Chloroplast and Cytoplasmic Enzymes: VI. Pea Leaf 3-Phosphoglycerate Kinases

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

Nitrosomonas europaea catalyzes the first step of the nitrification process (ammonia to nitrite). It has been recognized as one of the most important members of microbial communities of wastewater treatment processes. Genome-scale models are powerful tools in process optimization since they can predict the organism’s behavior under different growth conditions. The final genome-scale model of N. europaea ATCC19718, iGC535, can predict growth and oxygen uptake rates with 90.52% accuracy under chemolithotrophic and chemolitoorganotrophic conditions. Moreover, iGC535 can predict the simultaneous oxidation of ammonia and wastewater pollutants, such as benzene, toluene, phenol and, chlorobenzene. iGC535 represents the most comprehensive knowledge-base for a nitrifying organism available to date. The genome-scale model reconstructed in this work brings us closer to understanding N. europaea’s role in a community with other nitrifying bacteria.

Ectopic expression of Pokkali phosphoglycerate kinase-2 (OsPGK2-P) improves yield in tobacco plants under salinity stress

KEY MESSAGE

Our results indicate that OsPGK2a-P gene is differentially regulated in contrasting rice cultivars under stress and its overexpression confers salt stress tolerance in transgenic tobacco. Phosphoglycerate kinase (PGK; EC = 2.7.2.3) plays a major role for ATP production during glycolysis and 1, 3-bisphosphoglycerate production to participate in the Calvin cycle for carbon fixation in plants. Whole genome analysis of rice reveals the presence of four PGK genes (OsPgks) on different chromosomes. Comparative expression analysis of OsPgks in rice revealed highest level of transcripts for OsPgk2 at most of its developmental stages. Detailed characterization of OsPgk2 transcript and protein showed that it is strongly induced by salinity stress in two contrasting genotypes of rice, i.e., cv IR64 (salt sensitive) and landrace Pokkali (salt tolerant). Ectopic expression of OsPgk2a-P (isolated from Pokkali) in transgenic tobacco improved its salinity stress tolerance by higher chlorophyll retention and enhanced proline accumulation, besides maintaining better ion homeostasis. Ectopically expressing OsPgk2a-P transgenic tobacco plants showed tall phenotype with more number of pods than wild-type plants. Therefore, OsPgk2a-P appears to be a potential candidate for increasing salinity stress tolerance and enhanced yield in crop plants.

A non-radioactive method for measuring Rubisco activase activity in the presence of variable ATP: ADP ratios, including modifications for measuring the activity and activation state of Rubisco

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes carboxylation of ribulose-1,5-bisphosphate, the first in a series of reactions leading to the incorporation of atmospheric CO₂ into biomass. Rubisco requires Rubisco activase (RCA), an AAA+ ATPase that reactivates Rubisco by remodelling the conformation of inhibitor-bound sites. RCA is regulated by the ratio of ADP:ATP, with the precise response potentiated by redox regulation of the alpha-isoform. Measuring the effects of ADP on the activation of Rubisco by RCA using the well-established photometric assay is problematic because of the adenine nucleotide requirement of 3-phosphoglycerate (3-PGA) kinase. Described here is a novel assay for measuring RCA activity in the presence of variable ratios of ADP:ATP. The assay couples the formation of 3-PGA from ribulose 1,5-bisphosphate and CO₂ to NADH oxidation through cofactor-dependent phosphoglycerate mutase, enolase, PEP carboxylase and malate dehydrogenase. The assay was used to determine the effects of Rubisco and RCA concentration and ADP:ATP ratio on RCA activity, and to measure the activation of a modified Rubisco by RCA. Variations of the basic assay were used to measure the activation state of Rubisco in leaf extracts and the activity of purified Rubisco. The assay can be automated for high-throughput processing by conducting the reactions in two stages.

Conservation and duplication of isozymes in plants

Many enzymes in plants have isozymes because the same catalytic reaction is often present in several subcellular compartments, most frequently the plastids and the cytosol. The number and subcellular locations of the isozymes appear to be highly conserved in plant evolution. However, gene duplication in diploid species and the addition of genomes in polyploid species have increased the number of isozymes.

