Redox-shuttling between chloroplast and cytosol: integration of intra-chloroplast and extra-chloroplast metabolism

Multi-Omics Analyses of Lettuce (Lactuca sativa) Reveals Primary Metabolism Reorganization Supporting Distinct Features of Secondary Metabolism Induced by Supplementing UV-A Radiation

UV can serve as an effective light spectrum for regulating plant secondary metabolites, while relevant studies on UV-A are much less extensive than those on UV-B. A comprehensive understanding of the selective effects of UV-A on different secondary metabolites and the specific features of primary metabolism that drive these effects is still lacking. To address this knowledge gap, we conducted a study to analyze the dynamic changes in the metabolome and transcriptome of lettuce leaves irradiated with red plus UV-A light (monochromatic red light as control). Generally, UV-A promoted the synthesis of most phenylpropanoids and terpenoids originating from the shikimate and methylerythritol phosphate (MEP) pathway in plastids but sacrificed the synthesis of terpenoids derived from the mevalonate (MVA) pathway, particularly sesquiterpenes. Increased precursors supply for the shikimate and MEP pathway under UV-A was directly supported by the activation of the Calvin-Benson cycle and phosphoenolpyruvate transport. Whereas, along with phosphoenolpyruvate transport, the TCA cycle was restrained, causing deprivation of the MVA pathway precursor. In addition, UV-A also activated the plastidic oxidative branch of the pentose phosphate pathway, photorespiration, and malate shuttle, to ensure a sufficient supply of nitrogen, circulation homeostasis of the Calvin-Benson cycle, and energy balance, thus indirectly supporting UV-A-induced specific secondary metabolic output. This study provides a comprehensive framework for understanding the flexible primary-secondary metabolism interactions that are able to produce specific metabolites favorable for adaptation to environmental stimuli.

The fnr-like mutants confer isoxaben tolerance by initiating mitochondrial retrograde signalling

Isoxaben is a pre-emergent herbicide used to control broadleaf weeds. While the phytotoxic mechanism is not completely understood, isoxaben interferes with cellulose synthesis. Certain mutations in cellulose synthase complex proteins can confer isoxaben tolerance; however, these mutations can cause compromised cellulose synthesis and perturbed plant growth, rendering them unsuitable as herbicide tolerance traits. We conducted a genetic screen to identify new genes associated with isoxaben tolerance by screening a selection of Arabidopsis thaliana T-DNA mutants. We found that mutations in a FERREDOXIN-NADP(+) OXIDOREDUCTASE-LIKE (FNRL) gene enhanced tolerance to isoxaben, exhibited as a reduction in primary root stunting, reactive oxygen species accumulation and ectopic lignification. The fnrl mutant did not exhibit a reduction in cellulose levels following exposure to isoxaben, indicating that FNRL operates upstream of isoxaben-induced cellulose inhibition. In line with these results, transcriptomic analysis revealed a highly reduced response to isoxaben treatment in fnrl mutant roots. The fnrl mutants displayed constitutively induced mitochondrial retrograde signalling, and the observed isoxaben tolerance is partially dependent on the transcription factor ANAC017, a key regulator of mitochondrial retrograde signalling. Moreover, FNRL is highly conserved across all plant lineages, implying conservation of its function. Notably, fnrl mutants did not show a growth penalty in shoots, making FNRL a promising target for biotechnological applications in breeding isoxaben tolerance in crops.

Malate dehydrogenase in plants: evolution, structure, and a myriad of functions

Malate dehydrogenase (MDH) catalyzes the interconversion of oxaloacetate and malate coupled to the oxidation/reduction of coenzymes NAD(P)H/NAD(P)+. While most animals have two isoforms of MDH located in the cytosol and mitochondria, all major groups of land plants have at least six MDHs localized to the cytosol, mitochondria, plastids, and peroxisomes. This family of enzymes participates in important reactions in plant cells including photosynthesis, photorespiration, lipid metabolism, and NH4+ metabolism. MDH also helps to regulate the energy balance in the cell and may help the plant cope with various environmental stresses. Despite their functional diversity, all of the plant MDH enzymes share a similar structural fold and act as dimers. In this review, we will introduce readers to our current understanding of the plant MDHs, including their evolution, structure, and function. The focus will be on the MDH enzymes of the model plant Arabidopsis thaliana.

