The thermodynamic H+/ATP ratios of the H+-ATPsynthases from chloroplasts and Escherichia coli

Targeted blocking of EGFR and GLUT1 by compound H reveals a new strategy for treatment of triple-negative breast cancer and nasopharyngeal carcinoma

BACKGROUND

Cytoplasmic epidermal growth factor receptor (EGFR) is overexpressed in both nasopharyngeal carcinoma (NPC) and triple-negative breast cancer (TNBC), while clinical outcome and prognosis vary greatly among patients treated with gefitinib, and all patients eventually develop resistance to this agent. Therefore, we propose a new concept for synthesizing multitarget compounds and reveal new therapeutic strategies for NPC and TNBC expressing EGFR.

METHODS

Compound H was synthesized in our previous study. Molecular docking, and cell thermal shift assays (CETSAs) and drug affinity responsive target stability(DARTS) were used to confirm the binding of compound H to EGFR and GLUT1. Methylthiazolyldiphenyl-tetrazolium bromide(MTT), annexin V-PE assays, mitochondrial membrane potential (MMP) assays, and animal models were used to evaluate the inhibitory effect of compound H on TNBC cell lines. Energy metabolism tests, Western blotting, and immunofluorescence staining were performed to evaluate the synergistic effects on EGFR- and glucose transporter type 1(GLUT1)-mediated energy metabolism.

RESULTS

Compound H can simultaneously act on the EGFR tyrosine kinase ATP-binding site and inhibit GLUT1-mediated energy metabolism, resulting in reductions in ATP, MMP, intra-cellular lactic acid, and EGFR nuclear transfer. The anti-tumor activity of compound H is significantly superior to the combination of GLUT1 inhibitor BAY876 and EGFR inhibitor gefitinib. Compound H has remarkable anti-proliferative effects on TNBC MDA-MB231 cells, and importantly, no obvious toxicity effects of compound H were found in vivo.

CONCLUSIONS

Synergistic effects of inhibition of EGFR- and GLUT1-mediated energy metabolism by compound H may present a new strategy for the treatment of TNBC and NPC.

Mechanism of ADP-Inhibited ATP Hydrolysis in Single Proton-Pumping FoF1-ATP Synthase Trapped in Solution

F_oF₁-ATP synthases in mitochondria, in chloroplasts, and in most bacteria are proton-driven membrane enzymes that supply the cells with ATP made from ADP and phosphate. Different control mechanisms exist to monitor and prevent the enzymes' reverse chemical reaction of fast wasteful ATP hydrolysis, including mechanical or redox-based blockade of catalysis and ADP inhibition. In general, product inhibition is expected to slow down the mean catalytic turnover. Biochemical assays are ensemble measurements and cannot discriminate between a mechanism affecting all enzymes equally or individually. For example, all enzymes could work more slowly at a decreasing substrate/product ratio, or an increasing number of individual enzymes could be completely blocked. Here, we examined the effect of increasing amounts of ADP on ATP hydrolysis of single Escherichia coli F_oF₁-ATP synthases in liposomes. We observed the individual catalytic turnover of the enzymes one after another by monitoring the internal subunit rotation using single-molecule Förster resonance energy transfer (smFRET). Observation times of single FRET-labeled F_oF₁-ATP synthases in solution were extended up to several seconds using a confocal anti-Brownian electrokinetic trap (ABEL trap). By counting active versus inhibited enzymes, we revealed that ADP inhibition did not decrease the catalytic turnover of all F_oF₁-ATP synthases equally. Instead, increasing ADP in the ADP/ATP mixture reduced the number of remaining active enzymes that operated at similar catalytic rates for varying substrate/product ratios.

Conversion of Mevalonate to Isoprenol Using Light Energy in Escherichia coli without Consuming Sugars for ATP Supply

Bioconversion of key intermediate metabolites such as mevalonate into various useful chemicals is a promising strategy for microbial production. However, the conversion of mevalonate into isoprenoids requires a supply of adenosine triphosphate (ATP). Light-driven ATP regeneration using microbial rhodopsin is an attractive module for improving the intracellular ATP supply. In the present study, we demonstrated the ATP-consuming conversion of mevalonate to isoprenol using rhodopsin-expressing Escherichia coli cells as a whole-cell catalyst in a medium that does not contain energy cosubstrate, such as glucose. Heterologous genes for the synthesis of isoprenol from mevalonate, which requires three ATP molecules for the series of reactions, and a delta-rhodopsin gene derived from Haloterrigena turkmenica were cointroduced into E. coli. To evaluate the conversion efficiency of mevalonate to isoprenol, the cells were suspended in a synthetic medium containing mevalonate as the sole carbon source and incubated under dark or light illumination (100 μmol m^-2 s^-1). The specific isoprenol production rates were 10.0 ± 0.9 and 20.4 ± 0.7 μmol gDCW^-1 h^-1 for dark and light conditions, respectively. The conversion was successfully enhanced under the light condition. Furthermore, the conversion efficiency increased with increasing illumination intensity, suggesting that ATP regenerated by the proton motive force generated by rhodopsin using light energy can drive ATP-consuming reactions in the whole-cell catalyst.

The multiple facets of mitochondrial regulations controlling cellular thermogenesis

Understanding temperature production and regulation in endotherm organisms becomes a crucial challenge facing the increased frequency and intensity of heat strokes related to global warming. Mitochondria, located at the crossroad of metabolism, respiration, Ca²⁺ homeostasis, and apoptosis, were recently proposed to further act as cellular radiators, with an estimated inner temperature reaching 50 °C in common cell lines. This inner thermogenesis might be further exacerbated in organs devoted to produce consistent efforts as muscles, or heat as brown adipose tissue, in response to acute solicitations. Consequently, pathways promoting respiratory chain uncoupling and mitochondrial activity, such as Ca²⁺ fluxes, uncoupling proteins, futile cycling, and substrate supplies, provide the main processes controlling heat production and cell temperature. The mitochondrial thermogenesis might be further amplified by cytoplasmic mechanisms promoting the over-consumption of ATP pools. Considering these new thermic paradigms, we discuss here all conventional wisdoms linking mitochondrial functions to cellular thermogenesis in different physiological conditions.

