits with those of complex I of the respiratory electron transport chain.

The behavioural response of anaerobic Rhodobacter sphaeroides to temporal stimuli

The behavioural response of Rhodobacter sphaeroides to temporal changes in the concentration of chemoeffectors, and to stimuli affecting electron transport, was analysed using tethered cells. Populations of photosynthetically grown tethered cells of R. sphaeroides showed a transient response, a stop followed by adaptation, to a stepwise reduction in the concentration of chemoattractants (such as organic acids or sugars) and terminal electron acceptors. A step-down response was also measured in free swimming cells to a reduction in light intensity. As this response appears to apply to all effectors this suggests that there is a sensory pathway in anaerobically grown R. sphaeroides which responds primarily to a reduction in a stimulus. R. sphaeroides therefore responds when moving down a concentration gradient. This is the inverse of the classical Escherichia coli-Salmonella typhimurium model of bacterial sensory behaviour in which bacteria respond primarily when there is an increase in an attractant concentration, i.e. when moving up a gradient. R. sphaeroides does show a chemokinetic response to an increase in concentration of a limited number of compounds but this response is sustained and accompanied by an increase in the rate of flagellar rotation and therefore not simply equivalent to the transient increase in smooth swimming measured in E. coli on addition of an attractant.

Electron transport-dependent taxis in Rhodobacter sphaeroides

Rhodobacter sphaeroides showed chemotaxis to the terminal electron acceptors oxygen and dimethyl sulfoxide, and the responses to these effectors were shown to be influenced by the relative activities of the different electron transport pathways. R. sphaeroides cells tethered by their flagella showed a step-down response to a decrease in the oxygen or dimethyl sulfoxide concentration when using them as terminal acceptors. Bacteria using photosynthetic electron transport, however, showed a step-down response to oxygen addition. Addition of the proton ionophore carbonyl cyanide 4-trifluoromethoxyphenylhydrazone did not cause a transient behavioral response, although it decreased the electrochemical proton gradient (delta p) and increased the rate of electron transport. However, removal of the ionophore, which caused an increase in delta p and a decrease in the electron transport rate, resulted in a step-down response. Together, these data suggest that behavioral responses of R. sphaeroides to electron transport effectors are caused by changes in the rate of electron transport rather than changes in delta p.

ChrR positively regulates transcription of the Rhodobacter sphaeroides cytochrome c2 gene

Transcription of the Rhodobacter sphaeroides cytochrome c2 gene (cycA) is negatively regulated by both the presence of oxygen and intermediates in tetrapyrrole biosynthesis. A mutation responsible for uncoupling cycA transcription from tetrapyrrole availability was localized to a gene (chrR) that encodes a 357-amino-acid protein. Analysis of a defined chrR null mutation indicated that this protein positively regulated cycA transcription. From this and other results, it appeared that the positive action of ChrR on cycA transcription is blocked by altering the availability of either heme or some intermediate in tetrapyrrole biosynthesis. A single missense mutation which substitutes an Arg for a Cys at residue 182 of ChrR (C182R) was shown to be necessary and sufficient for the increased cycA transcription seen in the mutant strain Chr4. Thus, it appears that this C182R substitution generated an altered-function form of ChrR. In addition, by analyzing cycA transcription in delta ChrR strains, we showed that ChrR was not required for increased cycA transcription under anaerobic conditions. Instead, our results indicated that ChrR and the response regulator PrrA (J. M. Eraso and S. Kaplan, J. Bacteriol. 176:32-43, 1994) functioned independently at the upstream cycA promoter that is activated under anaerobic conditions.

