Disulphide proteomes and interactions with thioredoxin on the track towards understanding redox regulation in chloroplasts and cyanobacteria

The impact of light and thioredoxins on the plant thiol-disulfide proteome

Thiol-based redox regulation is a crucial posttranslational mechanism to acclimate plants to changing light availability. Here, we conducted a biotin switch-based redox proteomics study in Arabidopsis (Arabidopsis thaliana) to systematically investigate dynamics of thiol-redox networks in response to temporal changes in light availability and across genotypes lacking parts of the thioredoxin (Trx) or NADPH-Trx-reductase C (NTRC) systems in the chloroplast. Time-resolved dynamics revealed light led to marked decreases in the oxidation states of many chloroplast proteins with photosynthetic functions during the first 10 min, followed by their partial reoxidation after 2 to 6 h into the photoperiod. This involved f, m, and x-type Trx proteins showing similar light-induced reduction-oxidation dynamics, while NTRC, 2-Cys peroxiredoxins, and Trx y2 showed an opposing pattern, being more oxidized in light than dark. In Arabidopsis trxf1f2, trxm1m2, or ntrc mutants, most proteins showed increased oxidation states in the light compared to wild type, suggesting their light-dependent dynamics were related to NTRC/Trx networks. While NTRC deficiency had a strong influence in all light conditions, deficiencies in f- or m-type Trxs showed differential impacts on the thiol-redox proteome depending on the light environment, being higher in constant or fluctuating light, respectively. The results indicate plant redox proteomes are subject to dynamic changes in reductive and oxidative pathways to cooperatively fine-tune photosynthetic and metabolic processes in the light. The importance of the individual elements of the NTRC/Trx networks mediating these responses depend on the extent of light variability, with NTRC playing a crucial role to balance protein-redox states in rapidly fluctuating light.

PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions

Post-translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python-based workflow, called PTM-Psi, integrates several established open-source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non-standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S-nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM-Psi for interpreting sequence-structure-function relationships derived from thiol redox proteomics data. We demonstrate that the S-nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

The interplay of post-translational protein modifications in Arabidopsis leaves during photosynthesis induction

Diurnal dark to light transition causes profound physiological changes in plant metabolism. These changes require distinct modes of regulation as a unique feature of photosynthetic lifestyle. The activities of several key metabolic enzymes are regulated by light-dependent post-translational modifications (PTM) and have been studied at depth at the level of individual proteins. In contrast, a global picture of the light-dependent PTMome dynamics is lacking, leaving the response of a large proportion of cellular function undefined. Here, we investigated the light-dependent metabolome and proteome changes in Arabidopsis rosettes in a time resolved manner to dissect their kinetic interplay, focusing on phosphorylation, lysine acetylation, and cysteine-based redox switches. Of over 24 000 PTM sites that were detected, more than 1700 were changed during the transition from dark to light. While the first changes, as measured 5 min after onset of illumination, occurred mainly in the chloroplasts, PTM changes at proteins in other compartments coincided with the full activation of the Calvin-Benson cycle and the synthesis of sugars at later timepoints. Our data reveal connections between metabolism and PTM-based regulation throughout the cell. The comprehensive multiome profiling analysis provides unique insight into the extent by which photosynthesis reprograms global cell function and adds a powerful resource for the dissection of diverse cellular processes in the context of photosynthetic function.

Circadian regulation of metabolism across photosynthetic organisms

Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.

Microcystin aids in cold temperature acclimation: Differences between a toxic Microcystis wildtype and non-toxic mutant

For Microcystis aeruginosa PCC 7806, temperature decreases from 26 °C to 19 °C double the microcystin quota per cell during growth in continuous culture. Here we tested whether this increase in microcystin provided M. aeruginosa PCC 7806 with a fitness advantage during colder-temperature growth by comparing cell concentration, cellular physiology, reactive oxygen species damage, and the transcriptomics-inferred metabolism to a non-toxigenic mutant strain M. aeruginosa PCC 7806 ΔmcyB. Photo-physiological data combined with transcriptomic data revealed metabolic changes in the mutant strain during growth at 19 °C, which included increased electron sinks and non-photochemical quenching. Increased gene expression was observed for a glutathione-dependent peroxiredoxin during cold treatment, suggesting compensatory mechanisms to defend against reactive oxygen species are employed in the absence of microcystin in the mutant. Our observations highlight the potential selective advantages of a longer-term defensive strategy in management of oxidative stress (i.e., making microcystin) vs the shorter-term proactive strategy of producing cellular components to actively dissipate or degrade oxidative stress agents.

Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation

Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated.

Cool temperature acclimation in toxigenic Microcystis aeruginosa PCC 7806 and its non-toxigenic mutant

For Microcystis aeruginosa PCC 7806, temperature decreases from 26° C to 19° C double the microcystin quota per cell during growth in continuous culture. Here we tested whether this increase in microcystin provided M. aeruginosa PCC 7806 with a fitness advantage during colder-temperature growth by comparing cell concentration, cellular physiology, and the transcriptomics-inferred metabolism to a non-toxigenic mutant strain M. aeruginosa PCC 7806 ΔmcyB. Photo-physiological data combined with transcriptomic data revealed metabolic changes in the mutant strain during growth at 19° C, which included increased electron sinks and non-photochemical quenching. Increased gene expression was observed for a glutathione-dependent peroxiredoxin during cold treatment, suggesting compensatory mechanisms to defend against reactive oxygen species are employed in the absence of microcystin in the mutant. Our observations highlight the potential selective advantages of a longer-term defensive strategy in management of oxidative stress (i.e., making microcystin) vs the shorter-term proactive strategy of producing cellular components to actively dissipate or degrade oxidative stress agents.

SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features

Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin-like protein of the cyanobacterium Synechocystis sp. PCC 6803, forms ordered oligomers in solution. The 3.7 Å resolution cryo-EM structure of SynDLP oligomers reveals the presence of oligomeric stalk interfaces typical for eukaryotic dynamin-like proteins. The bundle signaling element domain shows distinct features, such as an intramolecular disulfide bridge that affects the GTPase activity, or an expanded intermolecular interface with the GTPase domain. In addition to typical GD-GD contacts, such atypical GTPase domain interfaces might be a GTPase activity regulating tool in oligomerized SynDLP. Furthermore, we show that SynDLP interacts with and intercalates into membranes containing negatively charged thylakoid membrane lipids independent of nucleotides. The structural characteristics of SynDLP oligomers suggest it to be the closest known bacterial ancestor of eukaryotic dynamin.

