Feedforward non-Michaelis–Menten mechanism for CO2 uptake by Rubisco: Contribution of carbonic anhydrases and photorespiration to optimization of photosynthetic carbon assimilation

Why is Brachiaria decumbens Stapf. a common species in the mining tailings of the Fundão dam in Minas Gerais, Brazil?

Currently, more than five years after the Fundão dam failure in Mariana, Minas Gerais, Brazil, Brachiaria decumbens Stapf. is the main grass in pasturelands affected by the mining tailings. The aim of this study was to investigate the reason for this fact as well as to determine the ecophysiological effects of mining tailings on B. decumbens and to test whether mixing the tailings with unaffected local soil enhances the affected soil properties. For the experiment, two different soils were collected, one unaffected soil without mining tailings (Ref) and the mining tailings (Tec), and we also created a mixture with 50 % of each soil type (Ref/Tec). We cultivated B. decumbens in the three soil treatments in a greenhouse for 110 days and evaluated soil physical-chemical properties and plant ecophysiology. Our results show that the tailings (Tec) compromised the normal ecophysiological state of B. decumbens. The species survived these adverse conditions due to its great efficiency in acquiring some elements. The soil management tested by this work mitigated the stress caused by tailings and can represent an alternative for the environmental recovery of the affected soils.

The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants

Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO) is the carbon-fixing enzyme present in most photosynthetic organisms, converting CO₂ into organic matter. Globally, photosynthetic efficiency in terrestrial plants has become increasingly challenged in recent decades due to a rapid increase in atmospheric CO₂ and associated changes toward warmer and dryer environments. Well adapted for these new climatic conditions, the C₄ photosynthetic pathway utilizes carbon concentrating mechanisms to increase CO₂ concentrations surrounding RuBisCO, suppressing photorespiration from the oxygenase catalyzed reaction with O₂. The energy efficiency of C₃ photosynthesis, from which the C₄ pathway evolved, is thought to rely critically on an uninterrupted supply of chloroplast CO₂. Part of the homeostatic mechanism that maintains this constancy of supply involves the CO₂ produced as a byproduct of photorespiration in a negative feedback loop. Analyzing the database of RuBisCO kinetic parameters, we suggest that in genera (Flaveria and Panicum) for which both C₃ and C₄ examples are available, the C₄ pathway evolved only from C₃ ancestors possessing much lower than the average carboxylase specificity relative to that of the oxygenase reaction (S _C/O=S _C/S _O), and hence, the higher CO₂ levels required for development of the photorespiratory CO₂ pump (C₂ photosynthesis) essential in the initial stages of C₄ evolution, while in the later stage (final optimization phase in the Flaveria model) increased CO₂ turnover may have occurred, which would have been supported by the higher CO₂ levels. Otherwise, C₄ RuBisCO kinetic traits remain little changed from the ancestral C₃ species. At the opposite end of the spectrum, C₃ plants (from Limonium) with higher than average S _C/O, which may be associated with the ability of increased CO₂, relative to O₂, affinity to offset reduced photorespiration and chloroplast CO₂ levels, can tolerate high stress environments. It is suggested that, instead of inherently constrained by its kinetic mechanism, RuBisCO possesses the extensive kinetic plasticity necessary for adaptation to changes in photorespiration that occur in the homeostatic regulation of CO₂ supply under a broad range of abiotic environmental conditions.

Explicit Treatment of Non-Michaelis-Menten and Atypical Kinetics in Early Drug Discovery*

Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential to sustain life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were mostly tested and implemented for cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more-complex systems (for instance, multiprotein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis-Menten (MM) kinetics are rendered inadequate, and the development of a new kind of kinetic analysis to study these systems is required. This review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents initial ideas on the design and analysis of experiments in early drug-discovery for such systems, to enable effective screening and characterisation of small-molecule inhibitors with desirable physiological outcomes.

Citrate valve integrates mitochondria into photosynthetic metabolism

While in heterotrophic cells and in darkness mitochondria serve as main producers of energy, during photosynthesis this function is transferred to chloroplasts and the main role of mitochondria in bioenergetics turns to be the balance of the level of phosphorylation of adenylates and of reduction of pyridine nucleotides to avoid over-energization of the cell and optimize major metabolic fluxes. This is achieved via the establishment and regulation of local equilibria of the tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase and fumarase in one branch and aconitase and isocitrate dehydrogenase in another branch. In the conditions of elevation of redox level, the TCA cycle is transformed into a non-cyclic open structure (hemicycle) leading to the export of the tricarboxylic acid (citrate) to the cytosol and to the accumulation of the dicarboxylic acids (malate and fumarate). While the buildup of NADPH in chloroplasts provides operation of the malate valve leading to establishment of NADH/NAD⁺ ratios in different cell compartments, the production of NADH by mitochondria drives citrate export by establishing conditions for the operation of the citrate valve. The latter regulates the intercompartmental NADPH/NADP⁺ ratio and contributes to the biosynthesis of amino acids and other metabolic products during photosynthesis.