Salinity Mitigates the Negative Effect of Elevated Temperatures on Photosynthesis in the C3-C4 Intermediate Species Sedobassia sedoides

The adaptation of plants to combined stresses requires unique responses capable of overcoming both the negative effects of each individual stress and their combination. Here, we studied the C3-C4 (C2) halophyte Sedobassia sedoides in response to elevated temperature (35 °C) and salinity (300 mM NaCl) as well as their combined effect. The responses we studied included changes in water-salt balance, light and dark photosynthetic reactions, the expression of photosynthetic genes, the activity of malate dehydrogenase complex enzymes, and the antioxidant system. Salt treatment led to altered water-salt balance, improved water use efficiency, and an increase in the abundance of key enzymes involved in intermediate C3-C4 photosynthesis (i.e., Rubisco and glycine decarboxylase). We also observed a possible increase in the activity of the C2 carbon-concentrating mechanism (CCM), which allowed plants to maintain high photosynthesis intensity and biomass accumulation. Elevated temperatures caused an imbalance in the dark and light reactions of photosynthesis, leading to stromal overreduction and the excessive generation of reactive oxygen species (ROS). In response, S. sedoides significantly activated a metabolic pathway for removing excess NADPH, the malate valve, which is catalyzed by NADP-MDH, without observable activation of the antioxidant system. The combined action of these two factors caused the activation of antioxidant defenses (i.e., increased activity of SOD and POX and upregulation of FDI), which led to a decrease in oxidative stress and helped restore the photosynthetic energy balance. Overall, improved PSII functioning and increased activity of PSI cyclic electron transport (CET) and C2 CCM led to an increase in the photosynthesis intensity of S. sedoides under the combined effect of salinity and elevated temperature relative to high temperature alone.

Oscillations of chlorophyll fluorescence after plasma membrane excitation in Chara originate from nonuniform composition of signaling metabolites in the streaming cytoplasm

Excitable cells of higher plants and characean algae respond to stressful stimuli by generating action potentials (AP) whose regulatory influence on chlorophyll (Chl) fluorescence and photosynthesis extends over tens of minutes. Unlike plant leaves where the efficiency of photosystem II reaction (YII) undergoes a separate reversible depression after an individual AP, characean algae exhibit long-lasting oscillations of YII after firing AP, provided that Chl fluorescence is measured on microscopic cell regions. Internodal cells of charophytes feature an extremely fast cytoplasmic streaming that stops immediately during the spike and recovers within ~10 min after AP. In this study a possibility was examined that multiple oscillations of YII and Chl fluorescence parameters (F', Fm') result from the combined influence of metabolic rearrangements in chloroplasts and the cyclosis cessation-recovery cycle induced by the Ca2+ influx during AP. It is shown that the AP-induced Fm' and YII oscillations disappear when the fluidic communications between the analyzed area (AOI) and surrounding cell regions are restricted or eliminated. The microfluidic signaling was manipulated in two ways: by narrowing the illuminated cell area and by arresting the cytoplasmic streaming with cytochalasin D (CD). The inhibition of Fm' and YII oscillations was not caused by the loss of cell excitability, since CD-treated cells retained the capacity of AP generation. The mechanism of AP-induced oscillations of YII and Chl fluorescence seems to involve the lateral microfluidic transport of signaling substances in combination with the distribution pattern of these substances that was enhanced during the period of streaming cessation.

Genome-Wide Identification and Expression Analysis of Malate Dehydrogenase Gene Family in Sweet Potato and Its Two Diploid Relatives

Malate dehydrogenase (MDH; EC 1.1.1.37) plays a vital role in plant growth and development as well as abiotic stress responses, and it is widely present in plants. However, the MDH family genes have not been explored in sweet potato. In this study, nine, ten, and ten MDH genes in sweet potato (Ipomoea batatas) and its two diploid wild relatives, Ipomoea trifida and Ipomoea triloba, respectively, were identified. These MDH genes were unevenly distributed on seven different chromosomes among the three species. The gene duplications and nucleotide substitution analysis (Ka/Ks) revealed that the MDH genes went through segmental duplications during their evolution under purifying selection. A phylogenetic and conserved structure divided these MDH genes into five subgroups. An expression analysis indicated that the MDH genes were omni-presently expressed in distinct tissues and responded to various abiotic stresses. A transcription factor prediction analysis proved that Dof, MADS-box, and MYB were the main transcription factors of sweet potato MDH genes. These findings provide molecular features of the MDH family in sweet potato and its two diploid wild relatives, which further supports functional characterizations.