Compartmented metabolite pools in protoplasts from the green alga Chlamydomonas reinhardtii: changes after transition from aerobiosis to anaerobiosis in the dark

A rapid fractionation method for determination of metabolite levels in the chloroplast and the extrachloroplast compartment of Chlamydomonas reinhardtii has been developed. Protoplasts containing one large chloroplast were fractionated by passing them through a multilayer gradient containing digitonin, polyacrylamide, and a mixture of silicone oil and bromodecane. Lysis of the plasma membrane and the separation of the chloroplasts from most of the extrachloroplast material was achieved within less than 5 s. The chloroplast enriched fraction was contaminated with 3% fumarase (mitochondria) and 13% phosphoenol pyruvate carboxylase (cytosol). Metabolites of the upper glycolytic chain were detected mainly in the chloroplasts, whereas 2-phosphoglycerate was found only in the extrachloroplast compartment. Analysis of changes in metabolite concentrations after transition to anaerobic conditions in the dark pointed to a regulation of carbohydrate catabolism by chloroplast phosphofructokinase and by cytosolic pyruvatekinase.

Isolation of chloroplastic phosphoglycerate kinase : kinetics of the two-enzyme phosphoglycerate kinase/glyceraldehyde-3-phosphate dehydrogenase couple

We report here a method for the isolation of high specific activity phosphoglycerate kinase (EC 2.7.2.3) from chloroplasts. The enzyme has been purified over 200-fold from pea (Pisum sativum L.) stromal extracts to apparent homogeneity with 23% recovery. Negative cooperativity is observed with the two enzyme phosphoglycerate kinase/glyceraldehyde-3-P dehydrogenase (EC 1.2.1.13) couple restored from the purified enzymes when NADPH is the reducing pyridine nucleotide, consistent with earlier results obtained with crude chloroplastic extracts (J Macioszek, LE Anderson [1987] Biochim Biophys Acta 892: 185-190). Michaelis Menten kinetics are observed when 3-phosphoglycerate is held constant and phosphoglycerate kinase is varied, which suggests that phosphoglycerate kinase-bound 1,3-bisphosphoglycerate may be the preferred substrate for glyceraldehyde-3-P dehydrogenase in the chloroplast.

Separation, purification, and comparative properties of chloroplast and cytoplasmic phosphoglycerate kinase from barley leaves

The chloroplast and cytoplasmic isoenzymes of phosphoglycerate kinase (PGK) (EC. 2.7.2.3) from Hordeum vulgare leaves have been separated and purified for the first time to apparent homogeneity. The method for purifying the isoenzymes is described here and consists of DEAE Sephacel chromatography followed by affinity chromatography on ATP Sepharose. This consistently provided a 500- to 900-fold purification of each isoenzyme. Most of the total PGK in green barley leaves was found to be in the chloroplasts with only 10% in the cytoplasm. The immunological properties of the two isoenzymes were compared. The antisera raised to the separate isoenzymes showed cross-reactivity, although there is evidence that each isoenzyme possesses some distinct epitopes. The isoenzymes differ in overall charge with isoelectric points at 5.2 and 5.4 for the chloroplast and cytoplasmic isoenzymes, respectively. Molecular mass estimations by gel filtration and sodium dodecyl sulfate polyacrylamide gel electrophoresis provided similar values of approximately 38 kilodaltons for each isoenzyme, some 4 to 5 kilodaltons less than the values calculated from the cDNA sequences of the wheat isoenzymes. The isoenzymes have broadly similar pH optima of pH 7 to 8. The cytoplasmic isoenzyme is more thermally stable than the chloroplast isoenzyme. Further studies are now in progress to compare both the regulatory properties of the isoenzymes and also their three-dimensional structures as compared with the yeast enzyme.

Isolation and characterization of the cytosolic and chloroplastic 3-phosphoglycerate kinase from spinach leaves

The cytosol and chloroplast 3-phosphoglycerate kinases (3-PGK) from spinach (Spinacia oleracea L.) were purifled to apparent homogeneity. The procedure included a conventional anion-exchange chromatography on DEAE-cellulose and mainly a series of HPLC columns. The charge differences of the two isoenzymes were so small that separation was only successful by anion-exchange chromatography on a HPLC SynChropak AX 300 column. The portion of the two isoenzmyes in leaf tissue was estimated as 5% and 95%. The major 3-PGK was associated with isolated chloroplasts while the other 3-PGK was only found in the soluble cell fraction. The specific activity of the purified enzymes were in the order of 800 units (per milligram of protein). The molecular weight for the two 3-PGKs under nondenaturing (size exclusion chromatography) and denaturing (SDS-PAGE) conditions were in the order of 40 kilodaltons, with the cytosolic 3-PGK being slightly smaller than the chloroplastic 3-PGK. An antiserum against the chloroplastic 3-PGK showed only 4.6% cross-reaction of the chloroplastic 3-PGK with the cytosolic 3-PGK. The kinetics for glycerate-3-phosphate and MgATP(2-) were biphasic. The presence of Na(2)SO(4) changed the MgATP(2-) dependence to linearity but not the glycerate-3-phosphate dependence.

