Rate limiting factors in leaf photosynthesis. II. Electron transport

Chloroplast-associated molecular patterns as concept for fine-tuned operational retrograde signalling

Chloroplasts compose about one-quarter of the mesophyll cell volume and contain about 60% of the cell protein. Photosynthetic carbon assimilation is the dominating metabolism in illuminated leaves. To optimize the resource expenditure in these costly organelles and to control and adjust chloroplast metabolism, an intensive transfer of information between nucleus-cytoplasm and chloroplasts occurs in both directions as anterograde and retrograde signalling. Recent research identified multiple retrograde pathways that use metabolite transfer and include reaction products of lipids and carotenoids with reactive oxygen species (ROS). Other pathways use metabolites of carbon, sulfur and nitrogen metabolism, low molecular weight antioxidants and hormone precursors to carry information between the cell compartments. This review focuses on redox- and ROS-related retrograde signalling pathways. In analogy to the microbe-associated molecular pattern, we propose the term 'chloroplast-associated molecular pattern' which connects chloroplast performance to extrachloroplast processes such as nuclear gene transcription, posttranscriptional processing, including translation, and RNA and protein fate. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

A tribute to Ulrich Heber (1930-2016) for his contribution to photosynthesis research: understanding the interplay between photosynthetic primary reactions, metabolism and the environment

The dynamic and efficient coordination of primary photosynthetic reactions with leaf energization and metabolism under a wide range of environmental conditions is a fundamental property of plants involving processes at all functional levels. The present historical perspective covers 60 years of research aiming to understand the underlying mechanisms, linking major breakthroughs to current progress. It centers on the contributions of Ulrich Heber who had pioneered novel concepts, fundamental methods, and mechanistic understanding of photosynthesis. An important first step was the development of non-aqueous preparation of chloroplasts allowing the investigation of chloroplast metabolites ex vivo (meaning that the obtained results reflect the in vivo situation). Later on, intact chloroplasts, retaining their functional envelope membranes, were isolated in aqueous media to investigate compartmentation and exchange of metabolites between chloroplasts and external medium. These studies elucidated metabolic interaction between chloroplasts and cytoplasm during photosynthesis. Experiments with isolated intact chloroplasts clarified that oxygenation of ribulose-1.5-bisphosphate generates glycolate in photorespiration. The development of non-invasive optical methods enabled researchers identifying mechanisms that balance electron flow in the photosynthetic electron transport system avoiding its over-reduction. Recording chlorophyll a (Chl a) fluorescence allowed one to monitor, among other parameters, thermal energy dissipation by means of 'nonphotochemical quenching' of the excited state of Chl a. Furthermore, studies both in vivo and in vitro led to basic understanding of the biochemical mechanisms of freezing damage and frost tolerance of plant leaves, to SO₂ tolerance of tree leaves and dehydrating lichens and mosses.

A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species

PREMISE OF THE STUDY

RNA-seq analysis of plant transcriptomes poses unique challenges due to the highly duplicated nature of plant genomes. We address these challenges in the context of recently formed polyploid species and detail an RNA-seq experiment comparing the leaf transcriptome profile of an allopolyploid relative of soybean with the diploid species that contributed its homoeologous genomes.

METHODS

RNA-seq reads were obtained from the three species and were aligned against the genome sequence of Glycine max. Transcript levels were estimated for each gene, relative contributions of polyploidy-duplicated loci (homoeologues) in the tetraploid were identified, and comparisons of transcript profiles and individual genes were used to analyze the regulation of transcript levels.

KEY RESULTS

We present a novel metric developed to address issues arising from high degrees of gene space duplication and a method for dissecting a gene's measured transcript level in a polyploid species into the relative contribution of its homoeologues. We identify the gene family likely contributing to differences in photosynthetic rate between the allotetraploid and its progenitors and show that the tetraploid appears to be using the "redundant" gene copies in novel ways.

CONCLUSIONS

Given the prevalence of polyploidy events in plants, we believe many of the approaches developed here to be applicable, and often necessary, in most plant RNA-seq experiments. The deep sampling provided by RNA-seq allows us to dissect the genetic underpinnings of specific phenotypes as well as examine complex interactions within polyploid genomes.

