Regulation of autotrophic and heterotrophic carbon dioxide fixation in Hydrogenomonas facilis

Analyzing the causes of method-to-method variability among Rubisco kinetic traits: from the first to the current measurements

Due to the importance of Rubisco in the biosphere, its kinetic parameters have been measured by different methodologies in a large number of studies over the last 60 years. These parameters are essential to characterize the natural diversity in the catalytic properties of the enzyme and they are also required for photosynthesis and cross-scale crop modeling. The present compilation of Rubisco kinetic parameters in model species revealed a wide intraspecific laboratory-to-laboratory variability, which was partially solved by making corrections to account for differences in the assay buffer composition and in the acidity constant of dissolved CO2, as well as for differences in the CO2 and O2 solubilities. Part of the intraspecific variability was also related to the different analytical methodologies used. For instance, significant differences were found between the two main methods for the determination of the specificity factor (Sc/o), and also between Rubisco quantification methods, Rubisco purification versus crude extracts, and single-point versus CO2 curve measurements for the carboxylation turnover rate (kcatc) determination. Causes of the intraspecific laboratory-to-laboratory variability for Rubisco catalytic traits are discussed. This study provides a normalized kinetic dataset for model species to be used by the scientific community. Corrections and recommendations are also provided to reduce measurement variability, allowing the comparison of kinetic data obtained in different laboratories using different assay conditions.

Metabolic response of Pseudomonas putida to increased NADH regeneration rates

Pseudomonas putida efficiently utilizes many different carbon sources without the formation of byproducts even under conditions of stress. This implies a high degree of flexibility to cope with conditions that require a significantly altered distribution of carbon to either biomass or energy in the form of NADH. In the literature, co-feeding of the reduced C1 compound formate to Escherichia coli heterologously expressing the NAD⁺-dependent formate dehydrogenase of the yeast Candida boidinii was demonstrated to boost various NADH-demanding applications. Pseudomonas putida as emerging biotechnological workhorse is inherently equipped with an NAD⁺-dependent formate dehydrogenase encouraging us to investigate the use of formate and its effect on P. putida's metabolism. Hence, this study provides a detailed insight into the co-utilization of formate and glucose by P. putida. Our results show that the addition of formate leads to a high increase in the NADH regeneration rate resulting in a very high biomass yield on glucose. Metabolic flux analysis revealed a significant flux rerouting from catabolism to anabolism. These metabolic insights argue further for P. putida as a host for redox cofactor demanding bioprocesses.

CO(2) Fixation, Glutamate Labeling, and the Krebs Cycle in Ribose-grown Hydrogenomonas facilis

Exposure of ribose-grown Hydrogenomonas facilis to (14)CO(2) for 6 to 12 sec during ribose oxidation resulted in labeling of a number of compounds, three of which were glutamate, phosphoglycerate, and pyruvate. Phosphoglycerate and pyruvate were labeled almost exclusively in C(1), suggesting operation of the reductive pentose phosphate cycle. Glutamate was labeled initially to the extent of 90% in C(1) and 10% in C(5), and this was followed by a concentration of radioisotope in C(5). All of the enzymes of the tricarboxylic acid cycle were detectable in ribose-grown cells, and, in general, specific activities were similar to those found in yeast extract-grown cells. Reduced nicotinamide adenine dinucleotide oxidase, aconitase, and the dehydrogenases for pyruvate, alpha-ketoglutarate, and succinate appeared to be of particulate origin. In addition to enzymes of the tricarboxylic acid cycle, an acetyl coenzyme A-stimulated phosphoenolpyruvate carboxylase was found, as was isocitrate lyase. Possible participation of these catalysts in glutamate synthesis is discussed.