Membrane-associated cytochrome cy of Rhodobacter capsulatus is an electron carrier from the cytochrome bc1 complex to the cytochrome c oxidase during respiration

We have recently established that the facultative phototrophic bacterium Rhodobacter capsulatus has two different pathways for reduction of the photooxidized reaction center during photosynthesis (F.E. Jenney and F. Daldal, EMBO J. 12:1283-1292, 1993; F.E. Jenney, R.C. Prince, and F. Daldal, Biochemistry 33:2496-2502, 1994). One pathway is via the well-characterized, water-soluble cytochrome c2 (cyt c2), and the other is via a novel membrane-associated c-type cytochrome named cyt cy. In this work, we probed the role of cyt cy in respiratory electron transport by isolating a set of R. capsulatus mutants lacking either cyt c2 or cyt cy, in the presence or in the absence of a functional quinol oxidase-dependent alternate respiratory pathway. The growth and inhibitor sensitivity patterns of these mutants, their respiratory rates in the presence of specific inhibitors, and the oxidation-reduction kinetics of c-type cytochromes monitored under appropriate conditions demonstrated that cyt cy, like cyt c2, connects the bc1 complex and the cyt c oxidase during respiratory electron transport. Whether cyt c2 and cyt cy are the only electron carriers between these two energy-transducing membrane complexes of R. capsulatus is unknown.

delta-Aminolevulinate couples cycA transcription to changes in heme availability in Rhodobacter sphaeroides

In this paper, the response of the transcriptional control region of the Rhodobacter sphaeroides cytochrome c2 gene, cycA, to intermediates in heme biosynthesis was studied. To determine if cycA transcription was regulated by heme availability, several precursors or analogs of tetrapyrroles were tested. Addition of delta-aminolevulinate (ALA), the first committed intermediate in heme biosynthesis, was shown to inhibit cycA transcription initiation at both the upstream and downstream promoter regions. In addition, an ALA auxotroph, which can grow in the presence of high levels of ALA, showed a 5 to 7-fold reduction in steady-state transcription from cycA::lacZYA operon fusions. To identify genetic elements responsible for negative regulation by ALA, trans-acting mutants with increased expression of cycA were isolated that were resistant to growth inhibition by the heme analog cohemin. These cohemin-resistant mutants (Chr) have elevated levels of several cycA transcripts and they contain cycA transcripts that had not previously been detected in wild-type cells. In addition, cycA transcription in the Chr mutants continues after the addition of ALA. Finally, we found that Chr mutants have increased ALA synthase activity, suggesting that synthesis of cytochrome c2 and ALA synthase are controlled by a common gene product whose activity has been modified in these mutants. A model is presented to explain how changes in tetrapyrrole intermediates could provide an effective signal to control both cycA transcription and ALA synthase synthesis in R. sphaeroides.

petR, located upstream of the fbcFBC operon encoding the cytochrome bc1 complex, is homologous to bacterial response regulators and necessary for photosynthetic and respiratory growth of Rhodobacter capsulatus

Interposon mutagenesis of a region upstream of the petABC(fbcFBC) operon, encoding the ubiquinol: cytochrome c2 oxidoreductase (bc1 complex) of the photosynthetic bacterium Rhodobacter capsulatus revealed the presence of two genes, petP and petR. DNA nucleotide sequence determination of this region indicated that petP and petR are transcribed in the same direction as the petABC(fbcFBC) operon, and are translationally coupled. A silent insertion located in the interoperonal region separating petPR and the petABC(fbcFBC) genes indicated that these clusters have separate promoters. The deduced amino acid sequence of the putative petR gene product is homologous to various bacterial response regulators, especially to those of the OmpR subgroup. Moreover, it was found that PetR mutants are unable to grow on rich or minimal media by either photosynthesis or respiration, demonstrating that these gene products are essential for growth of R. capsulatus.

Functional characterization of the lesion in the ubiquinol: cytochrome c oxidoreductase complex isolated from the nonphotosynthetic strain R126 of Rhodobacter capsulatus

The cytochrome bc1 complexes from the nonphotosynthetic strain R126 of Rhodobacter capsulatus and from its revertant MR126 were purified. Between both preparations, no difference could be observed in the stoichiometries of the cytochromes, in their spectral properties, and in their midpoint redox potentials. Both also showed identical polypeptide patterns after electrophoresis on polyacrylamide gels in the presence of sodium dodecylsulfate. The ubiquinol: cytochrome c oxidoreductase activity was strongly inhibited in the complex from the mutant compared to the one from the revertant. So was the oxidant-induced extra reduction of cytochrome b. Both preparations, however, showed an antimycin-induced red shift of cytochrome b, as well as antimycin-sensitive reduction of cytochrome b by ubiquinol. In accordance with a preceding study of chromatophores (Robertson et al. (1986). J. Biol. Chem. 261, 584-591), it is concluded that the mutation affects specifically the ubiquinol oxidizing site, leaving the ubiquinol reducing site unchanged.