Redox regulation and antioxidative defence in Arabidopsis leaves viewed from a systems biology perspective

Redox regulation is a central control element in cell metabolism. It is employed to adjust photosynthesis and the antioxidant defence system of leaves to the prevailing environment. During recent years progress has been made in describing the redox-dependent alterations in metabolism, the thiol/disulfide proteome, the redox-dependent and cross-talking signalling pathways and the target genes of redox regulation. Some transcription factors have been identified as proteins that perform thiol/disulfide transitions linked to the redox-regulation of specific plant promoters. In addition first mathematical models have been designed to simulate antioxidant defence and predict its response. Taken together, a profound experimental data set has been generated which allows to approach a systems biology type of understanding of antioxidant defence in photosynthesising cells in the near future. Since oxidative stress is likely to limit plant growth under stress, such a systematic understanding of antioxidant defence will help to define novel targets for breeding stress-tolerant plants.

Storage of light-driven transthylakoid proton motive force as an electric field (Deltapsi) under steady-state conditions in intact cells of Chlamydomonas reinhardtii

Proton motive force (pmf) is physiologically stored as either a DeltapH or a membrane potential (Deltapsi) across bacterial and mitochondrial energetic membranes. In the case of chloroplasts, previous work (Cruz et al. 2001, Biochemistry 40: 1226-1237) indicates that Deltapsi is a significant fraction of pmf, in vivo, and in vitro as long as the activities of counterions are relatively low. Kinetic analysis of light-induced changes in the electrochromic shift (ECS) in intact leaves was consistent with these observations. In this work, we took advantage of the spectroscopic properties of the green alga, Chlamydomonas reinhardtii, to demonstrate that light-driven Deltapsi was stored in vivo over the hours time scale. Analysis of the light-induced ECS kinetics suggested that the steady-state Deltapsi in 400 micromol photons m(-2) s(-1) red light was between 20 and 90 mV and that this represented about 60% of the light-induced increase in pmf. By extrapolation, it was surmised that about half of total (basal and light-induced) pmf is held as Deltapsi. It is hypothesized that Deltapsi is stabilized either by maintaining low chloroplast ionic strength or by active membrane ion transporters. In addition to the strong implications for regulation of photosynthesis by the xanthophyll cycle, these results imply that pmf partitioning is important across a wide range of species.

Photosystem I-dependent cyclic electron transport is important in controlling Photosystem II activity in leaves under conditions of water stress

Leaves of the C3 plant Brassica oleracea were illuminated with red and/or far-red light of different photon flux densities, with or without additional short pulses of high intensity red light, in air or in an atmosphere containing reduced levels of CO2 and/or oxygen. In the absence of CO2, far-red light increased light scattering, an indicator of the transthylakoid proton gradient, more than red light, although the red and far-red beams were balanced so as to excite Photosystem II to a comparable extent. On red background light, far-red supported a transthylakoid electrical field as indicated by the electrochromic P515 signal. Reducing the oxygen content of the gas phase increased far-red induced light scattering and caused a secondary decrease in the small light scattering signal induced by red light. CO2 inhibited the light-induced scattering responses irrespective of the mode of excitation. Short pulses of high intensity red light given to a background to red and/or far-red light induced appreciable additional light scattering after the flashes only, when CO2 levels were decreased to or below the CO2 compensation point, and when far-red background light was present. While pulse-induced light scattering increased, non-photochemical fluorescence quenching increased and F0 fluorescence decreased indicating increased radiationless dissipation of excitation energy even when the quinone acceptor QA in the reaction center of Photosystem II was largely oxidized. The observations indicate that in the presence of proper redox poising of the chloroplast electron transport chain cyclic electron transport supports a transthylakoid proton gradient which is capable of controlling Photosystem II activity. The data are discussed in relation to protection of the photosynthetic apparatus against photoinactivation.

Chloroplast energization and oxidation of P700/plastocyanin in illuminated leaves at reduced levels of CO2 or oxygen

Chlorophyll fluorescence, light scattering, the electrochromic shift P515 and levels of some photosynthetic intermediates were measured in illuminated leaves. Oxygen and CO2 concentrations in the gas phase were varied in order to obtain information on control of Photosystem II activity under conditions such as produced by water stress, when stomatal closure restricts access of CO2 to the photosynthetic apparatus. Light scattering and energy-dependent fluorescence quenching indicated a high level of chloroplast energization under high intensity illumination even when linear electron transport was curtailed in CO2-free air or in 1% oxygen with 35 μll(-1) CO2. Calculations of the phosphorylation potential based on measurements of phosphoglycerate, dihydroxyacetone phosphate and NADP revealed ratios of intrathylakoid to extrathylakoid proton concentrations, which were only somewhat higher in air containing 35 μl l(-1) CO2 than in CO2-free air or 1% oxygen/35 μl l(-1) CO2. Anaerobic conditions prevented appreciable chloroplast energization. Acceptor-limitation of electron flow resulted in a high reduction level of the electron transport chain, which is characterized by decreased oxidation of P700, not only under anaerobic conditions, but also in air, when CO2 was absent, and in 1% oxygen, when the CO2 concentration was reduced to 35 μll(-1). Efficient control of electron transport was indicated by the photoaccumulation of P700 (+) at or close to the CO2 compensation point in air. It is proposed to require the interplay between photorespiratory and photosynthetic electron flows, electron flow to oxygen and cyclic electron flow. The field-indicating electrochromic shift (P515) measured as a rapid absorption decrease on switching the light off followed closely the extent of photoaccumulation of P700 (+) in the light.