The atypical thioredoxin 'Alr2205', a newly identified partner of the typical 2-Cys-Peroxiredoxin, safeguards the cyanobacterium Anabaena from oxidative stress

Thioredoxins (Trxs) are ubiquitous proteins that play vital roles in several physiological processes. Alr2205, a thioredoxin-like protein from Anabaena PCC 7120, was found to be evolutionarily closer to the Trx-domain of the NADPH-Thioredoxin Reductase C than the other thioredoxins. The Alr2205 protein showed disulfide reductase activity despite the presence a non-canonical active site motif 'CPSC'. Alr2205 not only physically interacted with, but also acted as a physiological reductant of Alr4641 (the typical 2-Cys-Peroxiredoxin from Anabaena), supporting its peroxidase function. Structurally, Alr2205 was a monomeric protein that formed an intramolecular disulfide bond between the two active site cysteines (Cys-38 and Cys-41). However, the Alr2205C41S protein, wherein the resolving cysteine was mutated to serine, was capable of forming intermolecular disulfide bond and exist as a dimer when treated with H2O2. Overproduction of Alr2205 in E. coli protected cells from heavy metals, but not oxidative stress. To delve into its physiological role, Alr2205/Alr2205C41S was overexpressed in Anabaena, and the ability of the corresponding strains (An2205+ or An2205C41S+) to withstand environmental stresses was assessed. An2205+ showed higher resistance to H2O2 than An2205C41S+, indicating that the disulfide reductase function of this protein was critical to protect cells from this peroxide. Although, An2205+ did not show increased capability to withstand cadmium stress, An2205C41S+ was more susceptible to this heavy metal. This is the first study that provides a vital understanding into the function of atypical thioredoxins in countering the toxic effects of heavy metals/H2O2 in prokaryotes.

Cross Talk between Hydrogen Peroxide and Nitric Oxide in the Unicellular Green Algae Cell Cycle: How Does It Work?

The regulatory role of some reactive oxygen species (ROS) and reactive nitrogen species (RNS), such as hydrogen peroxide or nitric oxide, has been demonstrated in some higher plants and algae. Their involvement in regulation of the organism, tissue and single cell development can also be seen in many animals. In green cells, the redox potential is an important photosynthesis regulatory factor that may lead to an increase or decrease in growth rate. ROS and RNS are important signals involved in the regulation of photoautotrophic growth that, in turn, allow the cell to attain the commitment competence. Both hydrogen peroxide and nitric oxide are directly involved in algal cell development as the signals that regulate expression of proteins required for completing the cell cycle, such as cyclins and cyclin-dependent kinases, or histone proteins and E2F complex proteins. Such regulation seems to relate to the direct interaction of these signaling molecules with the redox-sensitive transcription factors, but also with regulation of signaling pathways including MAPK, G-protein and calmodulin-dependent pathways. In this paper, we aim to elucidate the involvement of hydrogen peroxide and nitric oxide in algal cell cycle regulation, considering the role of these molecules in higher plants. We also evaluate the commercial applicability of this knowledge. The creation of a simple tool, such as a precisely established modification of hydrogen peroxide and/or nitric oxide at the cellular level, leading to changes in the ROS-RNS cross-talk network, can be used for the optimization of the efficiency of algal cell growth and may be especially important in the context of increasing the role of algal biomass in science and industry. It could be a part of an important scientific challenge that biotechnology is currently focused on.

Redox and Hormonal Changes in the Transcriptome of Grape (Vitis vinifera) Berries during Natural Noble Rot Development

Noble rot is a favorable form of the interaction between grape (Vitis spp.) berries and the phytopathogenic fungus Botrytis cinerea. The transcriptome pattern of grapevine cells subject to natural noble rot development in the historic Hungarian Tokaj wine region has not been previously published. Furmint, a traditional white Tokaj variety suited to develop great quality noble rot was used in the experiments. Exploring a subset of the Furmint transcriptome redox and hormonal changes distinguishing between noble rot and bunch rot was revealed. Noble rot is defined by an early spike in abscisic acid (ABA) accumulation and a pronounced remodeling of ABA-related gene expression. Transcription of glutathione S-transferase isoforms is uniquely upregulated, whereas gene expression of some sectors of the antioxidative apparatus (e.g., catalases, carotenoid biosynthesis) is downregulated. These mRNA responses are lacking in berries exposed to bunch rot. Our results help to explain molecular details behind the fine and dynamic balance between noble rot and bunch rot development.

Current Knowledge on Mechanisms Preventing Photosynthesis Redox Imbalance in Plants

Photosynthesis includes a set of redox reactions that are the source of reducing power and energy for the assimilation of inorganic carbon, nitrogen and sulphur, thus generating organic compounds, and oxygen, which supports life on Earth. As sessile organisms, plants have to face continuous changes in environmental conditions and need to adjust the photosynthetic electron transport to prevent the accumulation of damaging oxygen by-products. The balance between photosynthetic cyclic and linear electron flows allows for the maintenance of a proper NADPH/ATP ratio that is adapted to the plant’s needs. In addition, different mechanisms to dissipate excess energy operate in plants to protect and optimise photosynthesis under adverse conditions. Recent reports show an important role of redox-based dithiol–disulphide interchanges, mediated both by classical and atypical chloroplast thioredoxins (TRXs), in the control of these photoprotective mechanisms. Moreover, membrane-anchored TRX-like proteins, such as HCF164, which transfer electrons from stromal TRXs to the thylakoid lumen, play a key role in the regulation of lumenal targets depending on the stromal redox poise. Interestingly, not all photoprotective players were reported to be under the control of TRXs. In this review, we discuss recent findings regarding the mechanisms that allow an appropriate electron flux to avoid the detrimental consequences of photosynthesis redox imbalances.

