Photosynthesis in Rhodospirillum rubrum. II. Photoheterotrophic carbon dioxide fixation

Carbon roadmap from syngas to polyhydroxyalkanoates in Rhodospirillum rubrum

The gasification of organic waste materials to synthesis gas (syngas), followed by microbial fermentation, provides a significant resource for generating bioproducts such as polyhydroxyalkanoates (PHA). The anaerobic photosynthetic bacterium, Rhodospirillum rubrum, is an organism particularly attractive for the bioconversion of syngas into PHAs. In this study, a quantitative physiological analysis of R. rubrum was carried out by implementing GC-MS and HPLC techniques to unravel the metabolic pathway operating during syngas fermentation that leads to PHA production. Further, detailed investigations of the central carbon metabolites using (13) C-labelled substrate showed significant CO2 assimilation (of 40%) into cell material and PHA from syngas carbon fraction. By a combination of quantitative gene expression and enzyme activity analyses, the main role of carboxylases from the central carbon metabolism in CO2 assimilation was shown, where the Calvin-Benson-Bassham cycle (CBB) played a minor role. This knowledge sheds light about the biochemical pathways that contribute to synthesis of PHA during syngas fermentation being valuable information to further optimize the fermentation process.

Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

Background

Purple nonsulfur bacteria (PNSB) are facultative photosynthetic bacteria and exhibit an extremely versatile metabolism. A central focus of research on PNSB dealt with the elucidation of mechanisms by which they manage to balance cellular redox under diverse conditions, in particular under photoheterotrophic growth.

Results

Given the complexity of the central metabolism of PNSB, metabolic modeling becomes crucial for an integrated analysis of the accumulated biological knowledge. We reconstructed a stoichiometric model capturing the central metabolism of three important representatives of PNSB (Rhodospirillum rubrum, Rhodobacter sphaeroides and Rhodopseudomonas palustris). Using flux variability analysis, the model reveals key metabolic constraints related to redox homeostasis in these bacteria. With the help of the model we can (i) give quantitative explanations for non-intuitive, partially species-specific phenomena of photoheterotrophic growth of PNSB, (ii) reproduce various quantitative experimental data, and (iii) formulate several new hypotheses. For example, model analysis of photoheterotrophic growth reveals that - despite a large number of utilizable catabolic pathways - substrate-specific biomass and CO₂ yields are fixed constraints, irrespective of the assumption of optimal growth. Furthermore, our model explains quantitatively why a CO₂ fixing pathway such as the Calvin cycle is required by PNSB for many substrates (even if CO₂ is released). We also analyze the role of other pathways potentially involved in redox metabolism and how they affect quantitatively the required capacity of the Calvin cycle. Our model also enables us to discriminate between different acetate assimilation pathways that were proposed recently for R. sphaeroides and R. rubrum, both lacking the isocitrate lyase. Finally, we demonstrate the value of the metabolic model also for potential biotechnological applications: we examine the theoretical capabilities of PNSB for photoheterotrophic hydrogen production and identify suitable genetic interventions to increase the hydrogen yield.

Conclusions

Taken together, the metabolic model (i) explains various redox-related phenomena of the versatile metabolism of PNSB, (ii) delivers new hypotheses on the operation and relevance of several metabolic pathways, and (iii) holds significant potential as a tool for rational metabolic engineering of PNSB in biotechnological applications.

L-malyl-coenzyme A/beta-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus

Cell extracts of Rhodobacter capsulatus grown on acetate contained an apparent malate synthase activity but lacked isocitrate lyase activity. Therefore, R. capsulatus cannot use the glyoxylate cycle for acetate assimilation, and a different pathway must exist. It is shown that the apparent malate synthase activity is due to the combination of a malyl-coenzyme A (CoA) lyase and a malyl-CoA-hydrolyzing enzyme. Malyl-CoA lyase activity was 20-fold up-regulated in acetate-grown cells versus glucose-grown cells. Malyl-CoA lyase was purified 250-fold with a recovery of 6%. The enzyme catalyzed not only the reversible condensation of glyoxylate and acetyl-CoA to L-malyl-CoA but also the reversible condensation of glyoxylate and propionyl-CoA to beta-methylmalyl-CoA. Enzyme activity was stimulated by divalent ions with preference for Mn(2+) and was inhibited by EDTA. The N-terminal amino acid sequence was determined, and a corresponding gene coding for a 34.2-kDa protein was identified and designated mcl1. The native molecular mass of the purified protein was 195 +/- 20 kDa, indicating a homohexameric composition. A homologous mcl1 gene was found in the genomes of the isocitrate lyase-negative bacteria Rhodobacter sphaeroides and Rhodospirillum rubrum in similar genomic environments. For Streptomyces coelicolor and Methylobacterium extorquens, mcl1 homologs are located within gene clusters implicated in acetate metabolism. We therefore propose that L-malyl-CoA/beta-methylmalyl-CoA lyase encoded by mcl1 is involved in acetate assimilation by R. capsulatus and possibly other glyoxylate cycle-negative bacteria.

Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms

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Structural gene regions of Rhodobacter sphaeroides involved in CO2 fixation

From studies conducted in both our laboratory and by Gibson, Tabita and colleagues, as well as drawing on the recent studies with Alcaligenes eutrophus, we describe two genetic regions which have been identified on the chromosome of Rhodobacter sphaeroides which code for a number of enzymes involved in CO2 fixation. One region was found to contain the genes coding for fructose 1,6-bisphosphatase (fbpA), phosphoribulokinase (prkA), a 37 kDa polypeptide (cfxA), and form I ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL, S). These genes appear to be expressed in the same transcriptional direction and are tandomly arranged. A second, apparently unlinked region of the chromosome contains a duplicate (with respect to functionality of gene products) but not identical set of these same four genes. Although the gene order in both regions is apparently identical, there is approximately 4 kb of DNA separating the 3'-end of prkB and the beginning of cfxB. The specific genetic organizations and proposed roles of these two genetic regions are discussed.

