Assimilatory Power in Photosynthesis: Photosynthetic phosphorylation by isolated chloroplasts is coupled with TPN reduction

Novel context-specific genome-scale modelling explores the potential of triacylglycerol production by Chlamydomonas reinhardtii

Gene expression data of cell cultures is commonly measured in biological and medical studies to understand cellular decision-making in various conditions. Metabolism, affected but not solely determined by the expression, is much more difficult to measure experimentally. Finding a reliable method to predict cell metabolism for expression data will greatly benefit metabolic engineering. We have developed a novel pipeline, OVERLAY, that can explore cellular fluxomics from expression data using only a high-quality genome-scale metabolic model. This is done through two main steps: first, construct a protein-constrained metabolic model (PC-model) by integrating protein and enzyme information into the metabolic model (M-model). Secondly, overlay the expression data onto the PC-model using a novel two-step nonconvex and convex optimization formulation, resulting in a context-specific PC-model with optionally calibrated rate constants. The resulting model computes proteomes and intracellular flux states that are consistent with the measured transcriptomes. Therefore, it provides detailed cellular insights that are difficult to glean individually from the omic data or M-model alone. We apply the OVERLAY to interpret triacylglycerol (TAG) overproduction by Chlamydomonas reinhardtii, using time-course RNA-Seq data. We show that OVERLAY can compute C. reinhardtii metabolism under nitrogen deprivation and metabolic shifts after an acetate boost. OVERLAY can also suggest possible 'bottleneck' proteins that need to be overexpressed to increase the TAG accumulation rate, as well as discuss other TAG-overproduction strategies.

An ancient function of PGR5 in iron delivery?

In all phototrophic organisms, the photosynthetic apparatus must be protected from light-induced damage. One important mechanism that mitigates photodamage in plants is antimycin A (AA)-sensitive cyclic electron flow (CEF), the evolution of which remains largely obscure. Here we show that proton gradient regulation 5 (PGR5), a key protein involved in AA-sensitive CEF, displays intriguing commonalities - including sequence and structural features - with a group of ferritin-like proteins. We therefore propose that PGR5 may originally have been involved in prokaryotic iron mobilization and delivery, which facilitated a primordial type of CEF as a side effect. The abandonment of the bacterioferritin system during the transformation of cyanobacterial endosymbionts into chloroplasts might have allowed PGR5 to functionally specialize in CEF.

Light-Powered Ion Pumping in a Cation-Selective Conducting Polymer Membrane

The simulation of the ion pumping against a proton gradient energized by light in photosynthesis is of significant importance for the energy conversion in a non-biological environment. Herein, we report light-powered ion pumping in a polystyrene sulfonate anion (PSS) doped polypyrrole (PPy) conducting polymer membrane (PSS-PPy) with a symmetric geometry. This PSS-PPy conducting polymer membrane exhibits a cationic selectivity and a light-responsive surface-charge-governed ion transport attributed to the negatively charged PSS groups. An asymmetric visible irradiation on one side of the PSS-PPy membrane induces a built-in electric field across the membrane due to the intrinsic photoelectronic property of PPy, which drives the cationic transport against the concentration gradient, demonstrating an ion-pumping effect. This work is a prototype that uses a geometry-symmetric conducting polymer membrane as a light-powered artificial ion pump for active ion transport, which exhibits potential applications in nanofluidic energy conversion.

The Physiological Functionality of PGR5/PGRL1-Dependent Cyclic Electron Transport in Sustaining Photosynthesis

The cyclic electron transport (CET), after the linear electron transport (LET), is another important electron transport pathway during the light reactions of photosynthesis. The proton gradient regulation 5 (PGR5)/PRG5-like photosynthetic phenotype 1 (PGRL1) and the NADH dehydrogenase-like complex pathways are linked to the CET. Recently, the regulation of CET around photosystem I (PSI) has been recognized as crucial for photosynthesis and plant growth. Here, we summarized the main biochemical processes of the PGR5/PGRL1-dependent CET pathway and its physiological significance in protecting the photosystem II and PSI, ATP/NADPH ratio maintenance, and regulating the transitions between LET and CET in order to optimize photosynthesis when encountering unfavorable conditions. A better understanding of the PGR5/PGRL1-mediated CET during photosynthesis might provide novel strategies for improving crop yield in a world facing more extreme weather events with multiple stresses affecting the plants.