OsMDH12: A Peroxisomal Malate Dehydrogenase Regulating Tiller Number and Salt Tolerance in Rice

Salinity is an important environmental factor influencing crop growth and yield. Malate dehydrogenase (MDH) catalyses the reversible conversion of oxaloacetate (OAA) to malate. While many MDHs have been identified in various plants, the biochemical function of MDH in rice remains uncharacterised, and its role in growth and salt stress response is largely unexplored. In this study, the biochemical function of OsMDH12 was determined, revealing its involvement in regulating tiller number and salt tolerance in rice. OsMDH12 localises in the peroxisome and is expressed across various organs. In vitro analysis confirmed that OsMDH12 converts OAA to malate. Seedlings of OsMDH12-overexpressing (OE) plants had shorter shoot lengths and lower fresh weights than wild-type (WT) plants, while osmdh12 mutants displayed the opposite. At maturity, OsMDH12-OE plants had fewer tillers than WT, whereas osmdh12 mutants had more, suggesting OsMDH12's role in tiller number regulation. Moreover, OsMDH12-OE plants were sensitive to salt stress, but osmdh12 mutants showed enhanced salt tolerance. The Na+/K+ content ratio increased in OsMDH12-OE plants and decreased in osmdh12 mutants, suggesting that OsMDH12 might negatively affect salt tolerance through influencing the Na+/K+ balance. These findings hint at OsMDH12's potential as a genetic tool to enhance rice growth and salt tolerance.

Comparative transcriptomics reveals the role of altered energy metabolism in the establishment of single-cell C4 photosynthesis in Bienertia sinuspersici

Single-cell C₄ photosynthesis (SCC₄) in terrestrial plants without Kranz anatomy involves three steps: initial CO₂ fixation in the cytosol, CO₂ release in mitochondria, and a second CO₂ fixation in central chloroplasts. Here, we investigated how the large number of mechanisms underlying these processes, which occur in three different compartments, are orchestrated in a coordinated manner to establish the C₄ pathway in Bienertia sinuspersici, a SCC₄ plant. Leaves were subjected to transcriptome analysis at three different developmental stages. Functional enrichment analysis revealed that SCC₄ cycle genes are coexpressed with genes regulating cyclic electron flow and amino/organic acid metabolism, two key processes required for the production of energy molecules in C₃ plants. Comparative gene expression profiling of B. sinuspersici and three other species (Suaeda aralocaspica, Amaranthus hypochondriacus, and Arabidopsis thaliana) showed that the direction of metabolic flux was determined via an alteration in energy supply in peripheral chloroplasts and mitochondria via regulation of gene expression in the direction of the C₄ cycle. Based on these results, we propose that the redox homeostasis of energy molecules via energy metabolism regulation is key to the establishment of the SCC₄ pathway in B. sinuspersici.

Encoded C4 homologue enzymes genes function under abiotic stresses in C3 plant

Plant organisms assimilate CO₂ through the photosynthetic pathway, which facilitates in the synthesis of sugar for plant development. As environmental elements including water level, CO₂ concentration, temperature and soil characteristics change, the plants may recruit series of genes to help adapt the hostile environments and challenges. C4 photosynthesis plants are an excellent example of plant evolutionary adaptation to diverse condition. Compared with C3 photosynthesis plants, C4 photosynthesis plants have altered leaf anatomy and new metabolism for CO₂ capture, with multiple related enzymes such as phosphoenolpyruvate carboxylase (PEPCase), pyruvate orthophosphate dikinase (PPDK), NAD(P)-malic enzyme (NAD(P)-ME), NAD(P) - malate dehydrogenase (NAD(P)-MDH) and carbonic anhydrases (CA), identified to participate in the carbon concentrating mechanism (CCM) pathway. Recently, great achievements about C4 CCM-related genes have been made in the dissection of C3 plant development processes involving various stresses. In this review, we describe the functions of C4 CCM-related homologous genes in carbon and nitrogen metabolism in C3 plants. We further summarize C4 CCM-related homologous genes' functions in response to stresses in C3 plants. The understanding of C4 CCM-related genes' function in response to abiotic stress in plant is important to modify the crop plants for climate diversification.

Live-cell imaging of the chloroplast outer envelope membrane using fluorescent dyes

Chloroplasts are organelles composed of sub-organellar compartments-stroma, thylakoids, and starch granules-and are surrounded by outer and inner envelope membranes (OEM and IEM, respectively). The chloroplast OEM and IEM play key roles not only as a barrier separating the chloroplast components from the cytosol but also in the interchange of numerous metabolites and proteins between the chloroplast interior and the cytosol. Fluorescent protein markers for the chloroplast OEM have been widely used to visualize the outermost border of chloroplasts. However, the use of marker proteins requires an established cellular genetic transformation method, which limits the plant species in which marker proteins can be used. Moreover, the high accumulation of OEM marker proteins often elicits abnormal morphological phenotypes of the OEM. Because the OEM can currently only be visualized using exogenous marker proteins, the behaviors of the chloroplast and/or its OEM remain unknown in wild-type cells of various plant species. Here, we visualized the OEM using live-cell staining with the fluorescent dyes rhodamine B and Nile red in several plant species, including crops. We propose rhodamine B and Nile red as new tools for visualizing the chloroplast OEM in living plant cells that do not require genetic transformation.