Emerging roles for carbonic anhydrase in mesophyll conductance and photosynthesis

Carbonic anhydrase (CA) is an abundant protein in most photosynthesizing organisms and higher plants. This review paper considers the physiological importance of the more abundant CA isoforms in photosynthesis, through their effects on CO₂ diffusion and other processes in photosynthetic organisms. In plants, CA has multiple isoforms in three different families (α, β and γ) and is mainly known to catalyze the CO₂↔HCO3- equilibrium. This reversible conversion has a clear role in photosynthesis, primarily through sustaining the CO₂ concentration at the site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Despite showing the same major reaction mechanism, the three main CA families are evolutionarily distinct. For different CA isoforms, cellular localization and total gene expression as a function of developmental stage are predicted to determine the role of each family in relation to the net assimilation rate. Reaction-diffusion modeling and observational evidence support a role for CA activity in reducing resistance to CO₂ diffusion inside mesophyll cells by facilitating CO₂ transfer in both gas and liquid phases. In addition, physical and/or biochemical interactions between CAs and other membrane-bound compartments, for example aquaporins, are suggested to trigger a CO₂ -sensing response by stomatal movement. In response to environmental stresses, changes in the expression level of CAs and/or stimulated deactivation of CAs may correspond with lower photosynthetic capacity. We suggest that further studies should focus on the dynamics of the relationship between the activity of CAs (with different subcellular localization, abundance and gene expression) and limitations due to CO₂ diffusivity through the mesophyll and supply of CO₂ to photosynthetic reactions.

Insights into the function of NADPH thioredoxin reductase C (NTRC) based on identification of NTRC-interacting proteins in vivo

Redox regulation in heterotrophic organisms relies on NADPH, thioredoxins (TRXs), and an NADPH-dependent TRX reductase (NTR). In contrast, chloroplasts harbor two redox systems, one that uses photoreduced ferredoxin (Fd), an Fd-dependent TRX reductase (FTR), and TRXs, which links redox regulation to light, and NTRC, which allows the use of NADPH for redox regulation. It has been shown that NTRC-dependent regulation of 2-Cys peroxiredoxin (PRX) is critical for optimal function of the photosynthetic apparatus. Thus, the objective of the present study was the analysis of the interaction of NTRC and 2-Cys PRX in vivo and the identification of proteins interacting with them with the aim of identifying chloroplast processes regulated by this redox system. To assess this objective, we generated Arabidopsis thaliana plants expressing either an NTRC-tandem affinity purification (TAP)-Tag or a green fluorescent protein (GFP)-TAP-Tag, which served as a negative control. The presence of 2-Cys PRX and NTRC in complexes isolated from NTRC-TAP-Tag-expressing plants confirmed the interaction of these proteins in vivo. The identification of proteins co-purified in these complexes by MS revealed the relevance of the NTRC-2-Cys PRX system in the redox regulation of multiple chloroplast processes. The interaction of NTRC with selected targets was confirmed in vivo by bimolecular fluorescence complementation (BiFC) assays.

Thermodynamic buffering, stable non-equilibrium and establishment of the computable structure of plant metabolism

The equilibria of coenzyme nucleotides and substrates established in plant cells generate simple rules that govern the plant metabolome and provide optimal conditions for the non-equilibrium fluxes of major metabolic processes such as ATP synthesis, CO₂ fixation, and mitochondrial respiration. Fast and abundant enzymes, such as adenylate kinase, carbonic anhydrase or malate dehydrogenase, provide constant substrate flux for these processes. These "buffering" enzymes follow the Michaelis-Menten (MM) kinetics and operate near equilibrium. The non-equilibrium "engine" enzymes, such as ATP synthase, Rubisco or the respiratory complexes, follow the modified version of MM kinetics due to their high concentration and low concentration of their substrates. The equilibrium reactions serve as control gates for the non-equilibrium flux through the engine enzymes establishing the balance of the fluxes of load and consumption of metabolic components. Under the coordinated operation of buffering and engine enzymes, the concentrations of free and Mg-bound adenylates and of free Mg²⁺ are set, serving as feedback signals from the adenylate metabolome. Those are linked to various cell energetics parameters, including membrane potentials. Also, internal levels of reduced and oxidized pyridine nucleotides are established in the coordinated operation of malate dehydrogenase and respiratory components, with proton concentration as a feedback from pyridine nucleotide pools. Non-coupled pathways of respiration serve to equilibrate the levels of pyridine nucleotides, adenylates, and as a pH stat. This stable non-equilibrium organizes the fluxes of energy spatially and temporally, controlling the rates of major metabolic fluxes that follow thermodynamically and kinetically defined computational principles.