β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study

Non-proteinogenic neurotoxic amino acid β-N-methylamino-L-alanine (BMAA) is synthesized by cyanobacteria, diatoms, and dinoflagellates, and is known to be a causative agent of human neurodegenerative diseases. Different phytoplankton organisms' ability to synthesize BMAA could indicate the importance of this molecule in the interactions between microalgae in nature. We were interested in the following: what kinds of mechanisms underline BMAA's action on cyanobacterial cells in different nitrogen supply conditions. Herein, we present a proteomic analysis of filamentous cyanobacteria Nostoc sp. PCC 7120 cells that underwent BMAA treatment in diazotrophic conditions. In diazotrophic growth conditions, to survive, cyanobacteria can use only biological nitrogen fixation to obtain nitrogen for life. Note that nitrogen fixation is an energy-consuming process. In total, 1567 different proteins of Nostoc sp. PCC 7120 were identified by using LC-MS/MS spectrometry. Among them, 123 proteins belonging to different functional categories were selected-due to their notable expression differences-for further functional analysis and discussion. The presented proteomic data evidences that BMAA treatment leads to very strong (up to 80%) downregulation of α (NifD) and β (NifK) subunits of molybdenum-iron protein, which is known to be a part of nitrogenase. This enzyme is responsible for catalyzing nitrogen fixation. The genes nifD and nifK are under transcriptional control of a global nitrogen regulator NtcA. In this study, we have found that BMAA impacts in a total of 22 proteins that are under the control of NtcA. Moreover, BMAA downregulates 18 proteins that belong to photosystems I or II and light-harvesting complexes; BMAA treatment under diazotrophic conditions also downregulates five subunits of ATP synthase and enzyme NAD(P)H-quinone oxidoreductase. Therefore, we can conclude that the disbalance in energy and metabolite amounts leads to severe intracellular stress that induces the upregulation of stress-activated proteins, such as starvation-inducible DNA-binding protein, four SOS-response enzymes, and DNA repair enzymes, nine stress-response enzymes, and four proteases. The presented data provide new leads into the ecological impact of BMAA on microalgal communities that can be used in future investigations.

Two chloroplast thioredoxin systems differentially modulate photosynthesis in Arabidopsis depending on light intensity and leaf age

Various regulatory mechanisms have evolved in plants to optimize photosynthetic activity under fluctuating light. Thioredoxins (TRX) are members of the regulatory network balancing activities of light and carbon fixation reactions in chloroplasts. We have studied the impact of two chloroplast TRX systems, the ferredoxin-dependent TRX reductase (FTR) and the NADPH-dependent TRX reductase C (NTRC) on regulation of photosynthesis by mutants lacking or overexpressing a component of either system. Plants were subjected to image-based phenotyping and chlorophyll fluorescence measurements that allow long-term monitoring of the development and photosynthetic activity of the rosettes, respectively. Our experiments demonstrate that NTRC and FTR systems respond differently to variation of light intensity. NTRC was an indispensable regulator of photosynthesis in young leaves, at light-intensity transitions and under low light intensities limiting photosynthesis, whereas steady-state exposure of plants to growth or higher light intensities diminished the need of NTRC in regulation of photosynthesis. In fluctuating light, overexpression of NTRC increased the quantum yield of Photosystem II (YII) at low light and stimulated the relaxation of non-photochemical quenching (NPQ) after high light exposure, indicating that overexpression of NTRC improves leaf capacity to convert light energy to chemical energy under these conditions. Overexpression of chimeric protein (NTR-TRXf) containing both the thioredoxin reductase and TRXf activity on an ntrc mutant background, did not completely recover either growth or steady-state photosynthetic activity, whereas OE-NTR-TRXf plants exposed to fluctuating light regained the wild-type level of Y(II) and NPQ.

Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana

Thiol-based redox regulation is a post-translational protein modification for controlling enzyme activity by switching oxidation/reduction states of Cys residues. In plant cells, numerous proteins involved in a wide range of biological systems have been suggested as the target of redox regulation; however, our knowledge on this issue is still incomplete. Here we report that 3-phosphoglycerate dehydrogenase (PGDH) is a novel redox-regulated protein. PGDH catalyzes the first committed step of Ser biosynthetic pathway in plastids. Using an affinity chromatography-based method, we found that PGDH physically interacts with thioredoxin (Trx), a key factor of redox regulation. The in vitro studies using recombinant proteins from Arabidopsis thaliana showed that a specific PGDH isoform, PGDH1, forms the intramolecular disulfide bond under nonreducing conditions, which lowers PGDH enzyme activity. MS and site-directed mutagenesis analyses allowed us to identify the redox-active Cys pair that is mainly involved in disulfide bond formation in PGDH1; this Cys pair is uniquely found in land plant PGDH. Furthermore, we revealed that some plastidial Trx subtypes support the reductive activation of PGDH1. The present data show previously uncharacterized regulatory mechanisms of PGDH and expand our understanding of the Trx-mediated redox-regulatory network in plants.

Photosynthesis in a Changing Global Climate: Scaling Up and Scaling Down in Crops

Photosynthesis is the major process leading to primary production in the Biosphere. There is a total of 7000bn tons of CO2 in the atmosphere and photosynthesis fixes more than 100bn tons annually. The CO2 assimilated by the photosynthetic apparatus is the basis of crop production and, therefore, of animal and human food. This has led to a renewed interest in photosynthesis as a target to increase plant production and there is now increasing evidence showing that the strategy of improving photosynthetic traits can increase plant yield. However, photosynthesis and the photosynthetic apparatus are both conditioned by environmental variables such as water availability, temperature, [CO2], salinity, and ozone. The "omics" revolution has allowed a better understanding of the genetic mechanisms regulating stress responses including the identification of genes and proteins involved in the regulation, acclimation, and adaptation of processes that impact photosynthesis. The development of novel non-destructive high-throughput phenotyping techniques has been important to monitor crop photosynthetic responses to changing environmental conditions. This wealth of data is being incorporated into new modeling algorithms to predict plant growth and development under specific environmental constraints. This review gives a multi-perspective description of the impact of changing environmental conditions on photosynthetic performance and consequently plant growth by briefly highlighting how major technological advances including omics, high-throughput photosynthetic measurements, metabolic engineering, and whole plant photosynthetic modeling have helped to improve our understanding of how the photosynthetic machinery can be modified by different abiotic stresses and thus impact crop production.

Plant Chloroplast Stress Response: Insights from Thiol Redox Proteomics

Significance: Plant chloroplasts generate reactive oxygen species (ROS) during photosynthesis, especially under stresses. The sulfhydryl groups of protein cysteine residues are susceptible to redox modifications, which regulate protein structure and function, and thus different signaling and metabolic processes. The ROS-governed protein thiol redox switches play important roles in chloroplasts. Recent Advances: Various high-throughput thiol redox proteomic approaches have been developed, and they have enabled the improved understanding of redox regulatory mechanisms in chloroplasts. For example, the thioredoxin-modulated antioxidant enzymes help to maintain cellular ROS homeostasis. The light- and dark-dependent redox regulation of photosynthetic electron transport, the Calvin/Benson cycle, and starch biosynthesis ensures metabolic coordination and efficient energy utilization. In addition, redox cascades link the light with the dynamic changes of metabolites in nitrate and sulfur assimilation, shikimate pathway, and biosynthesis of fatty acid hormone as well as purine, pyrimidine, and thiamine. Importantly, redox regulation of tetrapyrrole and chlorophyll biosynthesis is critical to balance the photodynamic tetrapyrrole intermediates and prevent oxidative damage. Moreover, redox regulation of diverse elongation factors, chaperones, and kinases plays an important role in the modulation of gene expression, protein conformation, and posttranslational modification that contribute to photosystem II (PSII) repair, state transition, and signaling in chloroplasts. Critical Issues: This review focuses on recent advances in plant thiol redox proteomics and redox protein networks toward understanding plant chloroplast signaling, metabolism, and stress responses. Future Directions: Using redox proteomics integrated with biochemical and molecular genetic approaches, detailed studies of cysteine residues, their redox states, cross talk with other modifications, and the functional implications will yield a holistic understanding of chloroplast stress responses.