Modelling and simulation of photosynthetic activities in C3 plants as affected by CO2

CO₂ concentration ([CO₂]) in a greenhouse may be a limiting factor for plant growth. Current greenhouse CO₂ control strategy usually depends on expert experience, which may control [CO₂] in a moderate range but cannot make it optimal due to lack of considering plant photochemistry reactions. A state-space kinetic model structure covering major photosynthetic reactions as affected by CO₂ is useful for [CO₂] control strategy development in a greenhouse because modern control theories are usually based on state-space models. In this work, a state-space kinetic model structure for photosynthesis was built, which describes the major reaction cascades of photophosphorylation, Calvin cycle, and biophysical processes such as CO₂ transport through the stomata under moderate [CO₂] range without considering photorespiration. Simulations were performed with a large range of model parameters to demonstrate the effect of [CO₂] on stable sugar production and the flexibilities of the developed model structure. The results clearly show whether increasing of CO₂ will lead to more production of sugar or not in different scenarios. The model structure may be extended to cover other photosynthetic influence factors such as temperature by using the well-known Arrhenius equation.

Thinking twice about the evolution of photosynthesis

Sam Granick opened his seminal 1957 paper titled 'Speculations on the origins and evolution of photosynthesis' with the assertion that there is a constant urge in human beings to seek beginnings (I concur). This urge has led to an incessant stream of speculative ideas and debates on the evolution of photosynthesis that started in the first half of the twentieth century and shows no signs of abating. Some of these speculative ideas have become commonplace, are taken as fact, but find little support. Here, I review and scrutinize three widely accepted ideas that underpin the current study of the evolution of photosynthesis: first, that the photochemical reaction centres used in anoxygenic photosynthesis are more primitive than those in oxygenic photosynthesis; second, that the probability of acquiring photosynthesis via horizontal gene transfer is greater than the probability of losing photosynthesis; and third, and most important, that the origin of anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis. I shall attempt to demonstrate that these three ideas are often grounded in incorrect assumptions built on more assumptions with no experimental or observational support. I hope that this brief review will not only serve as a cautionary tale but also that it will open new avenues of research aimed at disentangling the complex evolution of photosynthesis and its impact on the early history of life and the planet.

Features of cues and processes during chloroplast-mediated retrograde signaling in the alga Chlamydomonas

Retrograde signaling is an intracellular communication process defined by cues generated in chloroplast and mitochondria which traverse membranes to their destination in the nucleus in order to regulate nuclear gene expression and protein synthesis. The coding and decoding of such organellar message(s) involve gene medleys and metabolic components about which more is known in higher plants than the unicellular organisms such as algae. Chlamydomonas reinhardtii is an oxygenic microalgal model for genetic and physiological studies. It harbors a single chloroplast and is amenable for generating mutants. The focus of this review is on studies that delineate retrograde signaling in Chlamydomonas vis a vis higher plants. Thus, communication networks between chloroplast and nucleus involving photosynthesis- and ROS-generated signals, functional tetrapyrrole biosynthesis intermediates, and Ca²⁺-signaling that modulate nuclear gene expression in this alga are discussed. Conceptually, different signaling components converge to regulate either the same or functionally-overlapping gene products.

The antimycin A-sensitive pathway of cyclic electron flow: from 1963 to 2015

Cyclic electron flow has puzzled and divided the field of photosynthesis researchers for decades. This mainly concerns the proportion of its overall contribution to photosynthesis, as well as its components and molecular mechanism. Yet, it is irrefutable that the absence of cyclic electron flow has severe effects on plant growth. One of the two pathways mediating cyclic electron flow can be inhibited by antimycin A, a chemical that has also widely been used to characterize the mitochondrial respiratory chain. For the characterization of cyclic electron flow, antimycin A has been used since 1963, when ferredoxin was found to be the electron donor of the pathway. In 2013, antimycin A was used to identify the PGRL1/PGR5 complex as the ferredoxin:plastoquinone reductase completing the last puzzle piece of this pathway. The controversy has not ended, and here, we review the history of research on this process using the perspective of antimycin A as a crucial chemical for its characterization.