Significance Statement

We established a live-cell imaging method to visualize the chloroplast outer envelope membrane by staining living cells with fluorescent dyes. This method does not require genetic transformation and allows the observation of the chloroplast outer envelope membrane in various plant species.

Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling

Modelling higher plant growth is of strategic interest for modern agriculture as well as for the development of bioregenerative life support systems for space applications, where crop growth is expected to play an essential role. The capability of constraint-based metabolic models to cope the diel dynamics of plants growth is integrated into a multilevel modelling approach including mass and energy transfer and enzyme kinetics. Lactuca sativa is used as an exemplary crop to validate, with experimental data, the approach presented as well as to design a novel model-based predictive control strategy embedding metabolic information. The proposed modelling strategy predicts with high accuracy the dynamics of gas exchange and the distribution of fluxes in the metabolic network whereas the control architecture presented can be useful to manage higher plants chambers and open new ways of merging metabolome and control algorithms.

Drought-Induced Responses in Maize under Different Vapor Pressure Deficit Conditions

Water stress in plants depends on the soil water level and the evaporative demand. In this study, the physiological, biochemical, and molecular response of maize were examined under three evaporative demand conditions (low—1.00 kPa, medium—2.2 kPa, and high—4.00 kPa Vapor pressure deficit (VPD)) at three different soil water content (SWC); well-watered, 45%, and 35% SWC. Plants grown at 35% SWC under high VPD had significant (p < 0.01) lower leaf weight, leaf area, and leaf number than low VPD. Plants under low, medium, and high VPD with drought stress (45% and 35% SWC) showed a 30 to 60% reduction in their leaf area compared to well-watered plants. Gas exchange parameters including photosynthesis, stomatal conductance, and water use efficiency exhibited significant differences (p < 0.01) between treatments, with the highest reduction occuring at 35% SWC and high VPD. Both drought and VPD significantly (p < 0.01) increased C4 enzyme levels and some transcription factors with increased stress levels. Transcription factors primarily related to Abssisic Acid (ABA) synthesis were upregulated under drought, which might be related to high ABA levels. In summary, severe drought levels coupled with high VPD had shown a significant decrease in plant development by modifying enzymes, ABA, and transcription factors.

Network-Based Analysis to Identify Hub Genes Involved in Spatial Root Response to Mechanical Constrains

Previous studies report that the asymmetric response, observed along the main poplar woody bent root axis, was strongly related to both the type of mechanical forces (compression or tension) and the intensity of force displacement. Despite a large number of targets that have been proposed to trigger this asymmetry, an understanding of the comprehensive and synergistic effect of the antistress spatially related pathways is still lacking. Recent progress in the bioinformatics area has the potential to fill these gaps through the use of in silico studies, able to investigate biological functions and pathway overlaps, and to identify promising targets in plant responses. Presently, for the first time, a comprehensive network-based analysis of proteomic signatures was used to identify functions and pivotal genes involved in the coordinated signalling pathways and molecular activities that asymmetrically modulate the response of different bent poplar root sectors and sides. To accomplish this aim, 66 candidate proteins, differentially represented across the poplar bent root sides and sectors, were grouped according to their abundance profile patterns and mapped, together with their first neighbours, on a high-confidence set of interactions from STRING to compose specific cluster-related subnetworks (I-VI). Successively, all subnetworks were explored by a functional gene set enrichment analysis to identify enriched gene ontology terms. Subnetworks were then analysed to identify the genes that are strongly interconnected with other genes (hub gene) and, thus, those that have a pivotal role in the bent root asymmetric response. The analysis revealed novel information regarding the response coordination, communication, and potential signalling pathways asymmetrically activated along the main root axis, delegated mainly to Ca2+ (for new lateral root formation) and ROS (for gravitropic response and lignin accumulation) signatures. Furthermore, some of the data indicate that the concave side of the bent sector, where the mechanical forces are most intense, communicates to the other (neighbour and distant) sectors, inducing spatially related strategies to ensure water uptake and accompanying cell modification. This information could be critical for understanding how plants maintain and improve their structural integrity-whenever and wherever it is necessary-in natural mechanical stress conditions.

Prospects and environmental sustainability of phyconanotechnology: A review on algae-mediated metal nanoparticles synthesis and mechanism

In recent years, researchers have proven that the employment of natural green components in the biogenesis of nanoparticles from microalgae species is one of the ways to delight the global environment issues. The application of nanotechnology with the exploitation of phycochemical produced from algae species is known as 'phyconanotechnology'. The use of biological compounds by microalgae as reducing agents for the synthesis of inorganic nanoparticles has shown promising results such as cost-effective and environmentally friendly. Different classifications of algae such as brown algae, red algae, green algae, and cyanobacteria are studied for the synthesis of different types of metal nanoparticles. It is also an important motive to acknowledge the mechanisms of the microalgae-mediated biosynthesis of nanoparticles via an intracellular pathway or extracellular pathway. Besides, microalgae species as biogenic sources preclude the use of conventional methods reagents, such as sodium borohydride (NaBH₄) and N,N-dimethylformamide (DMF), which further consolidates their position as the best choice for sustainable (economically and environmentally) nanoparticle synthesis compared to the conventional nanoparticles synthesis pathway.

