Anaerobic respiration in the Rhodospirillaceae: characterisation of pathways and evaluation of roles in redox balancing during photosynthesis

Abstract Recent discoveries relating to pathways of anaerobic electron transport in the Rhodospirillaceae are reviewed. The main emphasis is on the organism Rhodobacter capsulatus ** but comparisons are made with Rhodobacter sphaeroides ** f. sp. denitrificans and Rhodopseudomonas palustris . The known electron acceptors for anaerobic respiration in Rhodobacter capsulatus are trimethylamine- N -oxide (TMAO), dimethyl sulphoxide (DMSO), nitrate and nitrous oxide. In each case respiration generates a proton electrochemical gradient and in some cases can support growth on non-fermentable carbon sources. However, the principal objective of this review is to discuss the possibility that, apart from a role in energy conservation, anaerobic respiration in the photosynthetic bacteria may have a special function in maintaining redox balance during photosynthetic metabolism. Thus the electron acceptors mentioned above may serve as auxiliary oxidants: (a) to maintain an optimal redox poise of the photosynthetic electron transport chain; (b) to provide a sink for electrons during phototrophic growth on highly reduced carbon substrates.
Molecular properties of the nitrate reductase, nitrous oxide reductase and a single enzyme responsible for reduction of TMAO and DMSO are discussed. These enzymes are all located in the periplasm. Electrons destined for all three enzymes can originate from the rotenone-sensitive NADH dehydrogenase but do not proceed through the antimycin- and myxothiazol-sensitive cytochrome b/c₁ complex. It is likely, therefor, that the pathways of anaerobic respiration overlap with the cyclic photosynthetic electron transport chain only at the level of the ubiquinone pool. Redox components which might be involved in the terminal branches of anaerobic respiration are discussed.     

Analysis of the fnrL gene and its function in Rhodobacter capsulatus.

The fnr gene encodes a regulatory protein involved in the response to oxygen in a variety of bacterial genera. For example, it was previously shown that the anoxygenic, photosynthetic bacterium Rhodobacter sphaeroides requires the fnrL gene for growth under anaerobic, photosynthetic conditions. Additionally, the FnrL protein in R. sphaeroides is required for anaerobic growth in the dark with an alternative electron acceptor, but it is not essential for aerobic growth. In this study, the fnrL locus from Rhodobacter capsulatus was cloned and sequenced. Surprisingly, an R. capsulatus strain with the fnrL gene deleted grows like the wild type under either photosynthetic or aerobic conditions but does not grow anaerobically with alternative electron acceptors such as dimethyl sulfoxide (DMSO) or trimethylamine oxide. It is demonstrated that the c-type cytochrome induced upon anaerobic growth on DMSO is not synthesized in the R. capsulatus fnrL mutant. In contrast to wild-type strains, R. sphaeroides and R. capsulatus fnrL mutants do not synthesize the anaerobically, DMSO-induced reductase. Mechanisms that explain the basis for FnrL function in both organisms are discussed.     

Halotolerance of the Phototrophic Bacterium Rhodobacter capsulatus E1F1 Is Dependent on the Nitrogen Source

Phototrophic growth of the moderate halotolerant Rhodobacter capsulatus strain E1F1 in media containing up to 0.3 M NaCl was dependent on the nitrogen source used. In these media, increased growth rates and growth levels were observed in the presence of reduced nitrogen sources such as ammonium and amino acids. When the medium contained an oxidized nitrogen source (dinitrogen or nitrate), increases in salinity severely inhibited phototrophic growth. However, the addition of glycine betaine promoted halotolerance and allowed the cells to grow in 0.2 M NaCl. Inhibition of diazotrophic growth by salinity was due to a decrease in nitrogenase activity which was no longer synthesized and reversibly inactivated, both effects being alleviated by the addition of glycine betaine. In R. capsulatus E1F1, inhibition of cell growth in nitrate by salt was due to a rapid inhibition of nitrate uptake, which led to a long-term decrease in nitrate reductase activity, probably caused by repression of the enzyme. Addition of glycine betaine immediately restored nitrate uptake, but the recovery of nitrate reductase activity required several hours. Neither ammonium uptake nor ammonium assimilation through the glutamine synthetase-glutamate synthase pathway was affected by NaCl.     