Kandelia candel Thioredoxin f Confers Osmotic Stress Tolerance in Transgenic Tobacco

Water deficit caused by osmotic stress and drought limits crop yield and tree growth worldwide. Screening and identifying candidate genes from stress-resistant species are a genetic engineering strategy to increase drought resistance. In this study, an increased concentration of mannitol resulted in elevated expression of thioredoxin f (KcTrxf) in the nonsecretor mangrove species Kandelia candel. By means of amino acid sequence and phylogenetic analysis, the mangrove Trx was classified as an f-type thioredoxin. Subcellular localization showed that KcTrxf localizes to chloroplasts. Enzymatic activity characterization revealed that KcTrxf recombinant protein possesses the disulfide reductase function. KcTrxf overexpression contributes to osmotic and drought tolerance in tobacco in terms of fresh weight, root length, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) production. KcTrxf was shown to reduce the stomatal aperture by enhancing K+ efflux in guard cells, which increased the water-retaining capacity in leaves under drought conditions. Notably, the abscisic acid (ABA) sensitivity was increased in KcTrxf-transgenic tobacco, which benefits plants exposed to drought by reducing water loss by promoting stomatal closure. KcTrxf-transgenic plants limited drought-induced H2O2 in leaves, which could reduce lipid peroxidation and retain the membrane integrity. Additionally, glutathione (GSH) contributing to reactive oxygen species (ROS) scavenging and transgenic plants are more efficient at regenerating GSH from oxidized glutathione (GSSG) under conditions of drought stress. Notably, KcTrxf-transgenic plants had increased glucose and fructose contents under drought stress conditions, presumably resulting from KcTrxf-promoted starch degradation under water stress. We conclude that KcTrxf contributes to drought tolerance by increasing the water status, by enhancing osmotic adjustment, and by maintaining ROS homeostasis in transgene plants.

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

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

Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins

Thioredoxin (Trx) is a redox-responsive protein that modulates the activities of its target proteins mostly by reducing their disulfide bonds. In chloroplasts, five Trx isoforms (Trx-f, Trx-m, Trx-x, Trx-y, and Trx-z) regulate various photosynthesis-related enzymes with distinct target selectivity. To elucidate the determinants of the target selectivity of each Trx isoform, here we investigated the residues responsible for target recognition by Trx-f, the most well-studied chloroplast-resident Trx. As reported previously, we found that positively-charged residues on the Trx-f surface are involved in the interactions with its targets. Moreover, several residues that are specifically conserved in Trx-f (e.g. Cys-126 and Thr-158) were also involved in interactions with target proteins. The validity of these residues was examined by the molecular dynamics simulation. In addition, we validated the impact of these key residues on target protein reduction by studying (i) Trx-m variants into which we introduced the key residues for Trx-f and (ii) Trx-like proteins, named atypical Cys His-rich Trx 1 (ACHT1) and ACHT2a, that also contain these key residues. These artificial or natural protein variants could reduce Trx-f-specific targets, indicating that the key residues for Trx-f are critical for Trx-f-specific target recognition. Furthermore, we demonstrate that ACHT1 and ACHT2a efficiently oxidize some Trx-f-specific targets, suggesting that its target selectivity also contributes to the oxidative regulation process. Our results reveal the key residues for Trx-f-specific target recognition and uncover ACHT1 and ACHT2a as oxidation factors of their target proteins, providing critical insight into redox regulation of photosynthesis.

Chloroplast thioredoxin systems dynamically regulate photosynthesis in plants

Photosynthesis is a highly regulated process in photoautotrophic cells. The main goal of the regulation is to keep the basic photosynthetic reactions, i.e. capturing light energy, conversion into chemical energy and production of carbohydrates, in balance. The rationale behind the evolution of strong regulation mechanisms is to keep photosynthesis functional under all conditions encountered by sessile plants during their lifetimes. The regulatory mechanisms may, however, also impair photosynthetic efficiency by overriding the photosynthetic reactions in controlled environments like crop fields or bioreactors, where light energy could be used for production of sugars instead of dissipation as heat and down-regulation of carbon fixation. The plant chloroplast has a high number of regulatory proteins called thioredoxins (TRX), which control the function of chloroplasts from biogenesis and assembly of chloroplast machinery to light and carbon fixation reactions as well as photoprotective mechanisms. Here, we review the current knowledge of regulation of photosynthesis by chloroplast TRXs and assess the prospect of improving plant photosynthetic efficiency by modification of chloroplast thioredoxin systems.

A Hard Day's Night: Cyanobacteria in Diel Cycles

Cyanobacteria are photosynthetic prokaryotes that are influential in global geochemistry and are promising candidates for industrial applications. Because the livelihood of cyanobacteria is directly dependent upon light, a comprehensive understanding of metabolism in these organisms requires taking into account the effects of day-night transitions and circadian regulation. These events synchronize intracellular processes with the solar day. Accordingly, metabolism is controlled and structured differently in cyanobacteria than in heterotrophic bacteria. Thus, the approaches applied to engineering heterotrophic bacteria will need to be revised for the cyanobacterial chassis. Here, we summarize important findings related to diurnal metabolism in cyanobacteria and present open questions in the field.

Structural rearrangements in the C-terminal domain homolog of Orange Carotenoid Protein are crucial for carotenoid transfer

A recently reported family of soluble cyanobacterial carotenoproteins, homologs of the C-terminal domain (CTDH) of the photoprotective Orange Carotenoid Protein, is suggested to mediate carotenoid transfer from the thylakoid membrane to the Helical Carotenoid Proteins, which are paralogs of the N-terminal domain of the OCP. Here we present the three-dimensional structure of a carotenoid-free CTDH variant from Anabaena (Nostoc) PCC 7120. This CTDH contains a cysteine residue at position 103. Two dimer-forming interfaces were identified, one stabilized by a disulfide bond between monomers and the second between each monomer's β-sheets, both compatible with small-angle X-ray scattering data and likely representing intermediates of carotenoid transfer processes. The crystal structure revealed a major positional change of the C-terminal tail. Further mutational analysis revealed the importance of the C-terminal tail in both carotenoid uptake and delivery. These results have allowed us to suggest a detailed model for carotenoid transfer via these soluble proteins.