Empowering roots-Some current aspects of root bioenergetics

Roots of higher plants provide the shoot with nutrients and water. In exchange, they receive photosynthates, which serve both as energy source and building blocks for maintenance and growth. While studies in plant bioenergetics used to focus on photosynthesis, several more recent findings also aroused or renewed interest in energy conversion and allocation in roots. Root building costs were identified as a long-undervalued trait, which turned out to be highly relevant for stress tolerance and nutrient use efficiency. Reduced building costs per root length (e.g., by aerenchyma formation or by increasing the cell size) are beneficial for exploring the soil for nutrient-rich patches, especially in low-input agrosystems. Also, an apparent mismatch was frequently found between the root energy budget in the form of the ATP pool on the one side and the apparent costs on the other side, particularly the costs of membrane transport under stress conditions, e.g., the Na⁺ detoxification costs resulting from Na⁺ sequestration at the plasma membrane. Ion transport across the plasma membrane (and also endomembranes) is coupled to the proton motive force usually believed to be exclusively generated by H⁺ ATPases. Recently, an alternative mechanism, the biochemical pH clamp, was identified which relies on H⁺ formation and binding in the apoplast and the cytosol, respectively, driven by metabolism (so-called active buffering). On this background, several aspects of root bioenergetics are discussed. These are (1) root respiration in soil, with a critical view on calorimetric vs. gas exchange measurements; (2) processes of energy conversion in mitochondria with a special focus on the role of the alternative oxidases, which allow adjusting carbon flow through metabolic pathways to membrane transport processes; and (3) energy allocation, in particular to transport across the plasma membrane forming the interface to soil solution. A concluding remark is dedicated to modeling root bioenergetics for optimizing further breeding strategies. Apparent "energy spoilers" may bestow the plant with a yet unidentified advantage only unfolding their beneficial effect under certain environmental conditions.

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

The bacterial respiratory electron transport system (ETS) is branched to allow condition-specific modulation of energy metabolism. There is a detailed understanding of the structural and biochemical features of respiratory enzymes; however, a holistic examination of the system and its plasticity is lacking. Here we generate four strains of Escherichia coli harboring unbranched ETS that pump 1, 2, 3, or 4 proton(s) per electron and characterized them using a combination of synergistic methods (adaptive laboratory evolution, multi-omic analyses, and computation of proteome allocation). We report that: (a) all four ETS variants evolve to a similar optimized growth rate, and (b) the laboratory evolutions generate specific rewiring of major energy-generating pathways, coupled to the ETS, to optimize ATP production capability. We thus define an Aero-Type System (ATS), which is a generalization of the aerobic bioenergetics and is a metabolic systems biology description of respiration and its inherent plasticity.

The bacterial respiratory electron transport system (ETS) is branched to allow condition-specific modulation of energy metabolism. Here the authors examine the systems level properties of aerobic electron transport system using adaptive laboratory evolution and multi-omics analyses.

Luciferase-Based Determination of ATP/NAD(H) Pools in a Marine (Environmental) Bacterium

In all living organisms, adenosine triphosphate (ATP) and NAD(H) represent universal molecular currencies for energy and redox state, respectively, and are thus widely applicable molecular proxies for an organism's viability and activity. To this end, corresponding luciferase-based assays in combination with a microplate reader were established with the marine model bacterium Phaeobacter inhibens DSM 17395 (Escherichia coli K12 served as reference). Grey multiwell plates best balanced sensitivity and crosstalk, and optimal incubation times were 5 min and 30 min for the ATP and NAD(H) assay, respectively, together allowing limits of detection of 0.042, 0.470 and 0.710 nM for ATP, NAD+, and NADH, respectively. Quenching of bacterial cell samples involved Tris-EDTA-DTAB and bicarbonate base-DTAB for ATP and NAD(H) assays, respectively. The ATP and NAD(H) yields determined for P. inhibens DSM 17395 at ¼ ODmax were found to reside well within the range previously reported for E. coli and other bacteria, e.g., 3.28 µmol ATP (g cellsdry)-1. Thus, the here described methods for luciferase-based determination of ATP/NAD(H) pools open a promising approach to investigate energy and redox states in marine (environmental) bacteria.

pH-dependent 11° F1FO ATP synthase sub-steps reveal insight into the FO torque generating mechanism

Most cellular ATP is made by rotary F₁F_O ATP synthases using proton translocation-generated clockwise torque on the F_O c-ring rotor, while F₁-ATP hydrolysis can force counterclockwise rotation and proton pumping. The F_O torque-generating mechanism remains elusive even though the F_O interface of stator subunit-a, which contains the transmembrane proton half-channels, and the c-ring is known from recent F₁F_O structures. Here, single-molecule F₁F_O rotation studies determined that the pKa values of the half-channels differ, show that mutations of residues in these channels change the pKa values of both half-channels, and reveal the ability of F_O to undergo single c-subunit rotational stepping. These experiments provide evidence to support the hypothesis that proton translocation through F_O operates via a Grotthuss mechanism involving a column of single water molecules in each half-channel linked by proton translocation-dependent c-ring rotation. We also observed pH-dependent 11° ATP synthase-direction sub-steps of the Escherichia coli c₁₀-ring of F₁F_O against the torque of F₁-ATPase-dependent rotation that result from H⁺ transfer events from F_O subunit-a groups with a low pKa to one c-subunit in the c-ring, and from an adjacent c-subunit to stator groups with a high pKa. These results support a mechanism in which alternating proton translocation-dependent 11° and 25° synthase-direction rotational sub-steps of the c₁₀-ring occur to sustain F₁F_O ATP synthesis.

Proton motive force in plant photosynthesis dominated by ΔpH in both low and high light

The proton motive force (pmf) across the thylakoid membrane couples photosynthetic electron transport and ATP synthesis. In recent years, the electrochromic carotenoid and chlorophyll absorption band shift (ECS), peaking ∼515 nm, has become a widely used probe to measure pmf in leaves. However, the use of this technique to calculate the parsing of the pmf between the proton gradient (ΔpH) and electric potential (Δψ) components remains controversial. Interpretation of the ECS signal is complicated by overlapping absorption changes associated with violaxanthin de-epoxidation to zeaxanthin (ΔA505) and energy-dependent nonphotochemical quenching (qE; ΔA535). In this study, we used Arabidopsis (Arabidopsis thaliana) plants with altered xanthophyll cycle activity and photosystem II subunit S (PsbS) content to disentangle these overlapping contributions. In plants where overlap among ΔA505, ΔA535, and ECS is diminished, such as npq4 (lacking ΔA535) and npq1npq4 (also lacking ΔA505), the parsing method implies the Δψ contribution is virtually absent and pmf is solely composed of ΔpH. Conversely, in plants where ΔA535 and ECS overlap is enhanced, such as L17 (a PsbS overexpressor) and npq1 (where ΔA535 is blue-shifted to 525 nm) the parsing method implies a dominant contribution of Δψ to the total pmf. These results demonstrate the vast majority of the pmf attributed by the ECS parsing method to Δψ is caused by ΔA505 and ΔA535 overlap, confirming pmf is dominated by ΔpH following the first 60 s of continuous illumination under both low and high light conditions. Further implications of these findings for the regulation of photosynthesis are discussed.

