Dynamics and mechanisms of oscillatory photosynthesis

Exploring microbial players for metagenomic profiling of carbon cycling bacteria in sundarban mangrove soils

The Sundarbans, the world's largest tidal mangrove forest, acts as a crucial ecosystem for production, conservation, and the cycling of carbon and nitrogen. The study explored the hypothesis that microbial communities in mangrove ecosystems exhibit unique taxonomic and functional traits that play a vital part in carbon cycling and ecosystem resilience. Using metagenomic analysis to evaluate microbial communities in mangrove and non-mangrove environment, evaluating their composition, functional functions, and ecological relevance. The analysis revealed distinct microbial profiles, in mangrove and non-mangrove environments, with bacteria, proteobacteria, and viruses being the most prevalent groups, with varying abundances in each environment. Functional and taxonomical analysis identified genes involved in carbon regulation, including Triacylglycerol lipase, NarG, DsrB, DNA-binding transcriptional dual regulator CRP, Vanillate O-demethylase oxygenase, succinate-CoA ligase, Tetrahydrofolate ligase, Carboxylase, Ribulose-1,5-bisphosphate carboxylase/oxygenase, Glycine hydroxymethyltransferase, MAG: urease, Endosymbiont of Oligobrachia haakonmosbiensis, Ribulose bisphosphate carboxylase, Aconitate hydratase AcnA, and nitrous oxide reductase, suggesting the metabolic versatility of these microbial communities for carbon cycling. The findings emphasize the key role of microbial activity in preserving mangrove ecosystem health and resilience, highlighting the intricate interplay between microbial diversity, functional capabilities, and environmental factors.

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.

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.

Role of organic acids in the integration of cellular redox metabolism and mediation of redox signalling in photosynthetic tissues of higher plants

Organic acids play a crucial role in numerous metabolic processes accompanied by transfer of electrons and protons and linked to the reduction/oxidation of major redox couples in plant cells, such as NAD, NADP, glutathione, and ascorbate. Fluxes through the pathways metabolizing organic acids modulate redox states in cell compartments, contribute to generation of reactive oxygen and nitrogen species, and mediate signal transduction processes. Organic acid metabolism not only functions to equilibrate the redox potential in plant cells but also to transfer redox equivalents between cell compartments supporting various metabolic processes. The most important role in this transfer belongs to different forms of malate dehydrogenase interconverting malate and oxaloacetate or forming pyruvate (malic enzymes). During photosynthesis malate serves as a major form of transfer of redox equivalents from chloroplasts to the cytosol and other compartments via the malate valve. On the other hand, mitochondria, via alterations of their redox potential, become a source of citrate that can be transported to the cytosol and support biosynthesis of amino acids. Citrate is also an important retrograde signalling compound that regulates transcription of several genes including those encoding the alternative oxidase. The alternative oxidase, which is activated by increased redox potential and by pyruvate, is, in turn, important for the maintenance of redox potential in mitochondria. The roles of organic acids in establishing redox equilibrium, supporting ionic gradients on membranes, acidification of the extracellular medium, and regulation of production of reactive oxygen and nitrogen species are discussed.

Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach

Oxygenic photosynthesis dominates global primary productivity ever since its evolution more than three billion years ago. While many aspects of phototrophic growth are well understood, it remains a considerable challenge to elucidate the manifold dependencies and interconnections between the diverse cellular processes that together facilitate the synthesis of new cells. Phototrophic growth involves the coordinated action of several layers of cellular functioning, ranging from the photosynthetic light reactions and the electron transport chain, to carbon-concentrating mechanisms and the assimilation of inorganic carbon. It requires the synthesis of new building blocks by cellular metabolism, protection against excessive light, as well as diurnal regulation by a circadian clock and the orchestration of gene expression and cell division. Computational modeling allows us to quantitatively describe these cellular functions and processes relevant for phototrophic growth. As yet, however, computational models are mostly confined to the inner workings of individual cellular processes, rather than describing the manifold interactions between them in the context of a living cell. Using cyanobacteria as model organisms, this contribution seeks to summarize existing computational models that are relevant to describe phototrophic growth and seeks to outline their interactions and dependencies. Our ultimate aim is to understand cellular functioning and growth as the outcome of a coordinated operation of diverse yet interconnected cellular processes.