The Unprecedented Versatility of the Plant‎ Thioredoxin System

Thioredoxins are ubiquitous enzymes catalyzing reversible disulfide-bond formation to regulate structure and function of many proteins in diverse organisms. In recent years, reverse genetics and biochemical approaches were used to resolve the functions, specificities, and interactions of the different thioredoxin isoforms and reduction systems in planta and revealed the most versatile thioredoxin system of all organisms. Here we review the emerging roles of the thioredoxin system, namely the integration of thylakoid energy transduction, metabolism, gene expression, growth, and development under fluctuating environmental conditions. We argue that these new developments help us to understand why plants organize such a divergent composition of thiol redox networks and provide insights into the regulatory hierarchy that operates between them.

Redox crisis underlies conditional light-dark lethality in cyanobacterial mutants that lack the circadian regulator, RpaA

Cyanobacteria evolved a robust circadian clock, which has a profound influence on fitness and metabolism under daily light-dark (LD) cycles. In the model cyanobacterium Synechococcus elongatus PCC 7942, a functional clock is not required for diurnal growth, but mutants defective for the response regulator that mediates transcriptional rhythms in the wild-type, regulator of phycobilisome association A (RpaA), cannot be cultured under LD conditions. We found that rpaA-null mutants are inviable after several hours in the dark and compared the metabolomes of wild-type and rpaA-null strains to identify the source of lethality. Here, we show that the wild-type metabolome is very stable throughout the night, and this stability is lost in the absence of RpaA. Additionally, an rpaA mutant accumulates excessive reactive oxygen species (ROS) during the day and is unable to clear it during the night. The rpaA-null metabolome indicates that these cells are reductant-starved in the dark, likely because enzymes of the primary nighttime NADPH-producing pathway are direct targets of RpaA. Because NADPH is required for processes that detoxify ROS, conditional LD lethality likely results from inability of the mutant to activate reductant-requiring pathways that detoxify ROS when photosynthesis is not active. We identified second-site mutations and growth conditions that suppress LD lethality in the mutant background that support these conclusions. These results provide a mechanistic explanation as to why rpaA-null mutants die in the dark, further connect the clock to metabolism under diurnal growth, and indicate that RpaA likely has important unidentified functions during the day.

Identification of dimedone-trapped sulfenylated proteins in plants under stress

In stressed plants, the reactive oxygen species (ROS) levels rise. Key to ROS signaling research are detection and identification of the protein cysteine sulfenylation (-SOH), the ROS-mediated oxidative product of a thiol (-SH). Arabidopsis thaliana seedlings were stressed with hydrogen peroxide (H₂O₂) and the sulfenylated proteins were tagged with dimedone. Dimedone-tagged sulfenic acid proteins were visualized on a two-dimensional electrophoresis (2DE) immunoblot with an anticysteine sulfenic acid antibody and were subsequently detected by mass spectrometry. We optimized the detection method for protein sulfenylation in Arabidopsis. We conclude that dimedone can penetrate the cell wall, does not stress plants, and can "read" the changes in the protein sulfenylation pattern under oxidative stress. We observed that the number of sulfenylated proteins in plants treated with 10 mM H₂O₂ was higher than that in untreated plants. A total of 39 sulfenylated protein spots were found on 2DE immunoblots. By means of mass spectrometry, 11 sulfenylated proteins were discovered involved in primary metabolism, redox regulation, translation and signaling pathways. Hence, by combining an immunochemical 2DE strategy with mass spectrometry, we were able to identify sulfenylated proteins in H₂O₂-stressed Arabidopsis seedlings. The sulfenylated proteins can be considered for further validation as redox regulators in plants.

Microcystin-Bound Protein Patterns in Different Cultures of Microcystis aeruginosa and Field Samples

Micocystin (MC) exists in Microcystis cells in two different forms, free and protein-bound. We examined the dynamic change in extracellular free MCs, intracellular free MCs and protein-bound MCs in both batch cultures and semi-continuous cultures, using high performance liquid chromatography and Western blot. The results showed that the free MC per cell remained constant, while the quantity of protein-bound MCs increased with the growth of Microcystis cells in both kinds of culture. Significant changes in the dominant MC-bound proteins occurred in the late exponential growth phase of batch cultures, while the dominant MC-bound proteins in semi-continuous cultures remained the same. In field samples collected at different months in Lake Taihu, the dominant MC-bound proteins were shown to be similar, but the amount of protein-bound MC varied and correlated with the intracellular MC content. We identified MC-bound proteins by two-dimensional electrophoresis immunoblots and mass spectrometry. The 60 kDa chaperonin GroEL was a prominent MC-bound protein. Three essential glycolytic enzymes and ATP synthase alpha subunit were also major targets of MC-binding, which might contribute to sustained growth in semi-continuous culture. Our results indicate that protein-bound MC may be important for sustaining growth and adaptation of Microcystis sp.

The Path to Thioredoxin and Redox Regulation in Chloroplasts

After a brief discussion of my graduate work at Duke University, I describe a series of investigations on redox proteins at the University of California, Berkeley. Starting with ferredoxin from fermentative bacteria, the Berkeley research fostered experiments that uncovered a pathway for fixing CO2 in bacterial photosynthesis. The carbon work, in turn, opened new vistas, including the discovery that thioredoxin functions universally in regulating the Calvin-Benson cycle in oxygenic photosynthesis. These experiments, which took place over a 50-year period, led to the formulation of a set of biological principles and set the stage for research demonstrating a role for redox in the regulation of previously unrecognized processes extending far beyond photosynthesis.

The chloroplast NADPH thioredoxin reductase C, NTRC, controls non-photochemical quenching of light energy and photosynthetic electron transport in Arabidopsis

High irradiances may lead to photooxidative stress in plants, and non-photochemical quenching (NPQ) contributes to protection against excess excitation. One of the NPQ mechanisms, qE, involves thermal dissipation of the light energy captured. Importantly, plants need to tune down qE under light-limiting conditions for efficient utilization of the available quanta. Considering the possible redox control of responses to excess light implying enzymes, such as thioredoxins, we have studied the role of the NADPH thioredoxin reductase C (NTRC). Whereas Arabidopsis thaliana plants lacking NTRC tolerate high light intensities, these plants display drastically elevated qE, have larger trans-thylakoid ΔpH and have 10-fold higher zeaxanthin levels under low and medium light intensities, leading to extremely low linear electron transport rates. To test the impact of the high qE on plant growth, we generated an ntrc-psbs double-knockout mutant, which is devoid of qE. This double mutant grows faster than the ntrc mutant and has a higher chlorophyll content. The photosystem II activity is partially restored in the ntrc-psbs mutant, and linear electron transport rates under low and medium light intensities are twice as high as compared with plants lacking ntrc alone. These data uncover a new role for NTRC in the control of photosynthetic yield.