Microfluidic interactions involved in chloroplast responses to plasma membrane excitation in Chara

Adaptation of plants to environmental changes involves the mechanisms of long-distance signaling. In characean algae, these mechanisms comprise the propagation of action potential (AP) and the rotational cytoplasmic streaming acting in cooperation with light-dependent exchange of ions and metabolites across the chloroplast envelope. Both excitability and cyclosis exert conspicuous effects on photosynthetic activity of chloroplasts but possible influence of cyclosis arrest on the coupling of AP stimulus to photosynthetic performance remained unexplored. In this study, fluidic interactions between anchored chloroplasts were allowed or restricted by illuminating the whole internode or a confined cell area (2 mm in diameter), respectively. Measurements of chlorophyll fluorescence parameters (F' and F_m') in cell regions located close to calcium crystal depositions revealed that the AP generation induced long-lasting F_m' oscillations that persisted in illuminated cells. The AP generation often induced the F' oscillations, whose number diminished upon the transfer of internodal cells from total to local background light. The results indicate that the AP-induced changes in photosynthetic parameters, F' in particular, have a complex origin and comprise the internal processes caused by the elevation of stromal Ca²⁺ concentration in the analyzed chloroplasts and the stages related to ion and metabolite exchange mediated by cytoplasmic streaming. It is supposed that the composition of flowing cytoplasm is heterogeneous due to the spatial alteration of calcified and noncalcified cell sites, but this heterogeneity is enhanced and can be visualized after the transient cessation and restoration of cytoplasmic streaming.

Suppression of metabolite shuttles for export of chloroplast and mitochondrial ATP and NADPH increases the cytosolic NADH:NAD+ ratio in tobacco leaves in the dark

The communication between chloroplasts and mitochondria, which depends on the inter-organellar exchange of carbon skeletons, energy, and reducing equivalents, is essential for maintaining efficient respiratory metabolism and photosynthesis. We devised a multi-transgene approach to manipulate the leaf energy and redox balance in tobacco (Nicotiana tabacum) while monitoring the in vivo cytosolic redox status of NAD(H) using the biosensor c-Peredox-mCherry. Our strategy involved altering the shuttling capacity of the chloroplast by (1) increasing the chloroplast malate valve capacity by overexpression of the chloroplast malate valve transporter pOMT from Arabidopsis (AtpOMT1) while (2) reducing the activity of the chloroplast triose-phosphate/3-phosphoglycerate shuttle by knocking down the cytosolic NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (NtGAPC). This was accompanied by (3) alterations to the export of reducing equivalents in the mitochondria by knocking down the mitochondrial malate dehydrogenase (NtmMDH) and (4) an increased expression of the mitochondrial fission regulator FIS1A from Arabidopsis (AtFIS1A). The multi-transgene tobacco plants were analysed in glasshouse conditions and showed significant increases in the cytosolic NADH:NAD+ in the dark when transcript levels for NtGAPC or NtmMDH were knocked down. In addition, principal component analysis and Spearman correlation analyses showed negative correlations between average transcript levels for the gene targets and parameters related to chlorophyll fluorescence and plant growth. Our results highlight the importance of the shuttling of energy and reducing equivalents from chloroplasts and mitochondria to support photosynthesis and growth and suggest an important role for the dual 2-oxoglutarate/malate and oxaloacetate/malate transporter (pOMT).

Effects of chloroplast-cytoplasm exchange and lateral mass transfer on slow induction of chlorophyll fluorescence in Characeae

Rapid cytoplasmic streaming in characean algae mediates communications between remote cell regions exposed to uneven irradiance. The metabolites exported from brightly illuminated chloroplasts spread along the internode with the liquid flow and cause transient changes in chlorophyll fluorescence at cell areas that are exposed to dim light or placed shortly in darkness. The largest distance to which the photometabolites can be transported has not yet been determined. Neither is it known if lateral transport has an influence on the induction of chlorophyll fluorescence. In this study, the relations between spatial connectivity of anchored chloroplasts in characean internodes and fluorescence induction curves were examined. Connectivity between remote cell parts was pronounced upon illumination of a cell spot at a distance up to 10 mm from the area of fluorescence measurement, provided the spot was located upstream in the cytoplasmic flow. Spatial interactions between distant cell sites were also manifested in strikingly different slow stages of fluorescence induction caused by narrow- and wide-field illumination. Cytochalasin D, cooling of bath solution, and inactivation of light-dependent envelope transporters were used to disturb cyclosis-mediated spatial interactions. Although fluorescence induction curves induced by narrow- and wide-field illumination differed greatly under control conditions, they became similar after the inhibition of cyclosis with cytochalasin D. The results indicate that cytoplasmic streaming not only drives the lateral translocation of photometabolites but also promotes the export of reducing power from illuminated chloroplasts due to flushing the chloroplast surface and keeping sharp concentration gradients.