Dissimilatory nitrate and dimethylsulphoxide reduction in Rhodopseudomonas capsulata

Abstract The electron flow to the dissimilatory nitrate reductase (NRII), and dimethylsulphoxide (DMSO) oxidoreductase in Rhodopseudomonas capsulata strains was studied. Our results support the view that DMSO reduction, like dissimilatory nitrate reduction was linked to the electron transfer chain and probably coupled to energy conservation.     

Nitrogen limited growth of a methanotrophic culture

Based on present knowledge to growth of Methanococcus capsulatus a model for the nitrogen limited growth in a chemostat with ammonia as nitrogen source is proposed. The model may predict excretion of nitrate and nitrite with excess of ammonia in broth.     

Dimethyl sulfoxide reductase activity by anaerobically grown Escherichia coli HB101.

Escherichia coli grew anaerobically on a minimal medium with glycerol as the carbon and energy source and dimethyl sulfoxide (DMSO) as the terminal electron acceptor. DMSO reductase activity, measured with an artificial electron donor (reduced benzyl viologen), was preferentially associated with the membrane fraction (77 +/- 10% total cellular activity). A Km for DMSO reduction of 170 +/- 60 microM was determined for the membrane-bound activity. Methyl viologen, reduced flavin mononucleotide, and reduced flavin adenine dinucleotide also served as electron donors for DMSO reduction. Methionine sulfoxide, a DMSO analog, could substitute for DMSO in both the growth medium and in the benzyl viologen assay. DMSO reductase activity was present in cells grown anaerobically on DMSO but was repressed by the presence of nitrate or by aerobic growth. Anaerobic growth on DMSO coinduced nitrate, fumarate, and and trimethylamine-N-oxide reductase activities. The requirement of a molybdenum cofactor for DMSO reduction was suggested by the inhibition of growth and a 60% reduction in DMSO reductase activity in the presence of 10 mM sodium tungstate. Furthermore, chlorate-resistant mutants chlA, chlB, chlE, and chlG were unable to grow anaerobically on DMSO. DMSO reduction appears to be under the control of the fnr gene.     

Conservation and variation between Rhodobacter capsulatus and Escherichia coli Tat systems

The Tat system allows the translocation of folded and often cofactor-containing proteins across biological membranes. Here, we show by an interspecies transfer of a complete Tat translocon that Tat systems are largely, but not fully, interchangeable even between different classes of proteobacteria. The Tat apparatus from the alpha-proteobacterium Rhodobacter capsulatus was transferred to a Tat-deficient Escherichia coli strain, which is a gamma-proteobacterium. Similar to that of E. coli, the R. capsulatus Tat system consists of three components, rc-TatA, rc-TatB, and rc-TatC. A fourth gene (rc-tatF) is present in the rc-tatABCF operon which has no apparent relevance for translocation. The translational starts of rc-tatC and rc-tatF overlap in four nucleotides (ATGA) with the preceding tat genes, pointing to efficient translational coupling of rc-tatB, rc-tatC, and rc-tatF. We show by a variety of physiological and biochemical assays that the R. capsulatus Tat system functionally targets the E. coli Tat substrates TorA, AmiA, AmiC, and formate dehydrogenase. Even a Tat substrate from a third organism is accepted, demonstrating that usually Tat systems and Tat substrates from different proteobacteria are compatible with each other. Only one exceptional Tat substrate of E. coli, a membrane-anchored dimethyl sulfoxide (DMSO) reductase, was not targeted by the R. capsulatus Tat system, resulting in a DMSO respiration deficiency. Although the general features of Tat substrates and translocons are similar between species, the data indicate that details in the targeting pathways can vary considerably.     