Redox regulation in the thylakoid lumen

Higher plants need to balance the efficiency of light energy absorption and dissipative photo-protection when exposed to fluctuations in light quantity and quality. This aim is partially realized through redox regulation within the chloroplast, which occurs in all chloroplast compartments except the envelope intermembrane space. In contrast to the chloroplast stroma, less attention has been paid to the thylakoid lumen, an inner, continuous space enclosed by the thylakoid membrane in which redox regulation is also essential for photosystem biogenesis and function. This sub-organelle compartment contains at least 80 lumenal proteins, more than 30 of which are known to contain disulfide bonds. Thioredoxins (Trx) in the chloroplast stroma are photo-reduced in the light, transferring reducing power to the proteins in the thylakoid membrane and ultimately the lumen through a trans-thylakoid membrane-reduced, equivalent pathway. The discovery of lumenal thiol oxidoreductase highlights the importance of the redox regulation network in the lumen for controlling disulfide bond formation, which is responsible for protein activity and folding and even plays a role in photo-protection. In addition, many lumenal members involved in photosystem assembly and non-photochemical quenching are likely required for reduction and/or oxidation to maintain their proper efficiency upon changes in light intensity. In light of recent findings, this review summarizes the multiple redox processes that occur in the thylakoid lumen in great detail, highlighting the essential auxiliary roles of lumenal proteins under fluctuating light conditions.

Advancing understanding of microbial bioenergy conversion processes by activity-based protein profiling

The development of renewable biofuels is a global priority, but success will require novel technologies that greatly improve our understanding of microbial systems biology. An approach with great promise in enabling functional characterization of microbes is activity-based protein profiling (ABPP), which employs chemical probes to directly measure enzyme function in discrete enzyme classes in vivo and/or in vitro, thereby facilitating the rapid discovery of new biocatalysts and enabling much improved biofuel production platforms. We review general design strategies in ABPP, and highlight recent advances that are or could be pivotal to biofuels processes including applications of ABPP to cellulosic bioethanol, biodiesel, and phototrophic production of hydrocarbons. We also examine the key challenges and opportunities of ABPP in renewable biofuels research. The integration of ABPP with molecular and systems biology approaches will shed new insight on the catalytic and regulatory mechanisms of functional enzymes and their synergistic effects in the field of biofuels production.

Photosystem II repair in plant chloroplasts--Regulation, assisting proteins and shared components with photosystem II biogenesis

Photosystem (PS) II is a multisubunit thylakoid membrane pigment-protein complex responsible for light-driven oxidation of water and reduction of plastoquinone. Currently more than 40 proteins are known to associate with PSII, either stably or transiently. The inherent feature of the PSII complex is its vulnerability in light, with the damage mainly targeted to one of its core proteins, the D1 protein. The repair of the damaged D1 protein, i.e. the repair cycle of PSII, initiates in the grana stacks where the damage generally takes place, but subsequently continues in non-appressed thylakoid domains, where many steps are common for both the repair and de novo assembly of PSII. The sequence of the (re)assembly steps of genuine PSII subunits is relatively well-characterized in higher plants. A number of novel findings have shed light into the regulation mechanisms of lateral migration of PSII subcomplexes and the repair as well as the (re)assembly of the complex. Besides the utmost importance of the PSII repair cycle for the maintenance of PSII functionality, recent research has pointed out that the maintenance of PSI is closely dependent on regulation of the PSII repair cycle. This review focuses on the current knowledge of regulation of the repair cycle of PSII in higher plant chloroplasts. Particular emphasis is paid on sequential assembly steps of PSII and the function of the number of PSII auxiliary proteins involved both in the biogenesis and repair of PSII. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Electron-transfer kinetics in cyanobacterial cells: methyl viologen is a poor inhibitor of linear electron flow

The inhibitor methyl viologen (MV) has been widely used in photosynthesis to study oxidative stress. Its effects on electron transfer kinetics in Synechocystis sp. PCC6803 cells were studied to characterize its electron-accepting properties. For the first hundreds of flashes following MV addition at submillimolar concentrations, the kinetics of NADPH formation were hardly modified (less than 15% decrease in signal amplitude) with a significant signal decrease only observed after more flashes or continuous illumination. The dependence of the P700 photooxidation kinetics on the MV concentration exhibited a saturation effect at 0.3 mM MV, a concentration which inhibits the recombination reactions in photosystem I. The kinetics of NADPH formation and decay under continuous light with MV at 0.3 mM showed that MV induces the oxidation of the NADP pool in darkness and that the yield of linear electron transfer decreased by only 50% after 1.5-2 photosystem-I turnovers. The unexpectedly poor efficiency of MV in inhibiting NADPH formation was corroborated by in vitro flash-induced absorption experiments with purified photosystem-I, ferredoxin and ferredoxin-NADP(+)-oxidoreductase. These experiments showed that the second-order rate constants of MV reduction are 20 to 40-fold smaller than the competing rate constants involved in reduction of ferredoxin and ferredoxin-NADP(+)-oxidoreductase. The present study shows that MV, which accepts electrons in vivo both at the level of photosystem-I and ferredoxin, can be used at submillimolar concentrations to inhibit recombination reactions in photosystem-I with only a moderate decrease in the efficiency of fast reactions involved in linear electron transfer and possibly cyclic electron transfer.

Plastidic type I signal peptidase 1 is a redox-dependent thylakoidal processing peptidase

Thylakoids are the photosynthetic membranes in chloroplasts and cyanobacteria. The aqueous phase inside the thylakoid known as the thylakoid lumen plays an essential role in the photosynthetic electron transport. The presence and significance of thiol-disulfide exchange in this compartment have been recognized but remain poorly understood. All proteins found free in the thylakoid lumen and some proteins associated to the thylakoid membrane require an N-terminal targeting signal, which is removed in the lumen by a membrane-bound serine protease called thylakoidal processing peptidase (TPP). TPP is homologous to Escherichia coli type I signal peptidase (SPI) called LepB. Genetic data indicate that plastidic SPI 1 (Plsp1) is the main TPP in Arabidopsis thaliana (Arabidopsis) although biochemical evidence had been lacking. Here we demonstrate catalytic activity of bacterially produced Arabidopsis Plsp1. Recombinant Plsp1 showed processing activity against various TPP substrates at a level comparable to that of LepB. Plsp1 and LepB were also similar in the pH optima, sensitivity to arylomycin variants and a preference for the residue at -3 to the cleavage site within a substrate. Plsp1 orthologs found in angiosperms contain two unique Cys residues located in the lumen. Results of processing assays suggested that these residues were redox active and formation of a disulfide bond between them was necessary for the activity of recombinant Arabidopsis Plsp1. Furthermore, Plsp1 in Arabidopsis and pea thylakoids migrated faster under non-reducing conditions than under reducing conditions on SDS-PAGE. These results underpin the notion that Plsp1 is a redox-dependent signal peptidase in the thylakoid lumen.