Dynamic reorganization of photosynthetic supercomplexes during environmental acclimation of photosynthesis

Plants and algae have acquired the ability to acclimate to ever-changing environments in order to survive. During photosynthesis, light energy is converted by several membrane protein supercomplexes into electrochemical energy, which is eventually used to assimilate CO2. The efficiency of photosynthesis is modulated by many environmental factors such as quality and quantity of light, temperature, drought, and CO2 concentration, among others. Accumulating evidence indicates that photosynthetic supercomplexes undergo supramolecular reorganization within a short time frame during acclimation to an environmental change. This reorganization includes state transitions that balance the excitation of photosystem I and II by shuttling peripheral antenna proteins between the two, thermal energy dissipation that occurs at energy-quenching sites within the light-harvesting antenna generated for negative feedback when excess light is absorbed, and cyclic electron flow that is facilitated between photosystem I and the cytochrome bf complex when cells demand more ATP and/or need to activate energy dissipation. This review will highlight the recent findings regarding these environmental acclimation events in model organisms with particular attention to the unicellular green alga C. reinhardtii and with reference to the vascular plant A. thaliana, which offers a glimpse into the dynamic behavior of photosynthetic machineries in nature.

Central carbon metabolism and electron transport in Chlamydomonas reinhardtii: metabolic constraints for carbon partitioning between oil and starch

The metabolism of microalgae is so flexible that it is not an easy task to give a comprehensive description of the interplay between the various metabolic pathways. There are, however, constraints that govern central carbon metabolism in Chlamydomonas reinhardtii that are revealed by the compartmentalization and regulation of the pathways and their relation to key cellular processes such as cell motility, division, carbon uptake and partitioning, external and internal rhythms, and nutrient stress. Both photosynthetic and mitochondrial electron transfer provide energy for metabolic processes and how energy transfer impacts metabolism and vice versa is a means of exploring the regulation and function of these pathways. A key example is the specific chloroplast localization of glycolysis/gluconeogenesis and how it impacts the redox poise and ATP budget of the plastid in the dark. To compare starch and lipids as carbon reserves, their value can be calculated in terms of NAD(P)H and ATP. As microalgae are now considered a potential renewable feedstock, we examine current work on the subject and also explore the possibility of rerouting metabolism toward lipid production.

Cyclic electron flow is redox-controlled but independent of state transition

Photosynthesis is the biological process that feeds the biosphere with reduced carbon. The assimilation of CO2 requires the fine tuning of two co-existing functional modes: linear electron flow, which provides NADPH and ATP, and cyclic electron flow, which only sustains ATP synthesis. Although the importance of this fine tuning is appreciated, its mechanism remains equivocal. Here we show that cyclic electron flow as well as formation of supercomplexes, thought to contribute to the enhancement of cyclic electron flow, are promoted in reducing conditions with no correlation with the reorganization of the thylakoid membranes associated with the migration of antenna proteins towards Photosystems I or II, a process known as state transition. We show that cyclic electron flow is tuned by the redox power and this provides a mechanistic model applying to the entire green lineage including the vast majority of the cases in which state transition only involves a moderate fraction of the antenna.

Rubisco mutagenesis provides new insight into limitations on photosynthesis and growth in Synechocystis PCC6803

Orthophosphate (Pi) stimulates the activation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) while paradoxically inhibiting its catalysis. Of three Pi-binding sites, the roles of the 5P- and latch sites have been documented, whereas that of the 1P-site remained unclear. Conserved residues at the 1P-site of Rubisco from the cyanobacterium Synechocystis PCC6803 were substituted and the kinetic properties of the enzyme derivatives and effects on cell photosynthesis and growth were examined. While Pi-stimulated Rubisco activation diminished for enzyme mutants T65A/S and G404A, inhibition of catalysis by Pi remained unchanged. Together with previous studies, the results suggest that all three Pi-binding sites are involved in stimulation of Rubisco activation, whereas only the 5P-site is involved in inhibition of catalysis. While all the mutations reduced the catalytic turnover of Rubisco (K(cat)) between 6- and 20-fold, the photosynthesis and growth rates under saturating irradiance and inorganic carbon (Ci) concentrations were only reduced 40-50% (in the T65A/S mutants) or not at all (G404A mutant). Analysis of the mutant cells revealed a 3-fold increase in Rubisco content that partially compensated for the reduced K(cat) so that the carboxylation rate per chlorophyll was one-third of that in the wild type. Correlation between the kinetic properties of Rubisco and the photosynthetic rate (P(max)) under saturating irradiance and Ci concentrations indicate that a >60% reduction in K(cat) can be tolerated before P(max) in Synechocystsis PCC6803 is affected. These results indicate that the limitation of Rubisco activity on the rate of photosynthesis in Synechocystis is low. Determination of Calvin cycle metabolites revealed that unlike in higher plants, cyanobacterial photosynthesis is constrained by phosphoglycerate reduction probably due to limitation of ATP or NADPH.