Choice between autotrophy and heterotrophy in Pseudomonas oxalaticus. Growth in mixed substrates

1. The type of metabolism adopted by Pseudomonas oxalaticus during growth on a variety of carbon sources was studied. 2. The only substrate upon which autotrophic growth was observed is formate. 3. In mixtures of formate and those substrates upon which the organism can grow faster than on formate, e.g. succinate, lactate or citrate, heterotrophic metabolism results. 4. In mixtures of formate and those substrates upon which the organism can grow at a similar rate to that on formate, e.g. glycollate or glyoxylate, the predominant mode of metabolism adopted is heterotrophic utilization of the C(2) substrate coupled with oxidation of formate as ancillary energy source. 5. P. oxalaticus grows on oxalate 30% slower than on formate. In mixtures of formate and oxalate, the predominant mode of metabolism adopted is autotrophic utilization of formate coupled with oxidation of oxalate as ancillary energy source. 6. In mixtures of formate and those substrates upon which the organism grows at a much lower rate than on formate, e.g. glycerol and malonate, the predominant mode of metabolism adopted is autotrophic utilization of formate. 7. It is concluded that synthesis of the enzymes involved in autotrophic metabolism is controlled by a combination of induction and metabolite repression.

Presence of duplicate genes encoding a phylogenetically new subgroup of form I ribulose 1,5-bisphosphate carboxylase/oxygenase in Mycobacterium sp. strain JC1 DSM 3803

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. Two sets of the structural genes for form I RubisCO were identified in Mycobacterium sp. strain JC1. The genes were clustered on the chromosome in the transcriptional order of cbbL-cbbS. Cloned cbbL-1 and cbbS-1 and cbbL-2 and cbbS-2 have open reading frames of 1431, 426, 1428, and 426 nucleotides, respectively. Primer extension analysis revealed that transcriptional start sites of cbbLS-1 and -2 genes were the nucleotides T and G located 99 and 41bp upstream of the cbbL start codons, respectively. CbbLS-1 and CbbLS-2 that were expressed in Escherichia coli exhibited RubisCO activity. A phylogeny of CbbL amino acid sequences revealed that the two enzymes in Mycobacterium sp. strain JC1 may form a new phylogenetic subgroup, type IE, in the 'red-like' group of the form I RubisCO family.

Growth of mycobacteria on carbon monoxide and methanol

Several mycobacterial strains, such as Mycobacterium flavescens, Mycobacterium gastri, Mycobacterium neoaurum, Mycobacterium parafortuitum, Mycobacterium peregrinum, Mycobacterium phlei, Mycobacterium smegmatis, Mycobacterium tuberculosis, and Mycobacterium vaccae, were found to grow on carbon monoxide (CO) as the sole source of carbon and energy. These bacteria, except for M. tuberculosis, also utilized methanol as the sole carbon and energy source. A CO dehydrogenase (CO-DH) assay, staining by activity of CO-DH, and Western blot analysis using an antibody raised against CO-DH of Mycobacterium sp. strain JC1 (formerly Acinetobacter sp. strain JC1 [J. W. Cho, H. S. Yim, and Y. M. Kim, Kor. J. Microbiol. 23:1-8, 1985]) revealed that CO-DH is present in extracts of the bacteria prepared from cells grown on CO. Ribulose bisphosphate carboxylase/oxygenase (RubisCO) activity was also detected in extracts prepared from all cells, except M. tuberculosis, grown on CO. The mycobacteria grown on methanol, except for M. gastri, which showed hexulose phosphate synthase activity, did not exhibit activities of classic methanol dehydrogenase, hydroxypyruvate reductase, or hexulose phosphate synthase but exhibited N,N-dimethyl-4-nitrosoaniline-dependent methanol dehydrogenase and RuBisCO activities. Cells grown on methanol were also found to have dihydroxyacetone synthase. Double immunodiffusion revealed that the antigenic sites of CO-DHs, RuBisCOs, and dihydroxyacetone synthases in all mycobacteria tested are identical with those of the Mycobacterium sp. strain JC1 enzymes.