Ups and downs in alfalfa: Proteomic and metabolic changes occurring in the growing stem

The expanding interest for using lignocellulosic biomass in industry spurred the study of the mechanisms underlying plant cell-wall synthesis. Efforts using genetic approaches allowed the disentanglement of major steps governing stem fibre synthesis. Nonetheless, little is known about the relations between the stem maturation and the evolution of its proteome. During Medicago sativa L. maturation, the different internodes grow asynchronously allowing the discrimination of various developmental stages on a same stem. In this study, the proteome of three selected regions of the stem of alfalfa (apical, intermediate and basal) was analyzed and combined with a compositional analysis of the different stem parts. Interestingly, the apical and the median regions share many similarities: high abundance of chloroplast- and mitochondrial-related proteins together with the accumulation of proteins acting in the early steps of fibre production. In the mature basal region, forisomes and stress-related proteins accumulate. The RT-qPCR assessment of the expression of genes coding for members of the cellulose synthase family likewise indicates that fibres and the machinery responsible for the deposition of secondary cell walls are predominantly formed in the apical section. Altogether, this study reflects the metabolic change from the fibre production in the upper stem regions to the acquisition of defence-related functions in the fibrous basal part.

Optimization of ATP synthase function in mitochondria and chloroplasts via the adenylate kinase equilibrium

The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg(2+), supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H(+), and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg(2+) contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg(2+), adenylate transport, and phosphate release and supply.

Control of Rubisco function via homeostatic equilibration of CO2 supply

Rubisco is the most abundant protein on Earth that serves as the primary engine of carbon assimilation. It is characterized by a slow rate and low specificity for CO2 leading to photorespiration. We analyze here the challenges of operation of this enzyme as the main carbon fixation engine. The high concentration of Rubisco exceeds that of its substrate CO2 by 2-3 orders of magnitude; however, the total pool of available carbon in chloroplast, i.e., mainly bicarbonate, is comparable to the concentration of Rubisco active sites. This makes the reactant stationary assumption (RSA), which is essential as a condition of satisfying the Michaelis-Menten (MM) kinetics, valid if we assume that the delivery of CO2 from this pool is not limiting. The RSA is supported by active carbonic anhydrases (CA) that quickly equilibrate bicarbonate and CO2 pools and supply CO2 to Rubisco. While the operation of stromal CA is independent of light reactions, the thylakoidal CA associated with PSII and pumping CO2 from the thylakoid lumen is coordinated with the rate of electron transport, water splitting and proton gradient across the thylakoid membrane. At high CO2 concentrations, CA becomes less efficient (the equilibrium becomes unfavorable), so a deviation from the MM kinetics is observed, consistent with Rubisco reaching its Vmax at approximately 50% lower level than expected from the classical MM curve. Previously, this deviation was controversially explained by the limitation of RuBP regeneration. At low ambient CO2 and correspondingly limited capacity of the bicarbonate pool, its depletion at Rubisco sites is relieved in that the enzyme utilizes O2 instead of CO2, i.e., by photorespiration. In this process, CO2 is supplied back to Rubisco, and the chloroplastic redox state and energy level are maintained. It is concluded that the optimal performance of photosynthesis is achieved via the provision of continuous CO2 supply to Rubisco by carbonic anhydrases and photorespiration.

Activity of the mitochondrial pyruvate dehydrogenase complex in plants is stimulated in the presence of malate

The effect of malate on the steady-state activity of the pea (Pisum sativum L.) and barley (Hordeum vulgare L.) leaf pyruvate dehydrogenase complex (PDC) has been studied in isolated mitochondria. The addition of malate was found to be stimulatory for the mitochondrial PDC, however there was no stimulation of chloroplast PDC. The stimulation was saturated below 1mM malate and was apparently related to а partially activated complex, which activity increased in the presence of malate by about twofold. Malate also reversed the reduction of PDC activity in the presence of glycine. Based on the obtained kinetic data, we suggest that the effect of malate is rather not a direct activation of PDC but involves the establishment of NAD-malate dehydrogenase equilibrium, decreasing concentration of NADH and relieving its inhibitory effect of PDC.