State transitions--the molecular remodeling of photosynthetic supercomplexes that controls energy flow in the chloroplast

In oxygen-evolving photosynthesis, the two photosystems-photosystem I and photosystem II-function in parallel, and their excitation levels must be balanced to maintain an optimal photosynthetic rate under natural light conditions. State transitions in photosynthetic organisms balance the absorbed light energy between the two photosystems in a short time by relocating light-harvesting complex II proteins. For over a decade, the understanding of the physiological consequences, the molecular mechanism, and its regulation has increased considerably. After providing an overview of the general understanding of state transitions, this review focuses on the recent advances of the molecular aspects of state transitions with a particular emphasis on the studies using the green alga Chlamydomonas reinhardtii. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts.

Photosynthetic electron transport from water to NADP driven by photosystem II in inside-out chloroplast vesicles

It is now widely held that the light-induced noncyclic (linear) electron transport from water to NADP(+) requires the collaboration in series of the two photosystems that operate in oxygen-evolving cells: photosystem II (PSII) photooxidizes water and transfers electrons to photosystem I (PSI); PSI photoreduces ferredoxin, which in turn reduces NADP(+) (the Z scheme). However, a recently described alternative scheme envisions that PSII drives the noncyclic electron transport from water to ferredoxin and NADP(+) without the collaboration of PSI, whose role is limited to cyclic electron transport [Arnon, D. I., Tsujimoto, H. Y. & Tang, G. M.-S. (1981) Proc. Natl. Acad. Sci. USA 78, 2942-2946]. Reported here are findings at variance with the Z scheme and consistent with the alternative scheme. Thylakoid membrane vesicles were isolated from spinach chloroplasts by the two-phase aqueous polymer partition method. Vesicles, originating mainly from appressed chloroplast membranes that are greatly enriched in PSII, were turned inside-out with respect to the original sidedness of the membrane. With added plastocyanin, ferredoxin, and ferredoxin-NADP(+) reductase, the inside-out vesicles enriched in PSII gave a significant photoreduction of NADP(+) with water as electron donor, under experimental conditions that appear to exclude the participation of PSI.

Proton transport in photooxidation of water: A new perspective on photosynthesis

The currently prevalent concept of the generation of photosynthetic reducing power in oxygen-evolving cells envisions a linear (noncyclic) electron flow from water to ferredoxin (and thence to NADP(+)) that requires the collaboration of photosystems I and II (PSI and PSII) joined by plastoquinone and other electron carriers (the Z scheme). The essence of the Z scheme is that only PSI can reduce ferredoxin-i.e., that, after being energized to an intermediate reducing potential by PSII, electrons from water are transported via plastoquinone to PSI which energizes the electrons to their ultimate reducing potential adequate for the reduction of ferredoxin. Basic to the Z scheme is the function of plastoquinone as the obligatory link in electron transport from PSII to PSI. However, we have found that, when plastoquinone function was inhibited, ferredoxin was photoreduced by water without the collaboration of PSI. We now report evidence for an important function of plastoquinone in the translocation of protons liberated inside the thylakoid membrane by photooxidation of water. When the oxygenic photoreduction (i.e., by water) of ferredoxin was blocked by plastoquinone inhibitors, dibromothymoquinone or dinitrophenol ether of iodonitrothymol, the photoreduction of ferredoxin was restored by each of four chemically diverse uncouplers, similar only in their ability to facilitate proton movement across membranes. Similar results were obtained for the oxygenic reduction of NADP(+). Our results suggest that the light-induced electron flow from water cannot be maintained unless the simultaneously liberated protons are removed from inside the membrane via plastoquinone. The new evidence is embodied in a concept of an oxygenic photosystem for photosynthetic electron and proton transport, which we propose as an alternative to the Z scheme, to account for photoreduction of ferredoxin-NADP(+) by water and the coupled oxygenic (formerly noncyclic) ATP formation without involving PSI. The role of the anoxygenic photosystem (formerly called PSI) is ATP formation by cyclic photophosphorylation.