Glycollate production and excretion by Alcaligenes eutrophus

Autotrophic cultures of the facultative chemolithotroph Alcaligenes eutrophus have been found to excrete glycollate. This excretion was greatly stimulated by the incorporation of up to 20% (v/v) oxygen in the hydrogen used for gassing. The stimulatory effect of oxygen was prevented by the addition of 10% (v/v) CO2 to the gassing mixture. Glycollate excretion only in the presence of oxygen was increased by the addition of 2-pyridyl-hydroxymethane sulphonic acid (HPMS), an inhibitor of glycollate oxidation, indicating that glycollate formation itself was stimulated by oxygen. No glycollate excretion by cultures grown heterotrophically on pyruvate was detected, either in the absence or presence of HPMS, under heterotrophic or autotrophic cells showed phosphoglycollate phosphatase and glycollate oxidoreductase activities, which were considerably lower in extracts prepared from pyruvate- or fructose-grown (heterotrophic) cells. The increase in activity of both enzymes upon cell transfer from heterotrophic to autotrophic growth was prevented by chloramphenicol and resembled the induction of D-ribulose 1,5-diphosphate carboxylase under the same conditions.

Enzymes of glycollate formation and oxidation in two members of the rhodospirillacae (purple non-sulphur bacteria)

1. Phototrophic cultures of Rhodomicrobium vanielii do not excrete glycollate when gassed anaerobically with nitrogen plus carbon dioxide, although the addition of alpha-hydroxy-2-pyridine methanesulphonate (HPMS) results in the excretion of a trace amount of glycollate. The inclucion of low amounts of oxygen in this gas mixture results in marked glycollate excretion, higher rates occurring in the presence of HPMS. 2. Cell extracts of Rhodomicrobium vannielii, and also of Rhodospirillum rubrum, which excretes glycollate only under aerobic conditions in the light, catalyze the formation of glycollate from phosphoglycollate and also the oxidation of glycollate to glyoxylate.

Influence of Light Intensity on Reductive Pentose Phosphate Cycle Activity during Photoheterotrophic Growth of Rhodospirillum rubrum

Light intensity during growth affects the proportion of carbon dioxide fixed by the reductive pentose phosphate cycle relative to that incorporated via C(4) acids in acetate phototrophs of Rhodospirillum rubrum. With cells grown at high light intensity (9000 lux) the specific activities of ribulose-1, 5-diphosphate and propionyl CoA carboxylases were increased compared with cells grown at low light intensity (1500 lux), although pyruvate carboxylase activity was unaltered.Kinetic experiments with cells assimilating acetate at high light intensity showed that when the cells had been grown at high light intensity there was a rapid incorporation of (14)CO(2) into phosphate esters compared with cells grown at low light intensity and fixing (14)CO(2) while assimilating acetate at low light intensity. The percentage of the total radioactivity present in phosphate esters plotted against time gave a negative slope for high light conditions compared with a positive slope for low light conditions. High light-grown cells assimilating acetate at high light intensity showed the greatest combined rate of (14)CO(2) fixation via the reductive pentose phosphate cycle and C(4) acids, and this corresponded to the shortest mean generation time. When cells were grown at high light intensity and allowed to assimilate (14)CO(2) at high light intensity but in the stationary phase, the pattern of (14)CO(2) fixation resembled that for low light-grown cells assimilating acetate and fixing (14)CO(2) at low light intensity, showing that both acetate assimilation and high light intensity were necessary for the rapid incorporation of (14)CO(2) via the reductive pentose phosphate cycle.

Identification of propionate as an endogenous CO2 acceptor in Rhodospirillum rubrum and properties of purified propionyl-coenzyme A carboxylase

A heat-stable endogenous CO(2) acceptor has been found in extracts of Rhodospirillum rubrum grown photoheterotrophically on acetate. Evidence is presented which suggests that this factor is propionic acid. Thus, paper and gas chromatographic analyses have indicated that propionic acid is present in boiled extracts prepared from R. rubrum cells. The products of (14)CO(2) fixation obtained with either the boiled extract or propionic acid as the CO(2) acceptor were identical and were identified as methylmalonic acid and succinic acid by paper chromatography. The enzyme which catalyzes the carboxylation of propionyl-coenzyme A (propionyl-CoA carboxylase) was purified from R. rubrum cells grown on acetate and its properties were studied. The enzyme is similar to propionyl-CoA carboxylases isolated from mammalian sources.

Photosynthesis in Rhodospirillum rubrum. 3. Metabolic control of reductive pentose phosphate and tricarboxylic acid cycle enzymes

Enzymes of the reductive pentose phosphate cycle including ribulose-diphosphate carboxylase, ribulose-5-phosphate kinase, ribose-5-phosphate isomerase, aldolase, glyceraldehyde-3-phosphate dehydrogenase and alkaline fructose-1,6-diphos-phatase were shown to be present in autotrophically grown Rhodospirillum rubrum. Enzyme levels were measured in this organism grown photo- and dark heterotrophically as well. Several, but not all, of these enzymes appeared to be under metabolic control, mediated by exogenous carbon and nitrogen compounds. Light had no effect on the presence or levels of any of these enzymes in this photosynthetic bacterium. The enzymes of the tricarboxylic acid cycle and enolase were shown to be present in R. rubrum cultured aerobically, autotrophically, or photoheterotrophically, both in cultures evolving hydrogen and under conditions where hydrogen evolution is not observed. Light had no clearly demonstrable effect on the presence or levels of any of these enzymes.