Evolution of a biochemical model of steady-state photosynthesis

On the occasion of the 40th anniversary of the publication of the landmark model by Farquhar, von Caemmerer & Berry on steady-state C₃ photosynthesis (known as the "FvCB model"), we review three major further developments of the model. These include: (1) limitation by triose phosphate utilization, (2) alternative electron transport pathways, and (3) photorespiration-associated nitrogen and C₁ metabolisms. We discussed the relation of the third extension with the two other extensions, and some equivalent extensions to model C₄ photosynthesis. In addition, the FvCB model has been coupled with CO₂ -diffusion models. We review how these extensions and integration have broadened the use of the FvCB model in understanding photosynthesis, especially with regard to bioenergetic stoichiometries associated with photosynthetic quantum yields. Based on the new insights, we present caveats in applying the FvCB model. Further research needs are highlighted.

Recording and Simulating Proton-Related Metabolism in Bacterial Cell Suspensions

Proton release and uptake induced by metabolic activities were measured in non-buffered cell suspensions by means of a pH electrode. Recorded data were used for simulating substrate turnover rates by means of a new freeware app (proton.exe). The program applies Michaelis-Menten or first-order kinetics to the metabolic processes and allows for parametrization of simultaneously ongoing processes. The simulation includes changes of the transmembrane ΔpH, membrane potential and ATP gains, and demonstrates the principles of chemiosmotic energy conservation. In our experiments, the versatile sulfate-reducing bacterium Desulfovibrio desulfuricans CSN (DSM 9104) was used as model organism. We analysed sulfate uptake by proton-sulfate symport, scalar alkalinization by sulfate reduction to sulfide, as well as nitrate and nitrite reduction to ammonia, and electron transport-coupled proton translocation. Two types of experiments were performed: In oxidant pulse experiments, cells were kept under H₂, and micromolar amounts of sulfate, nitrate or nitrite were added. For reductant pulse experiments, small amounts of H₂-saturated KCl were added to cells incubated under N₂ with an excess of one of the above-mentioned electron acceptors. To study electron-transport driven proton translocation, the membrane potential was neutralized by addition of KSCN (100 mM). H⁺/e^– ratios of electron-transport driven proton translocation were calculated by simulation with proton.exe. This method gave lower but more realistic values than logarithmic extrapolation. We could verify the kinetic simulation parameters found with proton.exe using series of increasing additions of the reactants. Our approach allows for studying a broad variety of proton-related metabolic activities at micromolar concentrations and time scales of seconds to minutes.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.

Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins

Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.

Thermodynamic marking of FOF1 ATP synthase

F_OF₁ ATP synthase is a ~100% efficient molecular machine for energy conversion in biology, and holds great lessons for man-made energy technology and nanotechnology. In light of formidable biocomplexity of the F_OF₁ machinery, its modeling from pure physical principles remains difficult and rare. Here we construct a thermodynamic model of F_OF₁ from experimentally accessible quantities plus a single entropy production that generally has vanishingly small values (<1k_B). Based on the physical inputs, this model captures F_OF₁ performance observed over an exhaustively wide range of proton-motive force and nucleotide concentrations. The model predicts a distinct 1/8k_BT slope for ATP synthesis rate versus proton-motive force, which is verified by experimental data and represents a profound thermodynamic marking of this amazingly efficient machine operating near a universal limit of the 2nd law of thermodynamics. The model further predicts two symmetries of heat productions, which are testable by available experimental techniques and offer quantitative constraints on F_OF₁'s possible mechanisms behind its ~100% efficiency.

Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches

Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.

How potassium came to be the dominant biological cation: of metabolism, chemiosmosis, and cation selectivity since the beginnings of life

In the cytoplasm of practically all living cells, potassium is the major cation while sodium dominates in the media (seawater, extracellular fluids). Both prokaryotes and eukaryotes have elaborate mechanisms and spend significant energy to maintain this asymmetric K⁺ /Na⁺ distribution. This essay proposes an original line of evidence to explain how bacteria selected potassium at the very beginning of the evolutionary process and why it remains essential for eukaryotes.

Genome-scale metabolic modeling of Acetobacter pasteurianus 386B reveals its metabolic adaptation to cocoa fermentation conditions

Acetobacter pasteurianus 386B has been selected as a candidate functional starter culture to better control the cocoa fermentation process. Previously, its genome has been sequenced and a genome-scale metabolic model (GEM) has been reconstructed. To understand its metabolic adaptation to cocoa fermentation conditions, different flux balance analysis (FBA) simulations were performed and compared with experimental data. In particular, metabolic flux distributions were simulated for two phases that characterize the growth of A. pasteurianus 386B under cocoa fermentation conditions, predicting a switch in respiratory chain usage in between these phases. The possible influence on the resulting energy production was shown using a reduced version of the GEM. FBA simulations revealed the importance of the compartmentalization of the ethanol oxidation reactions, namely in the periplasm or in the cytoplasm, and highlighted the potential role of ethanol as a source of carbon, energy, and NADPH. Regarding the latter, the physiological function of a proton-translocating NAD(P)⁺ transhydrogenase was further investigated in silico. This study revealed the potential of using a GEM to simulate the metabolism of A. pasteurianus 386B, and may provide a general framework toward a better physiological understanding of functional starter cultures in food fermentation processes.

Potentiometric detection of ATP based on the transmembrane proton gradient generated by ATPase reconstituted on a gold electrode

Adenosine triphosphate (ATP) is a key molecule as energy vector for living organisms, therefore its detection reveals the presence of microbial colonies. Environments where the existence of microbial pathogens suppose a health hazard can benefit from real time monitoring of such molecule. We report a potentiometric biosensor based on ATP-synthase from Escherichia coli reconstituted in a floating phospholipid bilayer over gold electrodes modified with a 4-aminothiophenol self-assembled monolayer. The use of a pH-dependent redox probe on the electrode surface allows a simple, specific and reliable on site determination of ATP concentration from 1 μM to 1 mM. The broad range ATP biosensor can offer an alternative way of measuring in a few minutes the presence of microbial contamination.