Measurement of the redox state of the ubiquinone pool in Rhodobacter capsulatus membrane fragments

The dependence of the respiratory rate on the redox poise of the quinone pool was investigated in wild type and mutant membranes of Rhodobacter capsulatus. A linear relationship has been found between these two parameters only when succinate was oxidized by the bc1 complex. Conversely, a marked nonlinear relationship was observed between the Q-pool reduction level and the respiratory rate when O2 uptake occurred via the alternative oxidase. In addition, it was found that this latter pathway was not engaged until Q-pool reduction level reached approximately 25%. These results are discussed within the framework of a homogeneous pool regulating both photosynthetic and respiratory fluxes.

Isolation of a Rhodobacter capsulatus mutant that lacks c-type cytochromes and excretes porphyrins

A Rhodobacter capsulatus mutant lacking cytochrome oxidase activity was isolated by Tn5 mutagenesis. Difference spectroscopy of crude extracts and extracted c-type cytochromes demonstrated that this mutant completely lacked all c-type cytochromes. The strain did, however, synthesize normal amounts of b-type cytochromes and nonheme iron. This mutant also excreted large amounts of coproporphyrin and protoporphyrin and synthesized reduced amounts of bacteriochlorophyll, suggesting a link between the synthesis of c-type cytochromes and the expression of the tetrapyrrole biosynthetic pathway.

Prediction and comparison of the haem-binding sites in membrane haemoproteins

This article contains a comparative review of the structural properties of membrane haemoproteins, with particular emphasis on the possible similarities of the haem-binding peptides. A procedure is suggested for identifying the peptides which may bind membrane-buried haems on the basis of the primary sequences of the proteins. The integration of this procedure with the information deduced by refined hydropathy analysis indicates that the basic structural model for the haemoproteins which interact with quinones may be a transmembrane helical bundle containing the haem(s) at its centre. Structural similarities exist in the sequence of hydrophobic segments that are predicted to bind the membrane-buried haems of b-cytochromes which interact with quinones. The predicted haem-binding sites show similarities also with the peptides that bind the non-haem iron in the bacterial reaction centres, and this may be correlated to the common function of interacting with quinones and their intermediates. The analysis of the amino-acid composition of the proposed ligand peptides in the membrane haemoproteins examined has provided a molecular rationale for explaining the highly anisotropic low-spin EPR signal which is characteristic of many membrane-bound b-cytochromes.

Expression of the Rhodobacter sphaeroides cytochrome c2 structural gene

A Rhodobacter sphaeroides mutant (CYCA1) lacking cytochrome c2 (cyt c2) was previously constructed (T. J. Donohue, A. G. McEwan, S. Van Doren, A. R. Crofts, and S. Kaplan, Biochemistry, 27: 1918-1924, 1988) by a combination of in vivo and in vitro molecular genetic techniques. CYCA1 was incapable of photosynthetic growth (PS-); in this presentation, we show that chemoheterotrophically grown CYCA1 contained significant quantities of a high potential soluble c-type cytochrome(s) with an alpha band of approximately 554 nm which had previously gone undetected under these physiological conditions in wild-type cells. In addition, the PS- phenotype of CYCA1 can be complemented in trans with stable low-copy-number (approximately 5 to 9 per R. sphaeroides genome) broad-host-range plasmids containing the wild-type cyt c2 structural gene (cycA) and upstream regulatory sequences. cyt c2 and cycA-specific mRNA levels were elevated in both the wild type and CYCA1 derivatives harboring intact cycA genes in trans, presumably as a result of increased gene dosage. Although photosynthetically grown wild-type cells contained approximately twofold more cycA-specific transcripts than chemoheterotrophically grown cells, there was an approximately four- to sevenfold increase in cyt c2 levels under photosynthetic conditions. Similarly, complemented CYCA1 strains contained between 1.3- and 2.3-fold more cycA mRNA under photosynthetic conditions than under chemoheterotrophic conditions and had 6- to 12-fold higher steady-state levels of cyt c2 under the same physiological conditions. These data are discussed in terms of possible posttranscriptional control over cyt c2.