Coregulation of electron transport and Benson-Calvin cycle activity in isolated spinach chloroplasts: studies on glycerate 3-phosphate reduction

Glycerate 3-phosphate-dependent O2 evolution was measured in intact chloroplasts in the absence of CO2. At all concentrations of added glycerate 3-phosphate oxygen evolution ceased before stoichiometric amounts of oxygen were evolved. The inhibition of glycerate 3-phosphate-dependent-O2 evolution increased with increasing concentrations of substrate added. A similar response was observed in chloroplasts treated with KCN which inhibits ribulose-1,5-bisphosphate carboxylase-oxygenase. Oxygen uptake via the oxygenase activity of this enzyme is therefore not the cause of the discrepancy in stoichiometry of oxygen release in this system. The addition of NaHCO3 to chloroplasts in which oxygen evolution was inhibited by glycerate 3-phosphate caused an immediate sustained rate of oxygen evolution in the absence of KCN but not with KCN present. Simultaneous measurements of chlorophyll a fluorescence showed that qQ remained oxidized, although net O2 evolution had ceased. As O2 evolution decreased, qE and delta pH increased. Upon the addition of the NaHCO3, QA became more oxidized while delta pH and qE were decreased, suggesting that the inhibition of electron transport at high glycerate 3-phosphate concentrations was mediated by photosynthetic control via delta pH. However, the levels of ATP, ADP, ribulose 1,5-bisphosphate, and Pi concentrations and ATP/ADP ratio. The stromal glycerate 3-phosphate content declined upon illumination until O2 evolution ceased. At this time a constant stromal glycerate 3-phosphate concentration of 8-10 mM was maintained while net import of glycerate 3-phosphate into the stroma had virtually ceased. The stromal triosephosphate content remained at a constant low level throughout but the glycerate 3-phosphate level increased slightly after addition of NaHCO3. The data provided by the measurements of thylakoid reactions and stromal metabolites suggest that photosynthetic electron transport is tightly coupled to the requirements of the stroma for ATP and NADPH. Glycerate 3-phosphate reduction requires much less ATP than the operation of the complete Benson-Calvin cycle since the stoichiometry of ATP and NADPH utilization is reduced to 1:1. We conclude that thylakoid electron flow is not sufficiently flexible to maintain NADPH and ATP production in the ratio of 1:1. This situation will favor overenergization of the thylakoid membrane, increased leakiness of protons, increased electron drainage to O2, and result in progressive inhibition of noncyclic electron flow.

Photosynthetic carbon metabolism in isolated pea chloroplasts: metabolite levels and enzyme activities

We report here that enzyme activation precedes the rise in metabolite levels, which appear to limit photosynthetic CO2 fixation during induction in pea leaf chloroplasts. Therefore light activation may be required for the build-up of photosynthetic intermediates and hence for photosynthesis in isolated chloroplasts. Analysis of metabolite levels and the known kinetic properties of the chloroplast enzymes indicates that the reductive pentose phosphate cycle is subject to control which fluctuates between several points during induction and when CO2 fixation is maximal. The transketolase-aldolase-catalyzed reactions around sedoheptulose-biphosphatase appear to provide a simple and effective primary control for photosynthetic CO2 fixation. When substrate levels and enzyme active site concentrations are taken into account, there is insufficient glyceraldehyde 3-phosphate dehydrogenase, aldolase, and transketolase activity to support photosynthetic CO2 fixation at observed rates. These results suggest that there may be direct transfer of glyceraldehyde 3-phosphate among these enzymes in the pea chloroplast.

Enzymes of Glucose Oxidation in Leaf Tissues : The Distribution of the Enzymes of Glycolysis and the Oxidative Pentose Phosphate Pathway between Epidermal and Mesophyll Tissues of C(3)-Plants and Epidermal, Mesophyll, and Bundle Sheath Tissues of C(4)-Plants

The distribution of the glycolytic enzymes, phosphofructokinase, aldolase, triosephosphate isomerase, phosphoglycerate kinase, pyruvate kinase, and the oxidative pentose phosphate pathway enzymes, glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, was determined in the leaf tissues of two C(3)-plants, pea and leek, and two C(4)-plants, maize and sorghum. All enzymes examined were found in epidermal tissue. In pea, maize, and sorghum leaves, the specific activities of these enzymes were usually higher in the nonphotosynthetic epidermal tissue than in the photosynthetic tissues of the leaves. In leek leaves, which were etiolated, specific activities were similar in both epidermal and mesophyll tissue. The distribution of the rate limiting enzymes of glycolysis and the oxidative pentose phosphate pathways probably reflects the capacity of each tissue to generate NADH, NADPH, and ATP from the oxidation of glucose. This capacity appears to be greater in leaf tissues unable to generate reducing equivalents and ATP by photosynthesis, that is, in epidermal tissues and etiolated mesophyll tissue.