Fermentation Revisited: How Do Microorganisms Survive Under Energy-Limited Conditions?

During fermentation F_OF₁ hydrolyzes ATP, coupling proton transport to proton-motive force (pmf) generation. Despite that, pmf generated by ATP hydrolysis does not satisfy the energy budget of a fermenting cell. However, pmf can also be generated by extrusion of weak organic acids such as lactate and by hydrogen cycling catalyzed by hydrogenases (Hyds). Here we highlight recent advances in our understanding of how the transport of weak organic acids and enzymes contributes to pmf generation during fermentation. The potential impact of these processes on metabolism and energy conservation during microbial fermentation have been overlooked and they not only expand on Mitchell's chemiosmotic theory but also are of relevance to the fields of microbial biochemistry and human and animal health.

Optimization of ATP Synthase c-Rings for Oxygenic Photosynthesis

The conversion of sunlight into useable cellular energy occurs via the proton-coupled electron transfer reactions of photosynthesis. Light is absorbed by photosynthetic pigments and transferred to photochemical reaction centers to initiate electron and proton transfer reactions to store energy in a redox gradient and an electrochemical proton gradient (proton motive force, pmf), composed of a concentration gradient (ΔpH) and an electric field (Δψ), which drives the synthesis of ATP through the thylakoid F_oF₁-ATP synthase. Although ATP synthase structure and function are conserved across biological kingdoms, the number of membrane-embedded ion-binding c subunits varies between organisms, ranging from 8 to 17, theoretically altering the H⁺/ATP ratio for different ATP synthase complexes, with profound implications for the bioenergetic processes of cellular metabolism. Of the known c-ring stoichiometries, photosynthetic c-rings are among the largest identified stoichiometries, and it has been proposed that decreasing the c-stoichiometry could increase the energy conversion efficiency of photosynthesis. Indeed, there is strong evidence that the high H⁺/ATP of the chloroplast ATP synthase results in a low ATP/nicotinamide adenine dinucleotide phosphate (NADPH) ratio produced by photosynthetic linear electron flow, requiring secondary processes such as cyclic electron flow to support downstream metabolism. We hypothesize that the larger c subunit stoichiometry observed in photosynthetic ATP synthases was selected for because it allows the thylakoid to maintain pmf in a range where ATP synthesis is supported, but avoids excess Δψ and ΔpH, both of which can lead to production of reactive oxygen species and subsequent photodamage. Numerical kinetic simulations of the energetics of chloroplast photosynthetic reactions with altered c-ring size predicts the energy storage of pmf and its effects on the photochemical reaction centers strongly support this hypothesis, suggesting that, despite the low efficiency and suboptimal ATP/NADPH ratio, a high H⁺/ATP is favored to avoid photodamage. This has important implications for the evolution and regulation of photosynthesis as well as for synthetic biology efforts to alter photosynthetic efficiency by engineering the ATP synthase.

The energy budget in C4 photosynthesis: insights from a cell-type-specific electron transport model

Extra ATP required in C₄ photosynthesis for the CO₂ -concentrating mechanism probably comes from cyclic electron transport (CET). As metabolic ATP : NADPH requirements in mesophyll (M) and bundle-sheath (BS) cells differ among C₄ subtypes, the subtypes may differ in the extent to which CET operates in these cells. We present an analytical model for cell-type-specific CET and linear electron transport. Modelled NADPH and ATP production were compared with requirements. For malic-enzyme (ME) subtypes, c. 50% of electron flux is CET, occurring predominantly in BS cells for standard NADP-ME species, but in a ratio of c. 6 : 4 in BS : M cells for NAD-ME species. Some C₄ acids follow a secondary decarboxylation route, which is obligatory, in the form of 'aspartate-malate', for the NADP-ME subtype, but facultative, in the form of phosphoenolpyruvate-carboxykinase (PEP-CK), for the NAD-ME subtype. The percentage for secondary decarboxylation is c. 25% and that for 3-phosphoglycerate reduction in BS cells is c. 40%; but these values vary with species. The 'pure' PEP-CK type is unrealistic because its is impossible to fulfil ATP : NADPH requirements in BS cells. The standard PEP-CK subtype requires negligible CET, and thus has the highest intrinsic quantum yields and deserves further studies in the context of improving canopy productivity.

Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks

Adipic acid, a nylon-6,6 precursor, has recently gained popularity in synthetic biology. Here, 16 different production routes to adipic acid were evaluated using a novel tool for network-embedded thermodynamic analysis of elementary flux modes. The tool distinguishes between thermodynamically feasible and infeasible modes under determined metabolite concentrations, allowing the thermodynamic feasibility of theoretical yields to be assessed. Further, patterns that always caused infeasible flux distributions were identified, which will aid the development of tailored strain design. A review of cellular efflux mechanisms revealed that significant accumulation of extracellular product is only possible if coupled with ATP hydrolysis. A stoichiometric analysis demonstrated that the maximum theoretical product carbon yield heavily depends on the metabolic route, ranging from 32 to 99% on glucose and/or palmitate in Escherichia coli and Saccharomyces cerevisiae metabolic models. Equally important, metabolite concentrations appeared to be thermodynamically restricted in several pathways. Consequently, the number of thermodynamically feasible flux distributions was reduced, in some cases even rendering whole pathways infeasible, highlighting the importance of pathway choice. Only routes based on the shikimate pathway were thermodynamically favorable over a large concentration and pH range. The low pH capability of S. cerevisiae shifted the thermodynamic equilibrium of some pathways toward product formation. One identified infeasible-pattern revealed that the reversibility of the mitochondrial malate dehydrogenase contradicted the current state of knowledge, which imposes a major restriction on the metabolism of S. cerevisiae. Finally, the evaluation of industrially relevant constraints revealed that two shikimate pathway-based routes in E. coli were the most robust.