The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis

Although most of the tens of thousands of diatom species are photoautotrophs, a small number of heterotrophic species no longer photosynthesize. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia Nitz4, to determine how carbon metabolism was altered in the wake of this trophic shift. Nitzschia Nitz4 has retained its plastid and plastid genome, but changes associated with the transition to heterotrophy were cellular-wide and included losses of photosynthesis-related genes from the nuclear and plastid genomes, elimination of isoprenoid biosynthesis in the plastid, and remodeling of mitochondrial glycolysis to maximize adenosine triphosphte (ATP) yield. The genome contains a β-ketoadipate pathway that may allow Nitzschia Nitz4 to metabolize lignin-derived compounds. Diatom plastids lack an oxidative pentose phosphate pathway (oPPP), leaving photosynthesis as the primary source of NADPH to support essential biosynthetic pathways in the plastid and, by extension, limiting available sources of NADPH in nonphotosynthetic plastids. The genome revealed similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids and highlighted the ancestral absence of a plastid oPPP as a potentially important constraint on loss of photosynthesis, a hypothesis supported by the higher frequency of transitions to parasitism or heterotrophy in lineages that have a plastid oPPP.

The Complementary Roles of Chloroplast Cyclic Electron Transport and Mitochondrial Alternative Oxidase to Ensure Photosynthetic Performance

Chloroplasts use light energy and a linear electron transport (LET) pathway for the coupled generation of NADPH and ATP. It is widely accepted that the production ratio of ATP to NADPH is usually less than required to fulfill the energetic needs of the chloroplast. Left uncorrected, this would quickly result in an over-reduction of the stromal pyridine nucleotide pool (i.e., high NADPH/NADP⁺ ratio) and under-energization of the stromal adenine nucleotide pool (i.e., low ATP/ADP ratio). These imbalances could cause metabolic bottlenecks, as well as increased generation of damaging reactive oxygen species. Chloroplast cyclic electron transport (CET) and the chloroplast malate valve could each act to prevent stromal over-reduction, albeit in distinct ways. CET avoids the NADPH production associated with LET, while the malate valve consumes the NADPH associated with LET. CET could operate by one of two different pathways, depending upon the chloroplast ATP demand. The NADH dehydrogenase-like pathway yields a higher ATP return per electron flux than the pathway involving PROTON GRADIENT REGULATION5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1 (PGRL1). Similarly, the malate valve could couple with one of two different mitochondrial electron transport pathways, depending upon the cytosolic ATP demand. The cytochrome pathway yields a higher ATP return per electron flux than the alternative oxidase (AOX) pathway. In both Arabidopsis thaliana and Chlamydomonas reinhardtii, PGR5/PGRL1 pathway mutants have increased amounts of AOX, suggesting complementary roles for these two lesser-ATP yielding mechanisms of preventing stromal over-reduction. These two pathways may become most relevant under environmental stress conditions that lower the ATP demands for carbon fixation and carbohydrate export.

Functional Relationship of Arabidopsis AOXs and PTOX Revealed via Transgenic Analysis

Alternative oxidase (AOX) and plastid terminal oxidase (PTOX) are terminal oxidases of electron transfer in mitochondria and chloroplasts, respectively. Here, taking advantage of the variegation phenotype of the Arabidopsis PTOX deficient mutant (im), we examined the functional relationship between PTOX and its five distantly related homologs (AOX1a, 1b, 1c, 1d, and AOX2). When engineered into chloroplasts, AOX1b, 1c, 1d, and AOX2 rescued the im defect, while AOX1a partially suppressed the mutant phenotype, indicating that AOXs could function as PQH₂ oxidases. When the full length AOXs were overexpressed in im, only AOX1b and AOX2 rescued its variegation phenotype. In vivo fluorescence analysis of GFP-tagged AOXs and subcellular fractionation assays showed that AOX1b and AOX2 could partially enter chloroplasts while AOX1c and AOX1d were exclusively present in mitochondria. Surprisingly, the subcellular fractionation, but not the fluorescence analysis of GFP-tagged AOX1a, revealed that a small portion of AOX1a could sort into chloroplasts. We further fused and expressed the targeting peptides of AOXs with the mature form of PTOX in im individually; and found that targeting peptides of AOX1a, AOX1b, and AOX2, but not that of AOX1c or AOX1d, could direct PTOX into chloroplasts. It demonstrated that chloroplast-localized AOXs, but not mitochondria-localized AOXs, can functionally compensate for the PTOX deficiency in chloroplasts, providing a direct evidence for the functional relevance of AOX and PTOX, shedding light on the interaction between mitochondria and chloroplasts and the complex mechanisms of protein dual targeting in plant cells.