Competition between hydrogen peroxide and nitrate for electrons from the respiratory chains of Thiosphaera pantotropha and Rhodobacter capsulatus

Abstract Thiosphaera pantotropha and some strains of Rhodobacter capsulatus express both a periplasmic nitrate reductase and cytochrome c peroxidase when grown under aerobic conditions. Harvested cell suspensions of either species can respire nitrate in the presence of 200 μM O₂ (∼ 80% air saturation), at 70–80% of the anaerobic rate. Addition of hydrogen peroxide to such cells causes a 90% inhibition of nitrate reduction under anaerobic or aerobic conditions. The duration of the inhibition is proportional to the concentration of hydrogen peroxide added and can be ascribed to the expression of periplasmic peroxidases that compete with the nitrate reductase for electrons from the respiratory chain. The results reveal a hitherto unrecognised interaction between reactions of denitrification and the reduction of hydrogen peroxide by a periplasmic peroxidase that may have implications for the denitrification in microaerobic environments. The creation of aerobic conditions in bacterial cultures by addition of hydrogen peroxide, and relying on the generation of oxygen by endogenous catalase activity, is a commonly used technique for studying respiratory processes. The observations presented here demonstrate that results derived from such experiments should be interpreted with caution.     

Derivatives of Rhodobacter capsulatus strain AD2 cured of their endogenous plasmid are unable to utilize nitrate

Abstract Derivatives of Rhodobacter capsulatus AD2 unable to grow with nitrate as sole N source were isolated after conjugation with a plasmid containing a cloned 3.4 kb Hin dIII fragment from the endogenous plasmid of this strain. These derivatives lacked the M _r 74 × 10⁶ plasmid found in the wild-type, and failed to revert to growth on nitrate. Cultures of the plasmid-cured strains also lacked dissimilatory nitrate reductase activity, suggesting that genes required for both assimilatory and dissimilatory nitrate reduction are located on the endogenous plasmid.     

Subdivision of Salmonella enteritidis PT 4 by pulsed-field gel electrophoresis: Potential for epidemiological surveillance

Abstract The capacity to reduce nitrate (NIT⁺ character) of wild-type and mutant strains of the purple nonsulfur bacterium Rhodobacter capsulatus was analysed by the methods of plasmid genetics and by DNA-DNA hybridization techniques. By conjugative introduction of the endogenous 115-kb plasmid of strain AD2 into a plasmid-free NIT⁻ mutant of the same strain the missing assimilatory nitrate reductase activity was restored. By analogous experimental techniques, the capacity to reduce nitrate was also temporarily established in the Rb. capsulatus NIT⁻ wild-type strain B10. DNA-DNA hybridization experiments with the narGHIJ operon of Escherichia coli and napA of Alcaligenes eutrophus yielded positive signals with an 11-kb Eco RI fragment of the AD2 plasmid.     

Isolation and characterization of <Emphasis Type="Italic">Sulfurospirillum carboxydovorans</Emphasis> sp. nov., a new microaerophilic carbon monoxide oxidizing epsilon Proteobacterium

A new microaerophilic, Gram-negative, motile, 2–3 m long and 0.3 m wide, vibrioid to spirillum-shaped, CO oxidizing bacterium, designated strain MV, isolated from marine sediment (The North Sea) is described. Strain MV was able to couple the oxidation of CO to the reduction of elemental sulphur, DMSO and thiosulphate. Growth occurred with up to 100% (v/v) CO in the headspace. Acetate was needed as carbon source. No growth on CO was observed with nitrate and selenate as electron acceptor. Sulphite, elemental sulphur, DMSO, thiosulphate, nitrate, nitrite, perchloroethylene, arsenate and selenate were used as electron acceptors with pyruvate as energy and carbon source. Microaerophilic growth was observed. In non-agitated cultures growth occurred at atmospheric oxygen concentrations in the headspace. Hydrogen (with acetate as carbon source), formate (with acetate as carbon source), pyruvate, lactate, succinate, fumarate, malate -ketoglutaric acid, aspartate and yeast extract (1% (w/v)) supported growth with nitrate as electron acceptor. Fumarate and malate were fermented. Vitamins were not required for growth. The strain was cytochrome C oxidase and catalase positive. The DNA mol G+C content was 30.5%. 16S rRNA gene sequence comparison showed that strain MV grouped within the genus Sulfurospirillum with Sulfurospirillum arcachonense (sequence similarity 98.3%) as closest relative. The relative DNA–DNA relatedness between strain MV and S. arcachonense was 33.1%. Based on a detailed phenotypic and phylogenetic analysis, inclusion of strain MV in the genus Sulfurospirillum as a well separated new species is proposed. As species name we propose Sulfurospirillum carboxydovorans. The type strain is strain MV (ATCC BAA-937 = DSM 16295, GenBank accession number: AY740528).     

