Dependence of the Calvin cycle activity on kinetic parameters for the interaction of non-equilibrium cycle enzymes with their substrates

Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation

Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated.

Highlighting the effects of coumarin on adult plants of Arabidopsis thaliana (L.) Heynh. by an integrated -omic approach

In this study, the effects of the allelochemical coumarin through a metabolomic, proteomic and morpho-physiological approach in Arabidopsis adult plants (25days old) were investigated. Metabolomic analysis evidenced an increment of amino acids and a high accumulation of soluble sugars, after 6days of coumarin treatment. This effect was accompanied by a strong decrease on plant fresh and dry weights, as well as on total protein content. On the contrary, coumarin did not affect leaf number but caused a reduction in leaf area. An alteration of water status was confirmed by a reduction of relative water content and an increase in leaf osmotic potential. Moreover, coumarin impaired plant bio-membranes through an increase of lipid peroxidation and H₂O₂ content suggesting that coumarin treatment might induce oxidative stress. Coumarin reduced the effective quantum yield of the photosystem II, the energy dissipation in the form of heat, the maximum PSII efficiency, the coefficient of the photochemical quenching and the estimated electron transport rate, while it significantly stimulated the fluorescence emission and the coefficient of the non photochemical quenching. Finally, the proteomic characterization of coumarin-treated plants revealed a down-regulation of the ROS detoxifying proteins, responsible of oxidative damage and consequently of physiological cascade effects.

Comparative proteome analysis of differentially expressed proteins induced by K+ deficiency inArabidopsis thaliana

Mineral nutrient deficiencies constitute major limitations for plant growth on agricultural soils around the world. To identify genes that possibly play roles in plant K(+) nutrition, we employed the comparative proteome analysis for proteins isolated from Arabidopsis seedlings treated with K(+) deficiency for 3 h and 7 d. We identified genes including those encoding putative transcription factors, protein kinases, and phosphatases, proteins involved in phytohormone biosynthesis or signaling, proteins involved in carbon and energy metabolism, and other proteins possibly involved in signal transduction pathway such as 14-3-3 proteins and small G-protein. Our results suggest that those proteins may play roles in signal transduction pathways linking changes in extracellular K(+) status to alterations in gene expression facilitating K(+) homeostasis. These results yield a comprehensive picture of the post-transcriptional response for deprivation of K(+) and serve as a basic platform for further characterization of gene function and regulation in plant mineral nutrition.

Metabolic signals that lead to control of CBB gene expression in Rhodobacter capsulatus

Various mutant strains were used to examine the regulation and metabolic control of the Calvin-Benson-Bassham (CBB) reductive pentose phosphate pathway in Rhodobacter capsulatus. Previously, a ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO)-deficient strain (strain SBI/II) was found to show enhanced levels of cbb(I) and cbb(II) promoter activities during photoheterotrophic growth in the presence of dimethyl sulfoxide. With this strain as the starting point, additional mutations were made in genes encoding phosphoribulokinase and transketolase and in the gene encoding the LysR-type transcriptional activator, CbbR(II). These strains revealed that a product generated by phosphoribulokinase was involved in control of CbbR-mediated cbb gene expression in SBI/II. Additionally, heterologous expression experiments indicated that Rhodobacter sphaeroides CbbR responded to the same metabolic signal in R. capsulatus SBI/II and mutant strain backgrounds.

Photosynthetic capacity is differentially affected by reductions in sedoheptulose-1,7-bisphosphatase activity during leaf development in transgenic tobacco plants

The impact of reduced sedoheptulose-1,7-bisphosphatase (SBPase) activity on photosynthetic capacity and carbohydrate status was examined during leaf expansion and maturation in antisense transgenic tobacco (Nicotiana tabacum L. cv Samsun) plants. In wild-type plants, photosynthetic capacity was lowest in young expanding leaves and reached a maximum in the fully expanded, mature leaves. In contrast, the transgenic antisense SBPase plants had the highest photosynthetic rates in the young expanding leaves and lowest rates in the mature leaves. In the mature, fully expanded leaves of the transgenic plants photosynthetic capacity was closely correlated with the level of SBPase activity. However, in the youngest leaves of the SBPase antisense plants, photosynthetic rates were close to, or higher than, those observed in wild-type plants, despite having a lower SBPase activity than the equivalent wild-type leaves. Reductions in SBPase activity affected carbohydrate levels in both the mature and young developing leaves. The overall trend was for decreased SBPase activity to lead to reductions in carbohydrate levels, particularly in starch. However, these changes in carbohydrate content were also dependent on the developmental status of the leaf. For example, in young expanding leaves of plants with the smallest reductions in SBPase activity, the levels of starch were higher than in wild-type plants. These data suggest that the source status of the mature leaves is an important determinant of photosynthetic development.