Isolation of the elusive supercomplex that drives cyclic electron flow in photosynthesis

Photosynthetic light reactions establish electron flow in the chloroplast's thylakoid membranes, leading to the production of the ATP and NADPH that participate in carbon fixation. Two modes of electron flow exist-linear electron flow (LEF) from water to NADP(+) via photosystem (PS) II and PSI in series and cyclic electron flow (CEF) around PSI (ref. 2). Although CEF is essential for satisfying the varying demand for ATP, the exact molecule(s) and operational site are as yet unclear. In the green alga Chlamydomonas reinhardtii, the electron flow shifts from LEF to CEF on preferential excitation of PSII (ref. 3), which is brought about by an energy balancing mechanism between PSII and PSI (state transitions). Here, we isolated a protein supercomplex composed of PSI with its own light-harvesting complex (LHCI), the PSII light-harvesting complex (LHCII), the cytochrome b(6)f complex (Cyt bf), ferredoxin (Fd)-NADPH oxidoreductase (FNR), and the integral membrane protein PGRL1 (ref. 5) from C. reinhardtii cells under PSII-favouring conditions. Spectroscopic analyses indicated that on illumination, reducing equivalents from downstream of PSI were transferred to Cyt bf, whereas oxidised PSI was re-reduced by reducing equivalents from Cyt bf, indicating that this supercomplex is engaged in CEF (Supplementary Fig. 1). Thus, formation and dissociation of the PSI-LHCI-LHCII-FNR-Cyt bf-PGRL1 supercomplex not only controlled the energy balance of the two photosystems, but also switched the mode of photosynthetic electron flow.

Effect of trifluoroacetate, a persistent degradation product of fluorinated hydrocarbons, on Phaseolus vulgaris and Zea mays

The aim of this study was to quantify the effect of the pollutant, trifluoroacetate (TFA), on growth and photosynthesis of Phaseolus vulgaris (C(3)) and Zea mays (C(4)) in order to elucidate the physiological and biochemical basis of its inhibitory action. In whole plant studies, photosynthetic gas exchange, fast phase fluorescence kinetics and Rubisco activity were measured in parallel over a 14-day period in plants cultivated in a water culture system with NaTFA added at concentrations ranging from 0.625 to 160mgl(-1). Although initial stimulation of some photosynthetic parameters was observed at low TFA concentrations early on in the experiment, marked inhibition occurred at higher concentrations. In general Z. mays was affected more severely than P. vulgaris showing a large TFA-induced decrease in both apparent carboxylation efficiency (ACE) and in vitro Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) activity. Analysis of photosynthetic gas exchange revealed that besides constraints on mesophyll processes such as Rubisco activity, stomatal limitation also increased with increasing TFA concentration, especially in P. vulgaris. In depth analysis of the fast phase fluorescence transients pointed at TFA-induced uncoupling of the oxygen evolving complex (OEC) and inhibition of electron transport beyond Q(a) including possible constraints on the reduction of end electron acceptors of photosystem I.