Concurrent measurements of oxygen- and carbon-dioxide exchange during lightflecks inAlocasia macrorrhiza (L.) G. Don

Oxygen and CO2 exchange were measured concurrently in leaves of shade-grownAlocasia macrorrhiza (L.) G. Don during lightflecks consisting of short periods of high photon flux density (PFD) superimposed on a low-PFD background illumination. Oxygen exchange was measured with a zirconium-oxide ceramic cell in an atmosphere containing 1 600 μbar O2 and 350 μbar CO2. Following an increase in PFD from 10 to 500 μmol photons·m(-2)·s(-1), O2 evolution immediately increased to a maximum rate that was about twice as high as the highest CO2-exchange rates that were observed. Oxygen evolution then decreased over the next 5-10 s to rates equal to the much more slowly increasing rates of CO2 uptake. When the PFD was decreased at the end of a lightfleck, O2 evolution decreased nearly instantaneously to the low-PFD rate while CO2 fixation continued at an elevated rate for about 20 s. When PFD during the lightfleck was at a level that was limiting for steady-state CO2 exchange, then the O2-evolution rate was constant during the lightfleck. This observed pattern of O2 evolution during lightflecks indicated that the maximum rate of electron transport exceeded the maximum rate of CO2 fixation in these leaves. In noninduced leaves, rates of O2 evolution for the first fraction of a second were about as high as rates in fully induced leaves, indicating that O2 evolution and the electron-transport chain are not directly affected by the leaf's induction state. Severalfold differences between induced and noninduced leaves in O2 evolution during a lightfleck were seen for lightflecks longer than a few seconds where the rate of O2 evolution appeared to be limited by the utilization of reducing power in CO2 fixation.

Fractional control of photosynthesis by the QB protein, the cytochrome f/b 6 complex and other components of the photosynthesic apparatus

In order to obtain information on fractional control of photosynthesis by individual catalysts, catalytic activities in photosynthetic electron transport and carbon metabolism were modified by the addition of inhibitors, and the effect on photosynthetic flux was measured using chloroplasts of Spinacia oleracea L. In thylakoids with coupled electron transport, light-limited electron flow to ferricyanide was largely controlled by the QB protein of the electron-transport chain. Fractional control by the cytochrome f/b 6 complex was insignificant under these conditions. Control by the cytochrome f/b 6 complex dominated at high energy fluence rates where the contribution to control of the QB protein was very small. Uncoupling shifted control from the cytochrome f/b 6 complex to the QB protein. Control of electron flow was more complex in assimilating chloroplasts than in thylakoids. The contributions of the cytochrome f/b 6 complex and of the QB protein to control were smaller in intact chloroplasts than in thylakoids. Thus, even though the transit time for an electron through the electron-transport chain may be below 5 ms in leaves, oxidation of plastohydroquinone was only partially responsible for limiting photosynthesis under conditions of light and CO2 saturation. The energy fluence rate influenced control coefficients. Fractional control of photosynthesis by the ATP synthetase, the cytochrome f/b 6 complex and by ribulose-1,5-bisphosphate carboxylase increased with increasing fluence rates, whereas the contributions of the QB protein and of enzymes sensitive to SH-blocking agents decreased. The results show that the burdens of control are borne by several components of the photosynthetic apparatus, and that burdens are shifted as conditions for photosynthesis change.

The analysis of photosynthesis in air and water of Ascophyllum nodosum (L.) Le Jol

The photosynthetic characteristics for the intertidal macroalga Ascophyllum nodosum were examined in air and water. Under ambient conditions of temperature (10° C) inorganic carbon concentrations (15.63 mmol CO₂ m^-3 or 2.0 mol TIC m^-3) and light (500 μmol photons m^-2 s^-1) photosynthesis was slightly greater by the exposed alga than by the submerged alga. In both environments photosynthesis was light saturated at 200 μmol photons m^-2 s^-1. The relationship between CO₂ concentration and photosynthesis in air could be accurately analysed using Michaelis-Menten kinetics, although the range of concentrations used were not saturating. In contrast the application of the Lineweaver-Burk and Woolf plots to aquatic photosynthesis was not suitable as the experimental data was similar to the Blackman type curves and not rectangular hyperbolae. This was reflected by the applicability of the Hill-Whittingham equation to describe the photosynthesis curves. The effect of unstirred layers and other limiting factors is discussed in relation to the kinetic parameters, V _max and K _m.