Control analysis of metabolic systems involving quasi-equilibrium reactions

Reactions for which the rates are extremely sensitive to changes in the concentrations of variable metabolite concentrations contribute little to the control of biochemical reaction networks. Yet they do interfere with the calculation of the system's behaviour, both in terms of numerical integration of the rate equations and in terms of the analysis of metabolic control. We here present a way to solve this problem systematically for systems with time hierarchies. We identify the fast reactions and fast metabolites, group them apart from the other ("slow") reactions and metabolites, and then apply the appropriate quasi-equilibrium condition for the fast subsystem. This then makes it possible to eliminate the fast reactions and their elasticity coefficients from the calculations, allowing the calculation of the control coefficients of the slow reactions in terms of the elasticity coefficients of the slow reactions. As expected, the elasticity coefficients of the fast reactions drop out of the calculations, and they are irrelevant for control at the time resolution of the steady state of the slow reactions. The analysis, when applied iteratively, is expected to be particularly valuable for the control analysis of living cells, where a time hierarchy exists, the fastest being at the level of enzyme kinetics and the slowest at gene expression.

Rapid enzyme assays investigating the variation in the glycolytic pathway in field-caught populations of Fundulus heteroclitus

Variation in enzyme expression may be important in evolutionary adaptation, yet is seldom studied. Furthermore, no studies have examined the expression of all enzymes in a defined metabolic pathway. Enzyme concentration is a measure of enzyme expression and was ascertained by assaying maximal activity. Presented here is an analysis of variation of maximal enzyme activity for all the enzymes in a single metabolic pathway, glycolysis, from three clinically distributed populations of the fish, Fundulus heteroclitus. Techniques for rapidly analyzing maximal enzyme activity for all the enzymes of an entire metabolic pathway from many individuals are described. The high degree of repeatability (mean coefficient of variation for replicates, 4.4%) and sensitivity (less than 3 mg of tissue is required to measure all 10 enzymes) of these assays demonstrate the utility of such an approach for analyzing variation among populations for a large numbers of enzymes. Results from these studies indicate that (1) the average coefficient of variation for all enzyme determinations within a population is 45.3% and (2) between populations, the activity of 5 of the 10 glycolytic enzymes are significantly different. This considerable variation occurs even in populations where there is little allelic variation. These data demonstrating substantial variation in enzyme expression support the idea that changes in gene regulation may be as important as, or even more important than, changes in biochemical kinetic parameters in evolutionary processes.

cDNA and gene sequences of wheat chloroplast sedoheptulose-1,7-bisphosphatase reveal homology with fructose-1,6-bisphosphatases

The nucleotide sequence encoding the chloroplast enzyme, sedoheptulose-1,7-bisphosphatase [Sed(1,7)P2ase], was obtained from wheat cDNA and genomic clones. The transcribed region of the Sed(1,7)P2ase gene has eight exons (72-507 bp) and seven introns (85-626 bp) and encodes a precursor polypeptide of 393 amino acids. Comparison of the deduced amino acid sequence of Sed(1,7)P2ase with those of fructose-1,6-bisphosphatase [Fru(1,6)P2ase] enzymes from a variety of sources reveals 19% identity, rising to 42% if conservative changes are considered. Most importantly, the amino acid residues which form the active site of Fru(1,6)P2ase are highly conserved in the Sed(1,7)P2ase molecule, indicating a common catalytic mechanism. Interestingly, although the activities of both Sed(1,7)P2ase and chloroplast Fru(1,6)P2ase are modulated by light via the thioredoxin system, the amino acid sequence motif identified as having a role in this regulation in chloroplast Fru(1,6)P2ase is not found in the Sed(1,7)P2ase enzyme.