In Silico Analysis of the Regulation of the Photosynthetic Electron Transport Chain in C3 Plants

We present a new simulation model of the reactions in the photosynthetic electron transport chain of C3 species. We show that including recent insights about the regulation of the thylakoid proton motive force, ATP/NADPH balancing mechanisms (cyclic and noncyclic alternative electron transport), and regulation of Rubisco activity leads to emergent behaviors that may affect the operation and regulation of photosynthesis under different dynamic environmental conditions. The model was parameterized with experimental results in the literature, with a focus on Arabidopsis (Arabidopsis thaliana). A dataset was constructed from multiple sources, including measurements of steady-state and dynamic gas exchange, chlorophyll fluorescence, and absorbance spectroscopy under different light intensities and CO2, to test predictions of the model under different experimental conditions. Simulations suggested that there are strong interactions between cyclic and noncyclic alternative electron transport and that an excess capacity for alternative electron transport is required to ensure adequate redox state and lumen pH. Furthermore, the model predicted that, under specific conditions, reduction of ferredoxin by plastoquinol is possible after a rapid increase in light intensity. Further analysis also revealed that the relationship between ATP synthesis and proton motive force was highly regulated by the concentrations of ATP, ADP, and inorganic phosphate, and this facilitated an increase in nonphotochemical quenching and proton motive force under conditions where metabolism was limiting, such as low CO2, high light intensity, or combined high CO2 and high light intensity. The model may be used as an in silico platform for future research on the regulation of photosynthetic electron transport.

Deleting the IF1-like ζ subunit from Paracoccus denitrificans ATP synthase is not sufficient to activate ATP hydrolysis

In oxidative phosphorylation, ATP synthases interconvert two forms of free energy: they are driven by the proton-motive force across an energy-transducing membrane to synthesize ATP and displace the ADP/ATP ratio from equilibrium. For thermodynamically efficient energy conversion they must be reversible catalysts. However, in many species ATP synthases are unidirectional catalysts (their rates of ATP hydrolysis are negligible), and in others mechanisms have evolved to regulate or minimize hydrolysis. Unidirectional catalysis by Paracoccus denitrificans ATP synthase has been attributed to its unique ζ subunit, which is structurally analogous to the mammalian inhibitor protein IF1 Here, we used homologous recombination to delete the ζ subunit from the P. denitrificans genome, and compared ATP synthesis and hydrolysis by the wild-type and knockout enzymes in inverted membrane vesicles and the F1-ATPase subcomplex. ATP synthesis was not affected by loss of the ζ subunit, and the rate of ATP hydrolysis increased by less than twofold, remaining negligible in comparison with the rates of the Escherichia coli and mammalian enzymes. Therefore, deleting the P. denitrificans ζ subunit is not sufficient to activate ATP hydrolysis. We close by considering our conclusions in the light of reversible catalysis and regulation in ATP synthase enzymes.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

Perfect chemomechanical coupling of FoF1-ATP synthase

F_oF₁-ATP synthase (F_oF₁) couples H⁺ flow in F_o domain and ATP synthesis/hydrolysis in F₁ domain through rotation of the central rotor shaft, and the H⁺/ATP ratio is crucial to understand the coupling mechanism and energy yield in cells. Although H⁺/ATP ratio of the perfectly coupling enzyme can be predicted from the copy number of catalytic β subunits and that of H⁺ binding c subunits as c/β, the actual H⁺/ATP ratio can vary depending on coupling efficiency. Here, we report actual H⁺/ATP ratio of thermophilic Bacillus F_oF₁, whose c/β is 10/3. Proteoliposomes reconstituted with the F_oF₁ were energized with ΔpH and Δψ by the acid-base transition and by valinomycin-mediated diffusion potential of K⁺ under various [ATP]/([ADP]⋅[Pi]) conditions, and the initial rate of ATP synthesis/hydrolysis was measured. Analyses of thermodynamically equilibrated states, where net ATP synthesis/hydrolysis is zero, show linear correlation between the chemical potential of ATP synthesis/hydrolysis and the proton motive force, giving the slope of the linear function, that is, H⁺/ATP ratio, 3.3 ± 0.1. This value agrees well with the c/β ratio. Thus, chemomechanical coupling between F_o and F₁ is perfect.

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

The metabolism of microorganisms is regulated through two main mechanisms: changes of enzyme capacities as a consequence of gene expression modulation (“hierarchical control”) and changes of enzyme activities through metabolite-enzyme interactions. An increasing body of evidence indicates that hierarchical control is insufficient to explain metabolic behaviors, but the system-wide impact of metabolic regulation remains largely uncharacterized. To clarify its role, we developed and validated a detailed kinetic model of Escherichia coli central metabolism that links growth to environment. Metabolic control analyses confirm that the control is widely distributed across the network and highlight strong interconnections between all the pathways. Exploration of the model solution space reveals that several robust properties emerge from metabolic regulation, from the molecular level (e.g. homeostasis of total metabolite pool) to the overall cellular physiology (e.g. coordination of carbon uptake, catabolism, energy and redox production, and growth), while allowing a large degree of flexibility at most individual metabolic steps. These properties have important physiological implications for E. coli and significantly expand the self-regulating capacities of its metabolism.

Metabolism is a fundamental biochemical process that enables cells to operate and grow by converting nutrients into ‘building blocks’ and energy. Metabolism happens through the work of enzymes, which are encoded by genes. Thus, genes and their regulation are often thought of controlling metabolism, somewhat at the top of a hierarchical control system. However, an increasing body of evidence indicates that metabolism plays an active role in the control of its own operation via a dense network of metabolite-enzyme interactions. The system-wide role of metabolic regulation is hard to dissect and so far remains largely uncharacterized. To better understand its role, we constructed a detailed kinetic model of the carbon and energy metabolism of the bacterium Escherichia coli, a model organism in Systems and Synthetic biology. Model simulations indicate that kinetic considerations of metabolism alone can explain data from hundreds of experiments, without needing to invoke regulation of gene expression. In particular, metabolic regulation is sufficient to coordinate carbon utilization, redox and energy production, and growth, while maintaining local flexibility at individual metabolic steps. These findings indicate that the self-regulating capacities of E. coli metabolism are far more significant than previously expected, and improve our understanding on how cells work.