Cytochrome c2-independent respiratory growth of Rhodobacter capsulatus

To assess the role of cytochrome c2 as a respiratory electron carrier, we obtained a double mutant of Rhodobacter capsulatus defective in cytochrome c2 and in the quinol oxidase260. This mutant was able to grow chemoheterotrophically, indicating that an electron pathway independent of cytochrome c2 was functional between the ubiquinol:cytochrome c2 oxidoreductase and the cytochrome oxidase410.

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.

Isolation of the structural genes for the Rieske Fe-S protein, cytochrome b and cytochrome c1 all components of the ubiquinol: cytochrome c2 oxidoreductase complex of Rhodopseudomonas capsulata

The structural genes for the Rieske Fe-S protein (petA), cytochrome b (petB) and cytochrome c1 (petC) subunits of the ubiquinol:cytochrome c2 oxidoreductase (bc1 complex) of Rhodopseudomonas capsulata have been cloned by complementation, using a mutant defective in this complex. The location of these genes on the obtained plasmid, pR14A, was determined using synthetic mixed oligonucleotide probes corresponding to highly conserved amino acid sequences of these proteins from various organisms. Their correct identity was established by partial sequencing. The petA, petB and petC genes were found to lie close to each other in this order, spanning two adjacent EcoRI fragments of 2.7 X 10(3) and 1.3 X 10(3) base-pairs, respectively. An insertion-deletion mutation, covering most of petB and all of petC and an insertion mutation, located in petB were constructed in vitro and were introduced into the chromosome of an otherwise wild-type strain by gene transfer agent-mediated genetic crosses. The bc-1 mutants obtained were defective in photosynthesis but, as expected, they could grow by respiration because of a branched respiratory pathway. Therefore, in R. capsulata a functional bc1 complex is essential in vivo for photosynthesis but not for respiration. Further, in the respiratory pathway the branch point must be before the bc1 complex, most likely at the quinone pool. These mutants were also proficient in anaerobic growth in the presence of dimethylsulfoxide, indicating that a functional bc1 complex is not required for this pathway. Several other insertions and deletions, located outside of the pet gene cluster, were also constructed. The ability of these latter mutants to grow photosynthetically suggested that no other gene essential for photosynthesis is located in the proximity of the pet cluster. The plasmid pR14A was shown to complement in trans the bc-1 insertion or insertion-deletion mutants, indicating that the pet genes were expressed in R. capsulata. Cross-hybridization experiments showed that the pet cluster was quite distinct from other known genes involved in photosynthesis.

Isolation and characterization of an aminolevulinate-requiring Rhodobacter capsulatus mutant

Using transposon Tn5 mutagenesis, we isolated a mutant strain of Rhodobacter capsulatus that requires aminolevulinate for growth. Southern blot analysis indicated that this strain has a single Tn5 insertion. The addition of 0.1 mM aminolevulinate to the medium allowed the mutant to grow either aerobically or photosynthetically with generation times similar to those of the parental strain. When grown photosynthetically, bacteriochlorophyll accumulation increased with increasing aminolevulinate concentration. The mutant strain had only 10% of the normal aminolevulinate synthase activity, but it had a normal level of porphobilinogen synthase activity. The requirement for aminolevulinate could be satisfied by porphobilinogen, hemin, or protoporphyrin. While the mutant grew well on agar plates containing any of these substrates, growth in liquid media containing hemin or protoporphyrin was poor. Introduction of an R' factor containing all the known R. capsulatus bch genes into the mutant strain did not relieve the requirement for aminolevulinate, suggesting that the Tn5 insertion is not within the bch region.