The flexibility of metabolic interactions between chloroplasts and mitochondria in Nicotiana tabacum leaf

To examine the effect of mitochondrial function on photosynthesis, wild-type and transgenic Nicotiana tabacum with varying amounts of alternative oxidase (AOX) were treated with different respiratory inhibitors. Initially, each inhibitor increased the reduction state of the chloroplast electron transport chain, most severely in AOX knockdowns and least severely in AOX overexpressors. This indicated that the mitochondrion was a necessary sink for photo-generated reductant, contributing to the 'P700 oxidation capacity' of photosystem I. Initially, the Complex III inhibitor myxothiazol and the mitochondrial ATP synthase inhibitor oligomycin caused an increase in photosystem II regulated non-photochemical quenching not evident with the Complex III inhibitor antimycin A (AA). This indicated that the increased quenching depended upon AA-sensitive cyclic electron transport (CET). Following 12 h with oligomycin, the reduction state of the chloroplast electron transport chain recovered in all plant lines. Recovery was associated with large increases in the protein amount of chloroplast ATP synthase and mitochondrial uncoupling protein. This increased the capacity for photophosphorylation in the absence of oxidative phosphorylation and enabled the mitochondrion to act again as a sink for photo-generated reductant. Comparing the AA and myxothiazol treatments at 12 h showed that CET optimized photosystem I quantum yield, depending upon the P700 oxidation capacity. When this capacity was too high, CET drew electrons away from other sinks, moderating the P700+ amount. When P700 oxidation capacity was too low, CET acted as an electron overflow, moderating the amount of reduced P700. This study reveals flexible chloroplast-mitochondrion interactions able to overcome lesions in energy metabolism.

Photorespiration: The Futile Cycle?

Photorespiration, or C₂ photosynthesis, is generally considered a futile cycle that potentially decreases photosynthetic carbon fixation by more than 25%. Nonetheless, many essential processes, such as nitrogen assimilation, C₁ metabolism, and sulfur assimilation, depend on photorespiration. Most studies of photosynthetic and photorespiratory reactions are conducted with magnesium as the sole metal cofactor despite many of the enzymes involved in these reactions readily associating with manganese. Indeed, when manganese is present, the energy efficiency of these reactions may improve. This review summarizes some commonly used methods to quantify photorespiration, outlines the influence of metal cofactors on photorespiratory enzymes, and discusses why photorespiration may not be as wasteful as previously believed.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.

Overexpression of the chloroplastic 2-oxoglutarate/malate transporter disturbs carbon and nitrogen homeostasis in rice

The chloroplastic 2-oxaloacetate (OAA)/malate transporter (OMT1 or DiT1) takes part in the malate valve that protects chloroplasts from excessive redox poise through export of malate and import of OAA. Together with the glutamate/malate transporter (DCT1 or DiT2), it connects carbon with nitrogen assimilation, by providing 2-oxoglutarate for the GS/GOGAT (glutamine synthetase/glutamate synthase) reaction and exporting glutamate to the cytoplasm. OMT1 further plays a prominent role in C4 photosynthesis: OAA resulting from phosphoenolpyruvate carboxylation is imported into the chloroplast, reduced to malate by plastidic NADP-malate dehydrogenase, and then exported for transport to bundle sheath cells. Both transport steps are catalyzed by OMT1, at the rate of net carbon assimilation. To engineer C4 photosynthesis into C3 crops, OMT1 must be expressed in high amounts on top of core C4 metabolic enzymes. We report here high-level expression of ZmOMT1 from maize in rice (Oryza sativa ssp. indica IR64). Increased activity of the transporter in transgenic rice was confirmed by reconstitution of transporter activity into proteoliposomes. Unexpectedly, overexpression of ZmOMT1 in rice negatively affected growth, CO2 assimilation rate, total free amino acid content, tricarboxylic acid cycle metabolites, as well as sucrose and starch contents. Accumulation of high amounts of aspartate and the impaired growth phenotype of OMT1 rice lines could be suppressed by simultaneous overexpression of ZmDiT2. Implications for engineering C4 rice are discussed.