Physiological Functions of Cyclic Electron Transport Around Photosystem I in Sustaining Photosynthesis and Plant Growth

The light reactions in photosynthesis drive both linear and cyclic electron transport around photosystem I (PSI). Linear electron transport generates both ATP and NADPH, whereas PSI cyclic electron transport produces ATP without producing NADPH. PSI cyclic electron transport is thought to be essential for balancing the ATP/NADPH production ratio and for protecting both photosystems from damage caused by stromal overreduction. Two distinct pathways of cyclic electron transport have been proposed in angiosperms: a major pathway that depends on the PROTON GRADIENT REGULATION 5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE 1 (PGRL1) proteins, which are the target site of antimycin A, and a minor pathway mediated by the chloroplast NADH dehydrogenase-like (NDH) complex. Recently, the regulation of PSI cyclic electron transport has been recognized as essential for photosynthesis and plant growth. In this review, we summarize the possible functions and importance of the two pathways of PSI cyclic electron transport.

Thermodynamics of proton transport coupled ATP synthesis

The thermodynamic H(+)/ATP ratio of the H(+)-ATP synthase from chloroplasts was measured in proteoliposomes after energization of the membrane by an acid base transition (Turina et al. 2003 [13], 418-422). The method is discussed, and all published data obtained with this system are combined and analyzed as a single dataset. This meta-analysis led to the following results. 1) At equilibrium, the transmembrane ΔpH is energetically equivalent to the transmembrane electric potential difference. 2) The standard free energy for ATP synthesis (reference reaction) is ΔG°(ref)=33.8±1.3kJ/mol. 3) The thermodynamic H(+)/ATP ratio, as obtained from the shift of the ATP synthesis equilibrium induced by changing the transmembrane ΔpH (varying either pH(in) or pH(out)) is 4.0±0.1. The structural H(+)/ATP ratio, calculated from the ratio of proton binding sites on the c-subunit-ring in F(0) to the catalytic nucleotide binding sites on the β-subunits in F(1), is c/β=14/3=4.7. We infer that the energy of 0.7 protons per ATP that flow through the enzyme, but do not contribute to shifting the ATP/(ADP·Pi) ratio, is used for additional processes within the enzyme, such as activation, and/or energy dissipation, due e.g. to internal uncoupling. The ratio between the thermodynamic and the structural H(+)/ATP values is 0.85, and we conclude that this value represents the efficiency of the chemiosmotic energy conversion within the chloroplast H(+)-ATP synthase.

Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine

Two haloalkaliphilic bacteria isolated from industrial brine solutions were characterized via molecular, physiological, and in silico metabolic pathway analyses. Genomes from the organisms, designated Halomonas BC1 and BC2, were sequenced; 16S ribosomal subunit-based phylogenetic analysis revealed a high level of similarity to each other and to Halomonas meridiana. Both strains were moderate halophiles with near optimal specific growth rates (≥60 % μ max) observed over <0.1-5 % (w/v) NaCl and pH ranging from 7.4 to 10.2. Isolate BC1 was further characterized by measuring uptake or synthesis of compatible solutes under different growth conditions; in complex medium, uptake and accumulation of external glycine betaine was observed while ectoine was synthesized de novo in salts medium. Transcriptome analysis of isolate BC1 grown on glucose or citrate medium measured differences in glycolysis- and gluconeogenesis-based metabolisms, respectively. The annotated BC1 genome was used to build an in silico, genome-scale stoichiometric metabolic model to study catabolic energy strategies and compatible solute synthesis under gradients of oxygen and nutrient availability. The theoretical analysis identified energy metabolism challenges associated with acclimation to high salinity and high pH. The study documents central metabolism data for the industrially and scientifically important haloalkaliphile genus Halomonas.

Thermodynamics and kinetics of the FoF1-ATPase: application of the probability isotherm

We use the results of recent publications as vehicles with which to discuss the thermodynamics of the proton-driven mitochondrial F o F1-ATP synthase, focusing particularly on the possibility that there may be dissociation between rotatory steps and ATP synthesis/hydrolysis. Such stoichiometric 'slippage' has been invoked in the literature to explain observed non-ideal behaviour. Numerical solution of the Rate Isotherm (the kinetic equivalent of the more fundamental Probability Isotherm) suggests that such 'slippage' is an unlikely explanation; instead, we suggest that the experimental results may be more consistent with damage to the enzyme caused by its isolation from the biomembrane and its experimental fixation, resulting in non-physiological friction within the enzyme's rotary mechanism. We emphasize the unavoidable constraint of the Second Law as instantiated by the obligatory dissipation of Gibbs Free Energy if the synthase is to operate at anything other than thermodynamic equilibrium. We use further numerical solution of the Rate Isotherm to demonstrate that there is no necessary association of low thermodynamic efficiency with high metabolic rates in a bio-world in which the dominating mechanism of metabolic control is multifactorial enzyme activation.

A mechano-chemiosmotic model for the coupling of electron and proton transfer to ATP synthesis in energy-transforming membranes: a personal perspective

ATP is synthesized using ATP synthase by utilizing energy either from the oxidation of organic compounds, or from light, via redox reactions (oxidative- or photo phosphorylation), in energy-transforming membranes of mitochondria, chloroplasts, and bacteria. ATP synthase undergoes several changes during its functioning. The generally accepted model for ATP synthesis is the well-known rotatory model (see e.g., Junge et al., Nature 459:364-370, 2009; Junge and Müller, Science 333:704-705, 2011). Here, we present an alternative modified model for the coupling of electron and proton transfer to ATP synthesis, which was initially developed by Albert Lester Lehninger (1917-1986). Details of the molecular mechanism of ATP synthesis are described here that involves cyclic low-amplitude shrinkage and swelling of mitochondria. A comparison of the well-known current model and the mechano-chemiosmotic model is also presented. Based on structural, and other data, we suggest that ATP synthase is a Ca(2+)/H(+)-K(+) Cl(-)-pump-pore-enzyme complex, in which γ-subunit rotates 360° in steps of 30°, and 90° due to the binding of phosphate ions to positively charged amino acid residues in the N-terminal γ-subunit, while in the electric field. The coiled coil b 2-subunits are suggested to act as ropes that are shortened by binding of phosphate ions to positively charged lysines or arginines; this process is suggested to pull the α 3 β 3-hexamer to the membrane during the energization process. ATP is then synthesized during the reverse rotation of the γ-subunit by destabilizing the phosphated N-terminal γ-subunit and b 2-subunits under the influence of Ca(2+) ions, which are pumped over from storage-intermembrane space into the matrix, during swelling of intermembrane space. In the process of ATP synthesis, energy is first, predominantly, used in the delivery of phosphate ions and protons to the α 3 β 3-hexamer against the energy barrier with the help of C-terminal alpha-helix of γ-subunit that acts as a lift; then, in the formation of phosphoryl group; and lastly, in the release of ATP molecules from the active center of the enzyme and the loading of ADP. We are aware that our model is not an accepted model for ATP synthesis, but it is presented here for further examination and test.