Loose association of ribulose 1,5-bisphosphate carboxylase/oxygenase with chloroplast thylakoid membranes

The intra-chloroplastic distribution of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) between thylakoid membranes and stroma was studied by determining the enzyme activities in the two fractions, obtained by the rapid centrifugation of hypotonically disrupted chloroplast preparations of spinach and pea leaf tissues. The membrane-associated form of RuBisCO was found to increase in proportion to the concentration of MgCl2 in the disrupting medium; with 20 mM MgCl2 approximately 20% of the total RuBisCO of spinach chloroplasts and 10% of that of pea chloroplasts became associated with thylakoid membranes. Once released from membranes in the absence of MgCl2, addition of MgCl2 did not cause reassociation of the enzyme. The inclusion of KCl in the hypotonic disruption buffer also caused the association of RuBisCO with membranes; however, up to 30 mM KCl, only minimal enzyme activities could be detected in the membranes, whereas above 40 mM KCl there was a sharp increase in the membrane-associated form of the enzyme.Higher concentrations of chloroplasts during the hypotonic disruption, as well as addition of purified preparations of RuBisCO to the hypotonic buffer, resulted in an increase of membrane-associated activity. Therefore, the association of the enzyme with thylakoid membranes appears to be dependent on the concentration of RuBisCO. P-glycerate kinase and aldolase also associated to the thylakoid membranes but NADP-linked glyceraldehyde-3-P dehydrogenase did not. The optimal conditions for enzyme association with the thylakoid membranes were examined; maximal association occurred at pH 8.0. The association was temperature-insensitive in the range of 4° to 25° C. RuBisCO associated with the thylakoid membranes could be gradually liberated to the soluble form upon shaking in a Vortex mixer at maximal speed, indicating that the association is loose.

Characterization of a Photosynthesizing Reconstituted Spinach Chloroplast Preparation : REGULATION BY PRIMER, ADENYLATES, FERREDOXIN, AND PYRIDINE NUCLEOTIDES

A particulate preparation (MgP) capable of photosynthetic CO(2) assimilation without the addition of stromal protein was obtained by rupturing whole spinach (Spinacia oleracea var. America) chloroplasts in 15 millimolar MgCl(2) buffered with Tricine at pH 8.5. This CO(2) assimilation was dependent upon light, inorganic phosphate, ferredoxin, ADP, NAD or NADP, and primer. Excepting glycolate, the products of CO(2) fixation by MgP were similar to those found with whole chloroplasts.Glycerate-3-phosphate (PGA), fructose-1, 6-bisphosphate (FBP), and ribose-5-phosphate (R5P) but not fructose-6-P (F6P) functioned as primers. Concentrations of PGA and FBP but not of R5P higher than 2 millimolar were inhibitory to CO(2) fixation. A lag of CO(2) fixation was observed with PGA and FBP but not with R5P. This lag as well as inhibition by NADP, ADP, and ATP in the FBP-primed preparation was eliminated by an equimolar mixture of FBP plus F6P indicating FBPase as the sensitive site. NADP, ADP, and ATP also blocked CO(2) fixation by the PGA-fortified preparation but inhibition was even more sensitive than that observed when FBP was added. Inhibition by AMP in the PGA and FBP-primed preparations was not affected by the addition of F6P. When R5P was the starting primer, inhibition of CO(2) fixation was relatively insensitive to the adenylates and NADP. In contrast to the parent whole chloroplast, CO(2) fixation by MgP was insensitive to high (5 millimolar) inorganic phosphate. Depending upon the ferredoxin concentration, NAD was as effective as NADP in supporting CO(2) fixation.

Light Modulation of Glyceraldehyde-3-phosphate Dehydrogenase and Glucose-6-phosphate Dehydrogenase by Photosynthetic Electron Flow in Pea Chloroplasts

Light activation of NADP-linked glyceraldehyde-3-P dehydrogenase (EC 1.2.1.13) and light inactivation of glucose-6-P dehydrogenase (EC 1.1.1.49) appear to be modulated within pea leaf chloroplasts by mediators which are reduced by photosynthetic electron flow from the photosystem I reaction center. Dichlorophenyl-1, 1-dimethylurea inhibition of this modulation can be completely reversed by ascorbate plus 2,6-dichlorophenolindophenol in broken chloroplasts, but not in intact chloroplasts. Intact chloroplasts are impermeable to 2,6-dichlorophenolindophenol at pH 7.5. Studies on the effect of light in reconstituted chloroplasts with photosystem I-enriched particles in the place of whole thylakoids revealed that photosystem I participates in the light modulation of NADP-linked glyceraldehyde-3-P dehydrogenase and of glucose-6-P dehydrogenase.