Evolutionary development of redox regulation in chloroplasts

SIGNIFICANCE

The post-translational modification of thiol groups stands out as a key strategy that cells employ for metabolic regulation and adaptation to changing environmental conditions. Nowhere is this more evident than in chloroplasts-the O2-evolving photosynthetic organelles of plant cells that are fitted with multiple redox systems, including the thioredoxin (Trx) family of oxidoreductases functional in the reversible modification of regulatory thiols of proteins in all types of cells. The best understood member of this family in chloroplasts is the ferredoxin-linked thioredoxin system (FTS) by which proteins are modified via light-dependent disulfide/dithiol (S-S/2SH) transitions.

RECENT ADVANCES

Discovered in the reductive activation of enzymes of the Calvin-Benson cycle in illuminated chloroplast preparations, recent studies have extended the role of the FTS far beyond its original boundaries to include a spectrum of cellular processes. Together with the NADP-linked thioredoxin reductase C-type (NTRC) and glutathione/glutaredoxin systems, the FTS also plays a central role in the response of chloroplasts to different types of stress.

CRITICAL ISSUES

The comparisons of redox regulatory networks functional in chloroplasts of land plants with those of cyanobacteria-prokaryotes considered to be the ancestors of chloroplasts-and different types of algae summarized in this review have provided new insight into the evolutionary development of redox regulation, starting with the simplest O2-evolving organisms.

FUTURE DIRECTIONS

The evolutionary appearance, mode of action, and specificity of the redox regulatory systems functional in chloroplasts, as well as the types of redox modification operating under diverse environmental conditions stand out as areas for future study.

Proteome-wide light/dark modulation of thiol oxidation in cyanobacteria revealed by quantitative site-specific redox proteomics

Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in photosynthetic organisms. Herein, we present proteome-wide quantitative and site-specific profiling of in vivo thiol oxidation modulated by light/dark in the cyanobacterium Synechocystis sp. PCC 6803, an oxygenic photosynthetic prokaryote, using a resin-assisted thiol enrichment approach. Our proteomic approach integrates resin-assisted enrichment with isobaric tandem mass tag labeling to enable site-specific and quantitative measurements of reversibly oxidized thiols. The redox dynamics of ∼2,100 Cys-sites from 1,060 proteins under light, dark, and 3-(3,4-dichlorophenyl)-1,1-dimethylurea (a photosystem II inhibitor) conditions were quantified. In addition to relative quantification, the stoichiometry or percentage of oxidation (reversibly oxidized/total thiols) for ∼1,350 Cys-sites was also quantified. The overall results revealed broad changes in thiol oxidation in many key biological processes, including photosynthetic electron transport, carbon fixation, and glycolysis. Moreover, the redox sensitivity along with the stoichiometric data enabled prediction of potential functional Cys-sites for proteins of interest. The functional significance of redox-sensitive Cys-sites in NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, peroxiredoxin (AhpC/TSA family protein Sll1621), and glucose 6-phosphate dehydrogenase was further confirmed with site-specific mutagenesis and biochemical studies. Together, our findings provide significant insights into the broad redox regulation of photosynthetic organisms.

Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria

Protein redox chemistry constitutes a major void in knowledge pertaining to photoautotrophic system regulation and signaling processes. We have employed a chemical biology approach to analyze redox sensitive proteins in live Synechococcus sp. PCC 7002 cells in both light and dark periods, and to understand how cellular redox balance is disrupted during nutrient perturbation. The present work identified 300 putative redox-sensitive proteins that are involved in the generation of reductant, macromolecule synthesis, and carbon flux through central metabolic pathways, and may be involved in cell signaling and response mechanisms. Furthermore, our research suggests that dynamic redox changes in response to specific nutrient limitations, including carbon and nitrogen limitations, contribute to the regulatory changes driven by a shift from light to dark. Taken together, these results contribute to a high-level understanding of post-translational mechanisms regulating flux distributions and suggest potential metabolic engineering targets for redirecting carbon toward biofuel precursors.

Thioredoxin-dependent regulatory networks in chloroplasts under fluctuating light conditions

Plants have adopted a number of mechanisms to restore redox homeostasis in the chloroplast under fluctuating light conditions in nature. Chloroplast thioredoxin systems are crucial components of this redox network, mediating environmental signals to chloroplast proteins. In the reduced state, thioredoxins control the structure and function of proteins by reducing disulfide bridges in the redox active site of a protein. Subsequently, an oxidized thioredoxin is reduced by a thioredoxin reductase, the two enzymes together forming a thioredoxin system. Plant chloroplasts have versatile thioredoxin systems, including two reductases dependent on ferredoxin and NADPH as reducing power, respectively, several types of thioredoxins, and the system to deliver thiol redox signals to the thylakoid membrane and lumen. Light controls the activity of chloroplast thioredoxin systems in two ways. First, light reactions activate the thioredoxin systems via donation of electrons to oxidized ferredoxin and NADP⁺, and second, light induces production of reactive oxygen species in chloroplasts which deactivate the components of the thiol redox network. The diversity and partial redundancy of chloroplast thioredoxin systems enable chloroplast metabolism to rapidly respond to ever-changing environmental conditions and to raise plant fitness in natural growth conditions.

Live cell chemical profiling of temporal redox dynamics in a photoautotrophic cyanobacterium

Protein reduction-oxidation (redox) modification is an important mechanism that allows microorganisms to sense environmental changes and initiate cellular responses. We have developed a quantitative chemical probe approach for live cell labeling and imaging of proteins that are sensitive to redox modifications. We utilize this in vivo strategy to identify 176 proteins undergoing ∼5-10-fold dynamic redox change in response to nutrient limitation and subsequent replenishment in the photoautotrophic cyanobacterium Synechococcus sp. PCC 7002. We detect redox changes in as little as 30 s after nutrient perturbation and oscillations in reduction and oxidation for 60 min following the perturbation. Many of the proteins undergoing dynamic redox transformations participate in the major components for the production (photosystems and electron transport chains) or consumption (Calvin-Benson cycle and protein synthesis) of reductant and/or energy in photosynthetic organisms. Thus, our in vivo approach reveals new redox-susceptible proteins and validates those previously identified in vitro.