Nitrous oxide reduction by members of the family Rhodospirillaceae and the nitrous oxide reductase of Rhodopseudomonas capsulata

After growth in the absence of nitrogenous oxides under anaerobic phototrophic conditions, several strains of Rhodopseudomonas capsulata were shown to possess a nitrous oxide reductase activity. The enzyme responsible for this activity had a periplasmic location and resembled a nitrous oxide reductase purified from Pseudomonas perfectomarinus. Electron flow to nitrous oxide reductase was coupled to generation of a membrane potential and inhibited by rotenone but not antimycin. It is suggested that electron flow to nitrous oxide reductase branches at the level of ubiquinone from the previously characterized electron transfer components of R. capsulata. This pathway of electron transport could include cytochrome c', a component hitherto without a recognized function. R. capsulata grew under dark anaerobic conditions in the presence of malate as carbon source and nitrous oxide as electron acceptor. This confirms that nitrous oxide respiration is linked to ATP synthesis. Phototrophically and anaerobically grown cultures of nondenitrifying strains of Rhodopseudomonas sphaeroides, Rhodopseudomonas palustris, and Rhodospirillum rubrum also possessed nitrous oxide reductase activity.

Genetic-physical mapping of a photosynthetic gene cluster from R. capsulata

Transposon mutagenesis and complementation analysis of the photosynthesis genes in Rhodopseudomonas capsulata is presented utilizing Tn5.7 mutagenized R-primes. The R-prime pRPS404 contains many of the genes necessary for the differentiation of the photosynthetic apparatus. Utilizing homologous recombination, 30 independent copies of Tn5.7 were inserted into the R. capsulata chromosome with subsequent deletion of wild-type alleles. Mutants were characterized by absorption spectroscopy, SDS-PAGE, and determination of capability for photosynthetic growth. Many mutations in the bacteriochlorophyll and carotenoid biosynthetic pathways were isolated. A regulatory mutation was isolated affecting reaction-center synthesis as well as a 44 kd heme-containing polypeptide. Complementation analysis using various pRPR404::Tn5.7 plasmids has led to the postulation of transcriptional units.

Electron flow to dimethylsulphoxide or trimethylamine-N-oxide generates a membrane potential in Rhodopseudomonas capsulata

Under dark and essentially anaerobic conditions electron flow to either dimethylsulphoxide or trimethylamine-N-oxide in cells of Rhodopseudomonas capsulata has been shown to generate a membrane potential. This conclusion is based on the observation of a red shift in the carotenoid absorption band which is a well characterised indicator of membrane potential in this bacterium. The magnitude of the dimethylsulphoxide- or trimethylamine-N-oxide-dependent membrane potential was reduced either by a protonophore uncoupler of oxidative phosphorylation or synergistically by a combination of a protonophore plus rotenone, an inhibitor of electron flow from NADH dehydrogenase. These findings, together with the observation that venturicidin, an inhibitor of the proton translocating ATPase, did not reduce the membrane potential, show that electron flow to dimethylsulphoxide or trimethylamine-N-oxide is coupled to proton translocation. Thus contrary to some previous proposals dark and anaerobic growth of Rps. capsulata in the presence of dimethylsulphoxide or trimethylamine-N-oxide cannot be regarded as purely fermentative.

Alignment of genetic and restriction maps of the photosynthesis region of the Rhodopseudomonas capsulata chromosome by a conjugation-mediated marker rescue technique

The restriction map of a 46-kilobase fragment of the Rhodopseudomonas capsulata chromosome was aligned with the genetic map of the photosynthesis region of that chromosome by a marker rescue technique. Marker rescue was effected by mobilization of vectors bearing fragments of R. capsulata DNA from Escherichia coli to a set of R. capsulata mutants. Plasmids pDPT51 and pDPT55 were constructed to mediate the intergeneric mobilization of pBR322 derivatives, and a mutant of R. capsulata with improved intergeneric recipient activity was isolated. Four previously unmapped genes affecting bacteriochlorophyll synthesis and two genes affecting photochemical reaction center synthesis have been located by marker rescue. Some of the fragments of R. capsulata DNA are capable of vector-independent complementation, implying that promoters are located on these fragments. Other fragments complement only in one orientation of insertion in the vector, implying transcription from promotors on the vectors and thereby fixing the direction of transcription for those fragments. Still other fragments of DNA show rescue only via recombination between homologous plasmid-borne DNA fragments and chromosomal mutations. The physical dimensions of the genetic map are 3.0 megadaltons per map unit, which agrees with previous estimates based on the size of the R. capsulata gene transfer agent.