Protoplasts as a means of studying chloroplast development in vitro

Protoplasts obtained enzymically from etiolated primary leaves of oat were illuminated in vitro, and the process of etioplast chloroplast transformation followed. Chloroplast development proceeded up to 6 hours of incubation in the light (20 C). During this period, complete photosynthetic light and dark reactions were constituted, in addition to prolamellar body-degrading protease activity.In parallel, electron microscopic investigations showed a pronounced decrease in prolamellar body area from 89.5 square micrometers at 0 hours to 40.6 square micrometers at 6 hours, whereas the length of the thylakoid membranes (prothylakoids, thylakoids) increased from 21 micrometers at 0 hour to about 293 micrometers at 6 hours. This was accompanied by the formation of grana (bi- and polythylakoids).A comparison of plastid structure and function, developed within isolated protoplasts and those of organelles greened in intact leaves up to 6 hours, showed that there was only a slight lag in development of plastids illuminated in vitro to those illuminated in vivo. However, times of in vitro illumination longer than 6 hours resulted in signs of deterioration and the lack of further development, except for photosystem I activities.

Modulation of Chloroplast Fructose-1,6-bisphosphatase Activity by Light

Inhibitor experiments indicate that light effect mediator(II) which is reductively activated by transfer of electrons from the photosynthetic electron transport system at or beyond ferredoxin, is involved in activation by light of fructose-1,6-bisphosphatase in the pea plant. Activation proceeds optimally when the pH is low and Mg(2+) is 10 millimolar. Modulation by light results in increases in maximal velocity, apparently as a result of changes in enzyme conformation. Pea leaf thylakoids are effective in modulating the activity of glyceraldehyde-3-phosphate dehydrogenase but not of fructose-1,6-bisphosphatase or glucose-6-phosphate dehydrogenase in Kalanchoë stromal extracts. There is apparently species specificity for modulation of some, but not all, of the modulatable enzymes.

The control of 3-phosphoglycerate reduction in isolated chloroplasts by the concentrations of ATP, ADP and 3-phosphoglycerate

1. Oxygen evolution by reconstituted chloroplasts with 3-phosphoglycerate as substrate was inhibited by ADP. This inhibition was overcome by increased concentrations of 3-phosphoglycerate or by the addition of excess ATP. 2. The initial rate of 3-phosphoglycerate reduction by chloroplast stromal extracts, measured as 3-phosphoglycerate-dependent oxidation of NADPH, was also dependent on the concentrations of 3-phosphoglycerate, ADP and ATP. 3. Within the range of concentrations of 3-phosphoglycerate, ADP and ATP expected to occur within intact chloroplasts, the rate of 3-phosphoglycerate (PGA) reduction by stromal extract was proportional to the ratio [ATP] [PGA]/[ADP]. 4. These results are consistent with the notion that the substrates and products of 3-phosphoglycerate kinase control the rate of 3-phosphoglycerate reduction via a mass action effect.

Regulation of the Biosynthesis of Ent-Kaurene from Mevalonate in the Endosperm of Immature Marah macrocarpus Seeds by Adenylate Energy Charge

The rate of kaurene biosynthesis from mevalonate in a cell-free enzyme preparation from the endosperm of immature seeds of Marah macrocarpus is regulated by adenylate energy charge. The response curve is typical of a biosynthetic energy-utilizing sequence in which the rate of biosynthesis increases sharply as the energy charge is increased above 0.80. ADP proved to be an effective inhibitor of this process. AMP gave no inhibition at concentrations up to 2 mm and orthophosphate gave no inhibition up to 15 mm. Measurement of the pool sizes of intermediates in the sequence showed that the presence of ADP caused an increase in the levels of 5-phosphomevalonate and 5-pyrophosphomevalonate and a decrease in the levels of isopentenyl pyrophosphate and kaurene. These results indicate that pyrophosphomevalonate decarboxylase is the enzyme most subject to regulation by adenylate energy charge. The rate of conversion of isopentenyl pyrophosphate to kaurene and the rate of utilization of mevalonate by mevalonate kinase were not influenced by variations in the adenylate energy charge.