Dimethylsulfoxide reduction by marine sulfate-reducing bacteria

Abstract Dimethylsulfoxide (DMSO) reduction occurred in five out of nine strains of sulfate-reducing bacteria from marine or saline environments, but not in three freshwater isolates. DMSO reduction supported growth in all positive strains. In Desulfovibrio desulfuricans strain PA2805, DMSO reduction occurred simultaneously with sulfate reduction and was not effectively inhibited by molybdate, a specific inhibitor of sulfate reduction. The growth yield per mol lactate was 26% higher with DMSO than with sulfate as electron acceptor. In extracts of cells of strain PA2805 grown on sulfate, a low level of DMSO-reducing activity was present (0.013 μmol (mg protein)⁻ min⁻); higher levels were found in cells grown on DMSO (0.56 μmol (mg protein)⁻ min⁻). In anoxic marine environments DMSO reduction by sulfate-reducing bacteria may lead to enhanced dimethylsulfide emission rates.     

Bacterial nitrate assimilation: gene distribution and regulation

In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism.     

Hydroxylamine assimilation by Rhodobacter capsulatus E1F1. requirement of the hcp gene (hybrid cluster protein) located in the nitrate assimilation nas gene region for hydroxylamine reduction

Rhodobacter capsulatus E1F1 grows phototrophically with nitrate as nitrogen source. Using primers designed for conserved motifs in bacterial assimilatory nitrate reductases, a 450-bp DNA was amplified by PCR and used for the screening of a genomic library. A cosmid carrying an insert with four SalI fragments of 2.8, 4.1, 4.5, and 5.8 kb was isolated, and DNA sequencing revealed that it contains a nitrate assimilation (nas) gene region, including the hcp gene coding for a hybrid cluster protein (HCP). Expression of hcp is probably regulated by a nitrite-sensitive repressor encoded by the adjacent nsrR gene. A His(6)-HCP was overproduced in Escherichia coli and purified. HCP contained about 6 iron and 4 labile sulfide atoms per molecule, in agreement with the presence of both [2Fe-2S] and [4Fe-2S-2O] clusters, and showed hydroxylamine reductase activity, forming ammonia in vitro with methyl viologen as reductant. The apparent K(m) values for NH(2)OH and methyl viologen were 1 mM and 7 microM, respectively, at the pH and temperature optima (9.3 and 40 degrees C). The activity was oxygen-sensitive and was inhibited by sulfide and iron reagents. R. capsulatus E1F1 grew phototrophically, but not heterotrophically, with 1 mM NH(2)OH as nitrogen source, and up to 10 mM NH(2)OH was taken up by anaerobic resting cells. Ammonium was transiently accumulated in the media, and its assimilation was prevented by L-methionine-D,L-sulfoximine, a glutamine synthetase inhibitor. In addition, hydroxylamine- or nitrite-grown cells showed the higher hydroxylamine reductase activities. However, R. capsulatus B10S, a strain lacking the whole hcp-nas region, did not grow with 1 mM NH(2)OH. Also, E. coli cells overproducing HCP tolerate hydroxyl-amine better during anaerobic growth. These results suggest that HCP is involved in assimilation of NH(2)OH, a toxic product that could be formed during nitrate assimilation, probably in the nitrite reduction step.     