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.

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.

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.

Intra-seasonal dynamics in metabolic processes of 13C/12C and 18O/16O in components of Scots pine twigs from southern Siberia interpreted with a conceptual framework based on the Carbon Metabolism Oscillatory Model

BACKGROUND

Carbon isotope data from conifer trees play an important role in research on the boreal forest carbon reservoir in the global carbon cycle. Carbon isotopes are routinely used to study interactions between the environment and tree growth. Moreover, carbon isotopes became an essential tool for the evaluation of carbon assimilation and transport from needles into reserve pools, as well as the allocation of stored assimilates within a tree. The successful application and interpretation of carbon isotopes rely on the coherence of isotopic fractionation modeling. This study employs a new Carbon Metabolism Oscillatory Model (CMOM) to interpret the experimental data sets on metabolic seasonal dynamics of 13C/12 C and 18O/16O ratios measured in twig components of Scots pine growing in southern Siberia (Russia).

RESULTS

The dynamics of carbon isotopic variables were studied in components of Pinus sylvestris L. in light and in dark chambers during the vegetation period from 14 June to 28 July 2006. At the beginning of this period water-soluble organic matter, mostly labile sugars (including sucrose as the main component) and newly formed bulk needle material, displayed relatively "light" δ13C values (depletion in 13 C). Then, 13 C content increased again with noticeable "depletion" events in the middle of the growth period. A gradual 13 C accumulation took place in the second half of the vegetation period. Similar effects were observed both in the light and in the dark with some temporal shifts. Environmental factors did not influence the δ13C values. A gradual 12C-depletion effect was noticed in needles of the previous year. The δ13C values of sucrose and proteins from needle biomass altered independently from each other in the light chamber. A distinct negative correlation between δ13C and δ18O values was revealed for all studied variables.

CONCLUSIONS

The abrupt 13C depletion recorded by all tested trees for the period from June to July provides clear evidence of the transition from the dominant role of reserve carbohydrate pool (RCP) during the first half of the growth season to the preferable current year carbohydrate pool (CCP) consumption by new needles during its second half. The investigation of the isotopic signatures of Pinus sylvestris L. emphasizes the pivotal role of the intra-seasonal dynamics in carbon metabolism through the transport of assimilates from autotrophic (needles) to heterotrophic (twigs) organs of the studied trees. This provides an explanation for changes of carbon isotopic values observed within the growth season. The CMOM-based results support the hypothesis of the integration of three carbohydrate pools by photosynthesizing cells. The fluctuations of the carbon isotope ratios in different carbohydrate pools underlie various physiological processes in the tree metabolism. The possible mechanisms and pathways of formation of these carbohydrate pools are further discussed. Hence, CMOM provides a reasonable explanation for the absence of the impact of environmental conditions on the needle isotopic variables, the 12C-depletion effects and the use of RCP in needles. The model explains the negative connections between δ13C and δ18O values in all studied variables.

Optimization of CO₂fixation in photosynthetic cells via thermodynamic buffering

Stable operation of photosynthesis is based on the establishment of local equilibria of metabolites in the Calvin cycle. This concerns especially equilibration of stromal contents of adenylates and pyridine nucleotides and buffering of CO₂ concentration to prevent its depletion at the sites of Rubisco. Thermodynamic buffering that controls the homeostatic flux in the Calvin cycle is achieved by equilibrium enzymes such as glyceraldehyde phosphate dehydrogenase, transaldolase and transketolase. Their role is to prevent depletion of ribulose-1,5-bisphosphate, even at high [CO₂], and to maintain conditions where the only control is exerted by the CO₂ supply. Buffering of adenylates is achieved mainly by chloroplastic adenylate kinase, whereas NADPH level is maintained by mechanisms involving alternative sinks for electrons both within the chloroplast (cyclic phosphorylation, chlororespiration, etc.) and shuttling of reductants outside chloroplast (malate valve). This results in optimization of carbon fixation in chloroplasts, illustrating the principle that the energy of light is used to support stable non-equilibrium which drives all living processes in plants.