On the dynamics of the adenylate energy system: homeorhesis vs homeostasis

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.

An exploration of how the thermodynamic efficiency of bioenergetic membrane systems varies with c-subunit stoichiometry of F₁F₀ ATP synthases

Recently the F0 portion of the bovine mitochondrial F1F0-ATP synthase was shown to contain eight 'c' subunits (n = 8). This surprised many in the field, as previously, the only other mitochondrial F0 (for yeast) was shown to have ten 'c' subunits. The metabolic implications of 'c' subunit copy number explored in this paper lead to several surprising conclusions: (1) Aerobically respiring E. coli (n = 10) and animal mitochondria (n = 8) both have very high F1F0 thermodynamic efficiencies of ≈90% under typical conditions, whereas efficiency is only ≈65% for chloroplasts (n = 14). Reasons for this difference, including the importance of transmembrane potential (∆Ψ) as a rotational catalyst, as opposed to an energy source, are discussed. (2) Maximum theoretical P/O ratios in animal mitochondria (n = 8) are calculated to be 2.73 ATP/NADH and 1.64 ATP/FADH2, yielding 34.5 ATP/glucose (assuming NADH import via the malate/aspartate shuttle). The experimentally measured values of 2.44 (±0.15), 1.47 (±0.13), and 31.3 (±1.5), respectively, are only about 10% lower, suggesting very little energy depletion via transmembrane proton leakage. (3) Finally, the thermodynamic efficiency of oxidative phosphorylation is not lower than that of substrate level phosphorylation, as previously believed. The overall thermodynamic efficiencies of oxidative phosphorylation, glycolysis, and the citric acid cycle are ≈80% in all three processes.

Rethinking the existence of a steady-state Δψ component of the proton motive force across plant thylakoid membranes

Light-driven photosynthetic electron transport is coupled to the movement of protons from the chloroplast stroma to the thylakoid lumen. The resulting proton motive force that is generated is used to drive the conformational rotation of the transmembrane thylakoid ATPase enzyme which converts ADP (adenosine diphosphate) and Pi (inorganic phosphate) into ATP (adenosine triphosphate), the energy currency of the plant cell required for carbon fixation and other metabolic processes. According to Mitchell's chemiosmotic hypothesis, the proton motive force can be parsed into the transmembrane proton gradient (ΔpH) and the electric field gradient (Δψ), which are thermodynamically equivalent. In chloroplasts, the proton motive force has been suggested to be split almost equally between Δψ and ΔpH (Kramer et al., Photosynth Res 60:151-163, 1999). One of the central pieces of evidence for this theory is the existence of a steady-state electrochromic shift (ECS) absorption signal detected ~515 nm in plant leaves during illumination. The interpretation of this signal is complicated, however, by a heavily overlapping absorption change ~535 nm associated with the formation of photoprotective energy dissipation (qE) during illumination. In this study, we present new evidence that dissects the overlapping contributions of the ECS and qE-related absorption changes in wild-type Arabidopsis leaves using specific inhibitors of the ΔpH (nigericin) and Δψ (valinomycin) and separately using leaves of the Arabidopsis lut2npq1 mutant that lacks qE. In both cases, our data show that no steady-state ECS signal persists in the light longer than ~60 s. The consequences of our observations for the suggesting parsing of steady-state thylakoid proton motive force between (ΔpH) and the electric field gradient (Δψ) are discussed.

Photosynthesis-related quantities for education and modeling

A quantitative understanding of the photosynthetic machinery depends largely on quantities, such as concentrations, sizes, absorption wavelengths, redox potentials, and rate constants. The present contribution is a collection of numbers and quantities related mainly to photosynthesis in higher plants. All numbers are taken directly from a literature or database source and the corresponding reference is provided. The numerical values, presented in this paper, provide ranges of values, obtained in specific experiments for specific organisms. However, the presented numbers can be useful for understanding the principles of structure and function of photosynthetic machinery and for guidance of future research.

Biased Brownian stepping rotation of FoF1-ATP synthase driven by proton motive force

FoF1-ATP synthase (FoF1) produces most of the ATP in cells, uniquely, by converting the proton motive force (pmf) into ATP production via mechanical rotation of the inner rotor complex. Technical difficulties have hampered direct investigation of pmf-driven rotation, which are crucial to elucidating the chemomechanical coupling mechanism of FoF1. Here we develop a novel supported membrane system for direct observation of the rotation of FoF1 driven by pmf that was formed by photolysis of caged protons. Upon photolysis, FoF1 initiated rotation in the opposite direction to that of the ATP-driven rotation. The step size of pmf-driven rotation was 120°, suggesting that the kinetic bottleneck is a catalytic event on F1 with threefold symmetry. The reaction equilibrium was slightly biased to ATP synthesis like under physiological conditions, and FoF1 showed highly stochastic behaviour, frequently making a 120° backward step. This new experimental system would be applicable to single-molecule study of other membrane proteins.

Comparative energetics and kinetics of autotrophic lipid and starch metabolism in chlorophytic microalgae: implications for biomass and biofuel production

Due to the growing need to provide alternatives to fossil fuels as efficiently, economically, and sustainably as possible there has been growing interest in improved biofuel production systems. Biofuels produced from microalgae are a particularly attractive option since microalgae have production potentials that exceed the best terrestrial crops by 2 to 10-fold. In addition, autotrophically grown microalgae can capture CO2 from point sources reducing direct atmospheric greenhouse gas emissions. The enhanced biomass production potential of algae is attributed in part to the fact that every cell is photosynthetic. Regardless, overall biological energy capture, conversion, and storage in microalgae are inefficient with less than 8% conversion of solar into chemical energy achieved. In this review, we examine the thermodynamic and kinetic constraints associated with the autotrophic conversion of inorganic carbon into storage carbohydrate and oil, the dominant energy storage products in Chlorophytic microalgae. We discuss how thermodynamic restrictions including the loss of fixed carbon during acetyl CoA synthesis reduce the efficiency of carbon accumulation in lipids. In addition, kinetic limitations, such as the coupling of proton to electron transfer during plastoquinone reduction and oxidation and the slow rates of CO2 fixation by Rubisco reduce photosynthetic efficiency. In some cases, these kinetic limitations have been overcome by massive increases in the numbers of effective catalytic sites, e.g. the high Rubisco levels (mM) in chloroplasts. But in other cases, including the slow rate of plastoquinol oxidation, there has been no compensatory increase in the abundance of catalytically limiting protein complexes. Significantly, we show that the energetic requirements for producing oil and starch relative to the recoverable energy stored in these molecules are very similar on a per carbon basis. Presently, the overall rates of starch and lipid synthesis in microalgae are very poorly characterized. Increased understanding of the kinetic constraints of lipid and starch synthesis, accumulation and turnover would facilitate the design of improved biomass production systems.