Photosynthetic free energy transduction related to the electric potential changes across the thylakoid membrane

A model based on our present knowledge of photosynthetic energy transduction is presented. Calculated electric potential profiles are compared with microelectrode recordings of the thylakoid electric potential during and after actinic illumination periods of intermediate duration. The information content of the measured electric response is disclosed by a comparison of experimental results with calculations. The proton flux through the ATP synthase complex is seen to markedly influence the electric response. Also the imbalance in maximum turnover rate between the two photosystems, common to obligate shade plants like Peperomia metallica used in the microelectrode experiments, is clearly reflected in the electric potential profile.

A comparative study of metabolite levels in plant leaf material in the dark

Metabolite levels have been compared in the dark and during photosynthesis in leaves and protoplasts from spinach, pea, wheat and barley. In protoplasts the subcellular distribution was also studied. The levels of triose phosphates and sugar bisphosphates were high in the light and low in the dark. The hexose phosphates and 3-phosphoglycerate levels in the dark were very variable depending on the plant material. In most conditions, hexose phosphates and triose phosphates were mainly in the extrachloroplast compartment, while 3-phosphoglycerate and the sugar bisphosphates were mainly in the chloroplast compartment. Leaves always had a very low triose phosphate: 3-phosphoglycerate ratio in the dark, but in protoplasts this ratio was higher. Detailed studies with spinach showed that metabolite levels were very dependent on the availability of carbohydrate in the leaf, particularly starch. Starch mobilisation is not controlled just by the availability of inorganic phosphate and accumulation of phosphorylated intermediates. Hydrolysis of starch may provide precursors for sucrose synthesis while phosphorolysis leads to provision of substrates for respiration. Starch breakdown generates high enough levels of hexose phosphate to support substantial rates of sucrose synthesis in the dark. Respiration is not greatly increased when metabolite levels are high during starch mobilisation. Higher levels of metabolites shorten the length of the induction phase of photosynthesis.

The relationship between the redox state of Q A and photosynthesis in leaves at various carbon-dioxide, oxygen and light regimes

The response of chlorophyll fluorescence elicited by a low-fluence-rate modulated measuring beam to actinic light and to superimposed 1-s pulses from a high-fluence-rate light source was used to measure the redox state of the primary acceptor Q A of photosystem II in leaves which were photosynthesizing under steady-state conditions. The leaves were exposed to various O2 and CO2 concentrations and to different energy fluence rates of actinic light to assess the relationship between rates of photosynthesis and the redox state of Q A. Both at low and high fluence rates, the redox state of Q A was little altered when the CO2 concentration was reduced from saturation to about 600 μl·l(-1) although photosynthesis was decreased particularly at high fluence rates. Upon further reduction in CO2 content the amount of reduced Q A increased appreciably even at low fluence rates where light limited CO2 reduction. Both in the presence and in the absence of CO2, a more reduced Q A was observed when the O2 concentration was below 2%. Q A was almost fully reduced when leaves were exposed to high fluence rates under nitrogen. Even at low fluence rates, Q A was more reduced in shade leaves of Asarum europaeum and Fagus sylvatica than in leaves of Helianthus annuus and Fagus sylvatica grown under high light. Also, in shade leaves the redox state of Q A changed more during a transition from air containing 350 μl·l(-1) CO2 to CO2-free air than in sun leaves. The results are discussed with respect to the energy status and the CO2-fixation rate of the leaves.

Chlorophyll a fluorescence and light-scattering kinetics displayed by leaves during induction of photosynthesis

Light-scattering, which can be taken as an indicator of the transthylakoid proton-gradient, and chlorophyll a fluorescence, have been followed simultaneously during re-illumination of spinach leaves at different energy fluence rates and carbon dioxide concentrations. The slow fluorescence transient ("M peak"), which has been associated with photosynthetic induction, was observed in air only at the lower fluence rates used. Data are presented that indicate that M peaks in chlorophyll fluorescence kinetics can only be observed if there is also a simultaneous transient in light-scattering and that these transients are observed when the dark period is relatively long, fluence rate relatively low, and CO2 concentration relatively high.The results are discussed in relation to the varying demands on ATP by carbon assimilation during induction of photosynthesis at different carbon dioxide concentrations and the manner in which these variations influence the quenching of chlorophyll a fluorescence.