Redox regulation of the Calvin-Benson cycle: something old, something new

Reversible redox post-translational modifications such as oxido-reduction of disulfide bonds, S-nitrosylation, and S-glutathionylation, play a prominent role in the regulation of cell metabolism and signaling in all organisms. These modifications are mainly controlled by members of the thioredoxin and glutaredoxin families. Early studies in photosynthetic organisms have identified the Calvin-Benson cycle, the photosynthetic pathway responsible for carbon assimilation, as a redox regulated process. Indeed, 4 out of 11 enzymes of the cycle were shown to have a low activity in the dark and to be activated in the light through thioredoxin-dependent reduction of regulatory disulfide bonds. The underlying molecular mechanisms were extensively studied at the biochemical and structural level. Unexpectedly, recent biochemical and proteomic studies have suggested that all enzymes of the cycle and several associated regulatory proteins may undergo redox regulation through multiple redox post-translational modifications including glutathionylation and nitrosylation. The aim of this review is to detail the well-established mechanisms of redox regulation of Calvin-Benson cycle enzymes as well as the most recent reports indicating that this pathway is tightly controlled by multiple interconnected redox post-translational modifications. This redox control is likely allowing fine tuning of the Calvin-Benson cycle required for adaptation to varying environmental conditions, especially during responses to biotic and abiotic stresses.

Plastid thioredoxins: a "one-for-all" redox-signaling system in plants

The sessile nature of plants forces them to face an ever-changing environment instead of escape from hostile conditions as animals do. In order to overcome this survival challenge, a fine monitoring and controlling of the status of the photosynthetic electron transport chain and the general metabolism is vital for these organisms. Frequently, evolutionary plant adaptation has consisted in the appearance of multigenic families, comprising an array of enzymes, structural components, or sensing, and signaling elements, in numerous occasions with highly conserved primary sequences that sometimes make it difficult to discern between redundancy and specificity among the members of a same family. However, all this gene diversity is aimed to sort environment-derived plant signals to efficiently channel the external incoming information inducing a right physiological answer. Oxygenic photosynthesis is a powerful source of reactive oxygen species (ROS), molecules with a dual oxidative/signaling nature. In response to ROS, one of the most frequent post-translational modifications occurring in redox signaling proteins is the formation of disulfide bridges (from Cys oxidation). This review is focused on the role of plastid thioredoxins (pTRXs), proteins containing two Cys in their active site and largely known as part of the plant redox-signaling network. Several pTRXs types have been described so far, namely, TRX f, m, x, y, and z. In recent years, improvements in proteomic techniques and the study of loss-of-function mutants have enabled us to grasp the importance of TRXs for the plastid physiology. We will analyze the specific signaling function of each TRX type and discuss about the emerging role in non-photosynthetic plastids of these redox switchers.

Understanding the roles of the thylakoid lumen in photosynthesis regulation

It has been known for a long time that the thylakoid lumen provides the environment for oxygen evolution, plastocyanin-mediated electron transfer, and photoprotection. More recently lumenal proteins have been revealed to play roles in numerous processes, most often linked with regulating thylakoid biogenesis and the activity and turnover of photosynthetic protein complexes, especially the photosystem II and NAD(P)H dehydrogenase-like complexes. Still, the functions of the majority of lumenal proteins in Arabidopsis thaliana are unknown. Interestingly, while the thylakoid lumen proteome of at least 80 proteins contains several large protein families, individual members of many protein families have highly divergent roles. This is indicative of evolutionary pressure leading to neofunctionalization of lumenal proteins, emphasizing the important role of the thylakoid lumen for photosynthetic electron transfer and ultimately for plant fitness. Furthermore, the involvement of anterograde and retrograde signaling networks that regulate the expression and activity of lumen proteins is increasingly pertinent. Recent studies have also highlighted the importance of thiol/disulfide modulation in controlling the functions of many lumenal proteins and photosynthetic regulation pathways.

Structure of the homodimeric glycine decarboxylase P-protein from Synechocystis sp. PCC 6803 suggests a mechanism for redox regulation

Glycine decarboxylase, or P-protein, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. P-protein from the cyanobacterium Synechocystis sp. PCC 6803 is an α2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apoenzyme shows the C terminus locked in a closed conformation by a disulfide bond between Cys(972) in the C terminus and Cys(353) located in the active site. The presence of the disulfide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. Reduction of the 353-972 disulfide releases the C terminus and allows access to the active site. PLP and the substrate glycine bind in the active site of this reduced enzyme and appear to cause further conformational changes involving a flexible surface loop. The observation of the disulfide bond that acts to stabilize the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier.

Oxidative folding in chloroplasts

SIGNIFICANCE

Disulfide-bonded proteins in chloroplasts from green plants exist in the envelope and the thylakoid membrane, and in the stroma and the lumen. The formation of disulfide bonds in proteins is referred to as oxidative folding and is linked to the import and folding of chloroplast proteins as well as the assembly and repair of thylakoid complexes. It is also important in the redox regulation of enzymes and signal transfer.

RECENT ADVANCES

Green-plant chloroplasts contain enzymes that can form and isomerize disulfide bonds in proteins. In Arabidopsis thaliana, four proteins are identified that are relevant for the catalysis of disulfide bond formation in chloroplast proteins. The proteins' low quantum yield of Photosystem II 1 (LQY1, At1g75690) and snowy cotyledon 2 (SCO2, At3g19220) exhibits protein disulfide isomerase activity and is suggested to function in the assembly and repair of Photosystem II (PSII), and the biogenesis of thylakoids in cotyledons, respectively. The thylakoid-located Lumen thiol oxidoreductase 1 (LTO1, At4g35760) can catalyze the formation of the disulfide bond of the extrinsic PsbO protein of PSII. In addition, the stroma-located protein disulfide isomerase PDIL1-3 (At3g54960) may have a role in oxidative folding.

CRITICAL ISSUES

Research on oxidative folding in chloroplasts plants is in an early stage and little is known about the mechanisms of disulfide bond formation in chloroplast proteins.

FUTURE DIRECTIONS

The close link between the import and folding of chloroplast proteins suggests that Hsp93, a component of the inner envelope's import apparatus, may have co-chaperones that can catalyze disulfide bond formation in newly imported proteins.