Dihydroxyacetone synthase from a methanol-utilizing carboxydobacterium, Acinetobacter sp. strain JC1 DSM 3803

Acinetobacter sp. strain JC1 DSM 3803, a carboxydobacterium, grown on methanol was found to show dihydroxyacetone synthase, dihydroxyacetone kinase, and ribulose 1,5-bisphosphate carboxylase, but no hydroxypyruvate reductase and very low hexulose 6-phosphate synthase, activities. The dihydroxyacetone synthase was found to be expressed earlier than the ribulose 1,5-bisphosphate carboxylase. The dihydroxyacetone synthase was purified 19-fold in eight steps to homogeneity, with a yield of 9%. The final specific activity of the purified enzyme was 1.12 micromol of NADH oxidized per min per mg of protein. The molecular weight of the native enzyme was determined to be 140,000. Sodium dodecyl sulfate-gel electrophoresis revealed a subunit of molecular weight 73,000. The optimum temperature and pH were 30 degrees C and 7.0, respectively. The enzyme was inactivated very rapidly at 70 degrees C. The enzyme required Mg2+ and thiamine pyrophosphate for maximal activity. Xylulose 5-phosphate was found to be the best substrate when formaldehyde was used as a glycoaldehyde acceptor. Erythrose 4-phosphate, glycolaldehyde, and formaldehyde were found to act as excellent substrates when xylulose 5-phosphate was used as a glycoaldehyde donor. The Kms for formaldehyde and xylulose 5-phosphate were 1.86 mM and 33.3 microM, respectively. The enzyme produced dihydroxyacetone from formaldehyde and xylulose 5-phosphate. The enzyme was found to be expressed only in cells grown on methanol and shared no immunological properties with the yeast dihydroxyacetone synthase.

Characterisation and purification of ribulose-bisphosphate carboxylase from heterotrophically grown halophilic archaebacterium, Haloferax mediterranei

The CO2-fixing enzyme of Calvin cycle ribulose-1,5-bisphosphate-carboxylase/oxygenase has been isolated from a halophilic bacterium, Haloferax mediterranei grown heterotrophically. A homogeneous preparation was obtained from sonicated extract of the cells by three steps, resulting in a specific activity of 52 nmol.min-1.mg protein-1. The physicochemical and catalytic properties of the enzyme were studied. The halobacterial ribulose-bisphosphate carboxylase is an oligomer of 54-kDa and 14-kDa subunits as detected by SDS/PAGE. By sucrose-density-gradient centrifugation, the molecular mass of the enzyme was estimated as approximately 500 kDa indicating a hexadecameric nature. No evidence for an additional form of the enzyme devoid of small subunits was obtained. The enzyme required Mg2+ for activity, KCl for activity and stability, and an optimal pH of 7.8. In contrast to many halophilic proteins, ribulose-bisphosphate carboxylase from H. mediterranei is not an acidic protein. From the comparison of amino acid composition of halobacterial enzyme with its counterparts from a few eukaryotic and eubacterial sources, the S delta Q values showed that these proteins share some compositional similarities.

Ribulose 1,5-bisphosphate dependent CO2 fixation in the halophilic archaebacterium, Halobacterium mediterranei

The cell extract of Halobacterium mediterranei catalyses incorporation of 14CO2 into 3-phosphoglycerate in the presence of ribulose bisphosphate suggesting the existence of ribulose bisphosphate carboxylase activity in this halophilic archaebacterium.

Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms

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Evidence for the presence of phosphoriboisomerase and ribulose-1,5-diphosphate carboxylase in extracts of Desulfovibrio vulgaris

Cell extracts of Desulfovibrio vulgaris were found to incorporate 14CO2 into acid-stable products when ribose-5-phosphate or ribulose-1,5-diphosphate was used as a substrate. This CO2 fixation required adenosine triphosphate and produced 3-phosphoglyceric acid as one of the products. The assimilation of CO2 by pentose phosphates was unrelated to the pyruvate-CO2 exchange reaction. The pyruvate-CO2 exchange did not require adenosine triphosphate, did not produce phosphorylated compounds, and, unlike the pentose phosphate system, required an acidic protein fraction for activity.