The function of glycine decarboxylase complex is optimized to maintain high photorespiratory flux via buffering of its reaction products

Oxidation of glycine in photorespiratory pathway is the major flux through mitochondria of C3 plants in the light. It sustains increased intramitochondrial concentrations of NADH and NADPH, which are required to engage the internal rotenone-insensitive NAD(P)H dehydrogenases and the alternative oxidase. We discuss here possible mechanisms of high photorespiratory flux maintenance in mitochondria and suggest that it is fulfilled under conditions where the concentrations of glycine decarboxylase reaction products NADH and CO2 achieve an equilibrium provided by malate dehydrogenase and carbonic anhydrase, respectively. This results in the removal of these products from the glycine decarboxylase multienzyme active sites and in the maintenance of their concentrations at levels sufficiently low to prevent substrate inhibition of the reaction.

Validity of the Michaelis-Menten equation--steady-state or reactant stationary assumption: that is the question

The Michaelis-Menten equation is generally used to estimate the kinetic parameters, V and K(M), when the steady-state assumption is valid. Following a brief overview of the derivation of the Michaelis-Menten equation for the single-enzyme, single-substrate reaction, a critical review of the criteria for validity of the steady-state assumption is presented. The application of the steady-state assumption makes the implicit assumption that there is an initial transient during which the substrate concentration remains approximately constant, equal to the initial substrate concentration, while the enzyme-substrate complex concentration builds up. This implicit assumption is known as the reactant stationary assumption. This review presents evidence showing that the reactant stationary assumption is distinct from and independent of the steady-state assumption. Contrary to the widely believed notion that the Michaelis-Menten equation can always be applied under the steady-state assumption, the reactant stationary assumption is truly the necessary condition for validity of the Michaelis-Menten equation to estimate kinetic parameters. Therefore, the application of the Michaelis-Menten equation only leads to accurate estimation of kinetic parameters when it is used under experimental conditions meeting the reactant stationary assumption. The criterion for validity of the reactant stationary assumption does not require the restrictive condition of choosing a substrate concentration that is much higher than the enzyme concentration in initial rate experiments.

Entropy production in oscillatory processes during photosynthesis

The flow of matter and heat and the rate of enzymatic reactions are examined using two models of photosynthesis that exhibit sustained and damped oscillatory dynamics, with the objective of calculating the rate of entropy generation and studying the effects of temperature and kinetic constants on the thermodynamic efficiency of photosynthesis. The global coefficient of heat transfer and the direct and inverse constants of the formation reaction of the RuBisCO-CO2 complex were used as control parameters. Results show that when the system moves from isothermal to non-isothermal conditions, the transition from a steady state to oscillations facilitates an increase in the energy efficiency of the process. The simulations were carried out for two photosynthetic models in a system on a chloroplast reactor scale.

Modelling (18)O2 and (16)O2 unidirectional fluxes in plants. IV: role of conductance and laws of its regulation in C3 plants

Numerous studies focus on the measurement of conductances for CO2 transfer in plants and especially on their regulatory effects on photosynthesis. Measurement accuracy is strongly dependent on the model used and on the knowledge of the flow of photochemical energy generated by light in chloroplasts. The only accurate and precise method to quantify the linear electron flux (responsible for the production of reductive energy) is the direct measurement of O2 evolution, by (18)O2 labelling and mass spectrometry. The sharing of this energy between the carboxylation (P) and the oxygenation of photorespiration (PR) depends on the plant specificity factor (Sp) and on the corresponding atmospheric concentrations of CO2 and O2 (André, 2013). The concept of plant specificity factor simplifies the equations of the model. It gives a new expression of the effect of the conductance (g) between atmosphere and chloroplasts. Its quantitative effect on photosynthesis is easy to understand because it intervenes in the ratio of the plant specificity factor (Sp) to the specificity of Rubisco (Sr). Using this 'simple' model with the data of (18)O2 experiments, the calculation of conductance variations in response to CO2 and light was carried out. The good fitting of experimental data of O2 and CO2 exchanges confirms the validity of the simple model. The calculation of conductance variation during the increase of external CO2 concentration reveals a linear law of regulation between external and internal CO2 concentrations. During CO2 variations, the effects of g regulation tend to maintain a higher level of oxygenation (PR) in expense of a better carboxylation (P). Contrary to CO2, the variation of O2 creates a negative feedback effect compatible with a stabilization of atmospheric O2. The regulation of g amplifies this result. The effect of light in combination with CO2 is more complex. Below 800μmolquantam(-2)s(-1) the ratio PR/P is maintained unchangeable in expense of carboxylation efficiency. Above that irradiance value, PR/P increases dramatically. It appears that the saturation curves of photosynthesis under high light could be simply due to the regulation by the conductance g and not by any biochemical or biophysical limitation. In conclusion, the regulatory effect of conductance operates in a way that it preserves the rate of photorespiration. This confirms a positive and protective role of photorespiration at the biochemical, whole plant and atmosphere levels. Since the effects of photorespiration are linked to the properties of Rubisco, they add new arguments for a co-evolution of plant and atmosphere, including the evolution of CO2 conductance.