Increase in respiratory cost at high growth temperature is attributed to high protein turnover cost in Petunia x hybrida petals

It is widely believed that turnover of nitrogenous (N) compounds (especially proteins) incurs a high respiratory cost. Thus, if protein turnover costs change with temperature, this would influence the dependence of respiration rate on growth temperature. Here, we examined the extent to which protein turnover cost explained differences in N-utilization costs (nitrate uptake/reduction, ammonium assimilation, amino acid and protein syntheses, protein turnover and amino acid export) and in respiration rate with changes in growth temperature. By measurements and literature data, we evaluated each N-utilization cost in Petunia x hybrida petals grown at 20, 25 or 35 degrees C throughout their whole lifespans. Protein turnover cost accounted for 73% of the integrated N-utilization cost on a whole-petal basis at 35 degrees C. The difference in this cost on a dry weight basis between 25 and 35 degrees C accounted for 75% of the difference in N-utilization cost and 45% of the difference in respiratory cost. The cost of nitrate uptake/reduction was high at low growth temperatures. We concluded that respiratory cost in petals was strongly influenced by protein turnover and nitrate uptake/reduction, and on the shoot basis, C investment in biomass was highest at 25 degrees C.     

Aerobic and anaerobic nitrate and nitrite reduction in free-living cells of Bradyrhizobium sp. (Lupinus)

Induction, energy gain, effect on growth, and interaction of nitrate and nitrite reduction of Bradyrhizobium sp. (Lupinus) USDA 3045 were characterized. Both nitrate and nitrite were reduced in air, although nitrite reduction was insensitive to ammonium inhibition. Anaerobic reduction of both ions was shown to be linked with energy conservation. A dissimilatory ammonification process was detected, which has not been reported in rhizobia so far. Nevertheless, anaerobic conversion of nitrate to ammonium was lower than 40%, which suggests the presence of an additional, nitrite reductase of denitrifying type. Nitrite toxicity caused a non-linear relationship between biomass produced and >2 mM concentrations of each N oxyanion consumed. At > or =5 mM initial concentrations of nitrate, a stoichiometric nitrite accumulation occurred and nitrite remained in the medium. This suggests an inhibition of nitrite reductase activity by nitrate, presumably due to competition with nitrate reductase for electron donors. Lowering of growth temperature almost completely diminished nitrite accumulation and enabled consumption as high as 10 mM nitrate, which confirms such a conclusion.     

A denitrifying strain of Rhodobacter capsulatus

Abstract Repeated subculturing of Rhodobacter capsulatus strain BK5 under phototrophic conditions on a medium containing butyrate and nitrate led to the appearance of cultures that, unlike the original, produced gas. Isolation of a pure culture of the gas-forming organism revealed that it was a derivative of R. capsulatus BK5 that by virtue of expressing a nitrite reductase can catalyse the complete sequence of the denitrification reactions. The nitrite reductase is of the type that contains copper rather than haem.     

Photocatabolism of acetone by nonsulfur purple bacteria

Abstract Tests for the capacity of nonsulfur purple bacteria to photocatabolize acetone revealed that certain strains of Rhodobacter (Rb.) capsulatus and Rhodomicribium (Rm.) vannielii could grow on this organic compound. Phototrophic growth of R. capsulatus strain B10 on acetone was CO₂ dependent. Dark anaerobic or dark aerobic growth of R. capsulatus on acetone was not observed, although microaerobic growth in the dark did occur. Of a total of 13 species of nonsulfur purple bacteria examined, only strains of Rb. capsulatus and Rm. vannielii were found capable of photoheterotrophic growth on acetone.     

Characterization of the assimilatory and dissimilatory nitrate-reducing systems in Rhodobacter: a comparative study

Abstract: Assimilatory nitrate reductase from Rhodobacter capsulatus E1F1 was found to be a cytosolic NADH-dependent enzyme whereas nitrite reductase was detected both in the periplasm and in the cytosol. In addition to nitrate and nitrite, organic nitro compounds were also able to induce nitrate reductase which was repressed in carbon-starved cells or under conditions producing low intracellular nitrate levels. By contrast, nitrate reductase from Rhodobacter sphaeroides DSM 158 was located in the periplasm, did not use NADH as electron donor in vitro and was induced independently from the carbon/nitrogen balance of the cells. Production of nitrogenous gases was never detected in either strain cultured anaerobically with nitrate or nitrite.