Hydrogenase and ribulose diphosphate carboxylase during autotrophic, heterotrophic, and mixotrophic growth of scotochromogenic mycobacteria

Two key autotrophic enzyme systems, hydrogenase and ribulose diphosphate carboxylase, were examined in Mycobacterium gordonae and two other chemolithotrophic, scotochromogenic mycobacteria under different cultural conditions. In all three organisms both enzymes were inducible and were produced in significant levels only in the presence of the specific substrate, hydrogen or carbon dioxide. M. gordonae exhibited increased growth rates and yields, indicating mixotrophic growth, in the presence of a number of single organic substrates, including acetate, pyruvate, glucose, fructose, and glycerol. In contrast to other aerobic hydrogen autotrophs, the presence of either acetate or pyruvate did not repress ribulose diphosphate carboxylase, and mixotrophic growth was rapid with these substrates. In the absence of carbon dioxide, growth in glycerol medium under an atmosphere of hydrogen and oxygen was severely inhibited, even with cells preadapted to heterotrophic growth on glycerol. Cyclic adenosine monophosphate was not effective in inducing hydrogenase or carboxylase in heterotrophic, mixotrophic, or hydrogen-inhibited cultures.

Purification and regulatory properties of phosphoribulokinase from Hydrogenomonas eutropha H 16

1. Phosphoribulokinase was purified 286-fold from extracts of autotrophically grown cells. 2. The enzyme had a molecular weight of 237000 and showed a pH optimum of 9.0 in both crude extracts and purified preparation. MgCl(2) was required for activity; full activation was obtained at 5mm-MgCl(2) and the K(m) was approx. 0.5mm. 3. The ATP-saturation curve was sigmoidal and the degree of positive co-operativity increased at higher MgCl(2) concentrations. The ATP-binding sites appeared to be non-interacting at low ribulose 5-phosphate concentrations. 4. Lineweaver-Burk plots for ribulose 5-phosphate showed abrupt transitions between apparently linear sections. The apparent K(m) and V(max.) values increased with increasing concentrations of ribulose phosphate. The transitions may be explained by a sequence of negative and positive co-operativity in the catalytic rate constants. 5. Phosphoribulokinase activity was inhibited by AMP and phosphoenolpyruvate and was activated by NADH. The presence of AMP or phosphoenolpyruvate increased s(0.5) (substrate concentration required for half-maximal velocity) for both ribulose 5-phosphate and ATP but V(max.) was not changed. The sigmoidicity of the ATP-saturation curve increased in the presence of AMP but was not affected by phosphoenolpyruvate. The transitions in the ribulose 5-phosphate-saturation curves were more abrupt in the presence of either inhibitor. NADH lowered the s(0.5) for both ribulose 5-phosphate and ATP. The activator did not affect the degree of positive co-operativity between ATP-binding sites, but the ribulose 5-phosphate-binding sites appeared to be non-interacting in its presence. 6. A sequence of positive and negative co-operativity in the interactions of AMP-binding sites was suggested by the Hill plots. In the presence of NADH (and phosphoenolpyruvate) the sensitivity to inhibition by AMP was less below a certain AMP concentration and increased above that concentration. 7. Examination of the interactions between ligands indicated that phosphoribulokinase can be regulated effectively by changes in effector concentrations similar to those reported to occur in vivo.

Utilization of glucose and the effect of organic compounds on the chemolithotroph Thiobacillus ferrooxidans

The utilization of glucose by the chemolithotroph Thiobacillus ferrooxidans results in a repression of the ability to oxidize iron, the substrate for autotrophic growth. An assay with resting cells was used to measure iron oxidation rates. Concomitant with the decreased iron oxidation rates, the enzyme responsible for carbon dioxide fixation, ribulose diphosphate (RuDP) carboxylase, was also repressed. Maximum iron oxidation rates precede peak RuDP carboxylase levels, consistent with the role of these processes in autotrophic metabolism in nonrepressed cells. The degree of iron oxidation repression depends on the organic substrate supplied, as does the level of RuDP carboxylase. The uptake of glucose parallels an increase in synthesis of glucose-6-phosphate dehydrogenase and the accumulation in cells of poly-beta-hydroxybutyrate. The organism is also capable of growing on glucose and other organic supplements in the absence of its inorganic energy source; growth rates depend on the organic substrate supplied.