Martin Gibbs and the peaceful uses of nuclear radiation, (14)C

This abstract is a prologue to this paper. Prior to his health failing, Martin Gibbs began writing remembrances of his education and beginning a science career, particularly on the peaceful uses of nuclear radiation, at the U.S. Brookhaven National Laboratory (BNL), Camp Upton, NY. Two years before his death Martin provided one of us (Govindjee) a draft text narrating his science beginnings in anticipation of publication in Photosynthesis Research. Govindjee edited his draft and returned it to him. Later, when it became difficult for him to complete it, he phoned Govindjee and expressed the desire that Govindjee publish this story, provided he kept it close to his original. Certain parts of Martin's narrations have appeared without references (Gibbs 1999). The Gibbs family made a similar request since the narrations contained numerous early personal accounts. Clanton Black recently presented an elegant tribute on Martin Gibbs and his entire science career (Black 2008). Clanton was given the draft, which he and Govindjee then agreed to finish. This chronicle is their effort to place Gibbs's narrations about his education and his maturation scientifically, in context with the beginnings of biological chemistry work with carbon-14 at the BNL (see Gibbs 1999). Further, these events are placed in context with those times of newly discovered radioisotopes which became available as part of the intensive nuclear research of World War II (WW II). Carbon-14, discovered during WW II nuclear research in 1940, was extremely useful and quickly led to the rapid discovery of new carbon metabolism pathways and biochemical cycles, e.g., photosynthetic carbon assimilation, within a decade after WW II.

Cyclic electron transport around photosystem I: genetic approaches

The light reactions in photosynthesis convert light energy into chemical energy in the form of ATP and drive the production of NADPH from NADP+. The reactions involve two types of electron flow in the chloroplast. While linear electron transport generates both ATP and NADPH, photosystem I cyclic electron transport is exclusively involved in ATP synthesis. The physiological significance of photosystem I cyclic electron transport has been underestimated, and our knowledge of the machineries involved remains very limited. However, recent genetic approaches using Arabidopsis thaliana have clarified the essential functions of this electron flow in both photoprotection and photosynthesis. Based on several lines of evidence presented here, it is necessary to reconsider the fundamental mechanisms of chloroplast energetics.

Photosynthetic phosphorylation

A brief history of the discovery of photosynthetic phosphorylation by chloroplasts and bacterial chromatophores is presented. Arnon early introduced the terminology of 'Cyclic' and 'Non-cyclic photophosphorylation' and 'Cyclic' and 'Non-Cyclic electron transport' to the processes observed in illuminated chloroplasts. He made major contributions to the elucidation of these processes and stressed their great biological significance. Investigations of the electron transport components of chromatophores have led to the isolation, purification and crystallization of bacterial reaction centers. The development of three-dimensional molecular structures, and the characterization of their electron transfer components have provided a great deal of information about the early reactions of bacterial photosynthesis. The electron transfer schemes presented clearly support the 'cyclic' nature of light-induced electron transfer. Recent developments in the understanding of ATP synthesis in oxidative phosphorylation by mitochondria and in photophosphorylation by chloroplasts and bacterial chromatophores are discussed.

Divergent pathways of photosynthetic electron transfer: The autonomous oxygenic and anoxygenic photosystems

The aim of this article is to assemble and integrate, from a personal perspective of a research participant, seldom examined evidence that is incompatible with some basic tenets of photosynthetic electron transport, the cornerstone of which is the Z scheme. The nonconforming evidence pertaining to the mode of ferredoxin reduction and the role of the copper redox protein, plastocyanin, indicates that contrary to the Z scheme ferredoxin is reduced in two experimentally distinguishable ways: oxygenically by PS II (renamed the oxygenic photosystem), without the participation of PS I, and anoxygenically by PS I (renamed the anoxygenic photosystem). It also indicates that plastocyanin is not only, as the Z scheme asserts, the electron donor to the reaction center chlorophyll of PS I (P700) but also to the reaction center chlorophyll of PS II (P680). Other unconventional findings include evidence that the fully functional oxygenic photosystem, when operating separately from the anoxygenic photosystem, reduces plastoquinone to plastoquinol and subsequently oxidizes plastoquinol by two pathways acting in concert: one being the universally recognized DBMIB-sensitive pathway via the Rieske iron-sulfur center of the cytochrome bf complex and the other, a hitherto unrecognized, DBMIB-insensitive electron transport pathway around P680 that centers on cytochrome b-559. These nonconforming findings form the basis of an alternate hypothesis of photosynthetic electron transport that modifies and complements the Z scheme.

Polyphenol oxidase and photosynthesis research

Very briefly, the present state of knowledge on the latent, lumen oriented polyphenol oxidase (PPO) of the chloroplast is reviewed. The location of PPO in the thylakoid membrane was described by D. Arnon 46 years ago. The N-terminus sequence of the spinach enzyme is reported. A historical sketch is given of the discovery of photophosphorylation and Arnon's visit to the admired O. Warburg.