Rotary catalysis of FoF1-ATP synthase

The synthesis of ATP, the key reaction of biological energy metabolism, is accomplished by the rotary motor protein; FoF1-ATP synthase (FoF1). In vivo, FoF1, located on the cell membrane, carries out ATP synthesis by using the proton motive force. This heterologous energy conversion is supposed to be mediated by the mechanical rotation of FoF1; however, it still remained unclear. Recently, we developed the novel experimental setup to reproduce the proton motive force in vitro and succeeded in directly observing the proton-driven rotation of FoF1. In this review, we describe the interesting working principles determined so far for FoF1 and then introduce results from our recent study.

Combined mathematical methods in the description of the F(o)F(1)-ATP synthase catalytic cycle

The FoF1-ATP synthase is one of the key enzymes in supplying energy production in almost all living systems. In this paper, we provide a theoretical description of its catalytic cycle using combined mathematical methods. These methods include Langevin dynamics for the rotation of the central protein core and the Monte-Carlo method to model nucleotide and proton binding. This model is the first in which ATP synthesis and hydrolysis can occur depending on the nucleotide concentration and system conditions. The main advantage of the presented model is the possibility of obtaining results for both single-molecular protein-machines and large ensembles of proteins. The calculated rates are close to the experimentally measured rates for a single enzyme. The model has been formalised as a computer simulation that allows researchers to evaluate ATP production in different types of living cells.

Microscopy of single F(o) F(1) -ATP synthases--the unraveling of motors, gears, and controls

Optical microscopy of single F(1) -ATPase and F(o) F(1) -ATP synthases started 15 years ago. Direct demonstration of ATP-driven subunit rotation by videomicroscopy became the new exciting tool to analyze the conformational changes of this enzyme during catalysis. Stimulated by these experiments, technical improvements for higher time resolution, better angular resolution, and reduced viscous drag were developed rapidly. Optics and single-molecule enzymology were entangled to benefit both biochemists and microscopists. Today, several single-molecule microscopy methods are established including controls for the precise nanomanipulation of individual enzymes in vitro. Förster resonance energy transfer, which has been used for simultaneous monitoring of conformational changes of different parts of this rotary motor, is one of them and may become the tool for the analysis of single F(o) F(1) -ATP synthases in membranes of living cells. Here, breakthrough experiments are critically reviewed and challenges are discussed for the future microscopy of single ATP synthesizing enzymes at work.

Twisting and subunit rotation in single F(O)(F1)-ATP synthase

F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.

Energy-converting respiratory Complex I: on the way to the molecular mechanism of the proton pump

In respiring organisms the major energy transduction flux employs the transmembrane electrochemical proton gradient as a physical link between exergonic redox reactions and endergonic ADP phosphorylation. Establishing the gradient involves electrogenic, transmembrane H(+) translocation by the membrane-embedded respiratory complexes. Among others, Complex I (NADH:ubiquinone oxidoreductase) is the most structurally complex and functionally enigmatic respiratory enzyme; its molecular mechanism is as yet unknown. Here we highlight recent progress and discuss the catalytic events during Complex I turnover in relation to their role in energy conversion and to the enzyme structure.

Uncoupling of substrate-level phosphorylation in Escherichia coli during glucose-limited growth

The respiratory chain of Escherichia coli contains three different cytochrome oxidases. Whereas the cytochrome bo oxidase and the cytochrome bd-I oxidase are well characterized and have been shown to contribute to proton translocation, physiological data suggested a nonelectrogenic functioning of the cytochrome bd-II oxidase. Recently, however, this view was challenged by an in vitro biochemical analysis that showed that the activity of cytochrome bd-II oxidase does contribute to proton translocation with an H(+)/e(-) stoichiometry of 1. Here, we propose that this apparent discrepancy is due to the activities of two alternative catabolic pathways: the pyruvate oxidase pathway for acetate production and a pathway with methylglyoxal as an intermediate for the production of lactate. The ATP yields of these pathways are lower than those of the pathways that have so far always been assumed to catalyze the main catabolic flux under energy-limited growth conditions (i.e., pyruvate dehydrogenase and lactate dehydrogenase). Inclusion of these alternative pathways in the flux analysis of growing E. coli strains for the calculation of the catabolic ATP synthesis rate indicates an electrogenic function of the cytochrome bd-II oxidase, compatible with an H(+)/e(-) ratio of 1. This analysis shows for the first time the extent of bypassing of substrate-level phosphorylation in E. coli under energy-limited growth conditions.

Mathematical review of the energy transduction stoichiometries of C(4) leaf photosynthesis under limiting light

A generalized model for electron (e(-) ) transport limited C(4) photosynthesis of NAD-malic enzyme and NADP-malic enzyme subtypes is presented. The model is used to review the thylakoid stoichiometries in vivo under strictly limiting light conditions, using published data on photosynthetic quantum yield and on photochemical efficiencies of photosystems (PS). Model review showed that cyclic e(-) transport (CET), rather than direct O(2) photoreduction, most likely contributed significantly to the production of extra ATP required for the C(4) cycle. Estimated CET, and non-cyclic e(-) transport supporting processes like nitrogen reduction, accounted for ca. 45 and 7% of total photosystem I (PSI) e(-) fluxes, respectively. The factor for excitation partitioning to photosystem II (PSII) was ca. 0.4. Further model analysis, in terms of the balanced NADPH: ATP ratio required for metabolism, indicated that: (1) the Q-cycle is obligatory; (2) the proton: ATP ratio is 4; and (3) the efficiency of proton pumping per e(-) transferred through the cytochrome b(6) /f complex is the same for CET and non-cyclic pathways. The analysis also gave an approach to theoretically assess CO(2) leakiness from bundle-sheath cells, and projected a leakiness of 0.07-0.16. Compared with C(3) photosynthesis, the most striking C(4) stoichiometry is its high fraction of CET.