Autotrophic and heterotrophic metabolism of hydrogenomonas: regulation of autotrophic growth by organic substrates

The effects of a number of organic substrates on the autotrophic metabolism of Hydrogenomonas eutropha were examined. Dual substrate (mixotrophic) cultivation in the presence of hydrogen plus either fructose or alanine allowed autotrophic growth to begin immediately after the exhaustion of the organic substrate. On the other hand, the presence of acetate, pyruvate, or glutamate caused a lengthy lag to occur before autotrophic growth commenced. With acetate or pyruvate this lag (plateau) in the dicyclic growth curve was due to the repression of ribulose diphosphate carboxylase (RDPC) synthesis during mixotrophic growth. During heterotrophic growth with glutamate, RDPC was partially repressed; however, during mixotrophic growth, RDPC activity was high. Thus the delay of autotrophic growth was not due to a repression of RDPC by glutamate. The data suggest that glutamate interferes with autotrophic metabolism by repressing the incorporation of inorganic nitrogen. The repression of these vital autotrophic functions by acetate, pyruvate, and glutamate occurred both in the presence and absence of hydrogen, i.e., during both heterotrophic and mixotrophic cultivation. The derepression of the affected systems during the plateau phase of the dicyclic growth curves was demonstrated. Carbon dioxide assimilation by whole cells agreed well with the RDPC activity of extracts from cells grown under similar conditions.

Mixotrophic growth of Hydrogenomonas eutropha

Mixotrophic growth conditions were established by the addition of lactate to cultures of Hydrogenomonas eutropha growing autotrophically in a gaseous environment of H(2), O(2), and CO(2) (6:2:1). The specific growth rate of mixotrophic cultures was double that of the autotrophic cultures, and lactate disappearance paralleled growth. Growth yields in mixotrophic cultures were significantly greater than those in heterotrophic cultures for equal quantities of lactate consumed. The magnitude of the increase in yield was directly proportional to the absolute growth rate at the time of lactate addition to the starting autotrophic culture and to the time under mixotrophic conditions. The specific activities of hydrogenase and ribulose diphosphate carboxylase decreased during mixotrophic growth; the total activities increased somewhat. The results suggested that the complete autotrophic and heterotrophic physiologies functioned simultaneously under mixotrophic contions.

Factors affecting the synthesis and degradation of ribulose-1,5-diphosphate carboxylase in Hydrogenomonas facilis and Hydrogenomonas eutropha

Hydrogenomonas facilis and H. eutropha cultured in fructose medium retained high levels of ribulose-1,5-diphosphate carboxylase only when the following conditions were fulfilled: low aeration, FeCl(3) addition to fructose medium, and cell harvest at or prior to mid-exponential phase of growth. Repression of carboxylase synthesis was demonstrated under conditions of high oxygen tension during growth of H. eutropha on fructose. Upon depletion of fructose in the growth medium, carboxylase activity fell abruptly in both organisms. The decline could not be attributed to a repressive mechanism. Rapid inactivation of carboxylase was promoted by transfer of mid-exponential-phase H. eutropha to a basal salts medium lacking fructose. During severe fructose starvation, N(2), H(2), 80% H(2) to 20% air, 2,4-dinitrophenol, actinomycin D, streptomycin, bicarbonate, and magnesium ion deficiency spared carboxylase. Nitrogen starvation or chloramphenicol afforded no protection during severe starvation. In vitro inactivation was also demonstrated in crude cell-free extracts from nonstarved, fructose-grown H. eutropha. Substrate bicarbonate protected against this loss. Inactivation of the carboxylase could not be demonstrated either by starvation of autotrophically grown cells or in autotrophic extracts. Autotrophic extracts mixed with heterotrophic extracts lost their carboxylase activity, but mixing with heterotrophic extracts that had been heated to 50 C resulted in no loss of activity. Mechanisms are proposed to accommodate these observations.