Distinctive mitochondrial and chloroplast components contributing to the maintenance of carbon balance during plant growth at elevated CO2

Plant carbon balance depends upon the difference between photosynthetic carbon gain and respiratory carbon loss. In C₃ plants, growth at an elevated atmospheric concentration of CO₂ (ECO₂) stimulates photosynthesis and raises the leaf carbohydrate status, but how respiration responds is less understood. In this study, growth of Nicotiana tabacum at ECO₂ increased the protein amount of the non-energy conserving mitochondrial alternative oxidase (AOX). Growth at ECO₂ increased AOX1a transcript amount, and the transcript amount of a putative sugar-responsive gene encoding a chloroplast glucose-6-phosphate/phosphate translocator (GPT3). We suggest that the elevated amounts of AOX and GPT3 represent distinctive mitochondrial and chloroplast mechanisms to manage an excessive cytosolic pool of sugar phosphates. AOX respiration could consume cytosolic sugar phosphates, without this activity being restricted by rates of ATP turnover. GPT3 could allow accumulating cytosolic glucose-6-phosphate to return to the chloroplast. This could feed starch synthesis or a glucose-6-phosphate shunt in the Calvin cycle. AOX and GPT3 activities could buffer against P_i depletions that might otherwise disrupt mitochondrial and chloroplast electron transport chain activities. AOX and GPT3 activities could also buffer against a down-regulation of photosynthetic capacity by preventing a persistent imbalance between photosynthetic carbon gain and the activity of carbon utilizing sinks.

Transient depletion of transported metabolites in the streaming cytoplasm of Chara upon shading the long-distance transmission pathway

Export of reducing power from chloroplasts to cytoplasm serves to balance the NADPH/ATP ratio that is optimal for CO₂ assimilation. Rapid cytoplasmic streaming in characean algae conveys the exported metabolites downstream towards the shaded plastids where envelope transporters may operate for the import of reducing power in accordance with the direction of concentration gradients. Import of reducing equivalents by chloroplasts in the analyzed area transiently enhances the pulse-modulated chlorophyll fluorescence F' controlled by the redox state of photosystem II acceptor Q_A. When the microfluidic pathway was transferred to darkness while the analyzed cell area remained in dim background light, the amplitude of cyclosis-mediated F' changes dropped sharply and then recovered within 5-10 min. The suppression of long-distance signaling indicates temporal depletion of transmitted metabolites in the streaming cytoplasm. The return to overall background illumination induced an exceptionally large F' response to the first local light pulse admitted to a remote cell region. This indicates the appearance of excess reductants in the streaming cytoplasm at a certain stage of photosynthetic induction. The results suggest highly dynamic exchange of metabolites between stationary chloroplasts lining the microfluidic pathway and the streaming cytoplasm upon light-dark and dark-light transitions. Evidence is obtained that slow stages of chlorophyll fluorescence induction in algae with rapid cytoplasmic streaming directly depend on cyclosis-mediated long-distance delivery of metabolites produced far beyond the analyzed cell area.

Structural and Functional Heat Stress Responses of Chloroplasts of Arabidopsis thaliana

Temperature elevations constitute a major threat to plant performance. In recent years, much was learned about the general molecular mode of heat stress reaction of plants. The current research focuses on the integration of the knowledge into more global networks, including the reactions of cellular compartments. For instance, chloroplast function is central for plant growth and survival, and the performance of chloroplasts is tightly linked to the general status of the cell and vice versa. We examined the changes in photosynthesis, chloroplast morphology and proteomic composition posed in Arabidopsis thaliana chloroplasts after a single or repetitive heat stress treatment over a period of two weeks. We observed that the acclimation is potent in the case of repetitive application of heat stress, while a single stress results in lasting alterations. Moreover, the physiological capacity and its adjustment are dependent on the efficiency of the protein translocation process as judged from the analysis of mutants of the two receptor units of the chloroplast translocon, TOC64, and TOC33. In response to repetitive heat stress, plants without TOC33 accumulate Hsp70 proteins and plants without TOC64 have a higher content of proteins involved in thylakoid structure determination when compared to wild-type plants.

Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant

The Arabidopsis mutant rcd1 is tolerant to methyl viologen (MV). MV enhances the Mehler reaction, i.e. electron transfer from Photosystem I (PSI) to O₂, generating reactive oxygen species (ROS) in the chloroplast. To study the MV tolerance of rcd1, we first addressed chloroplast thiol redox enzymes potentially implicated in ROS scavenging. NADPH-thioredoxin oxidoreductase type C (NTRC) was more reduced in rcd1. NTRC contributed to the photosynthetic and metabolic phenotypes of rcd1, but did not determine its MV tolerance. We next tested rcd1 for alterations in the Mehler reaction. In rcd1, but not in the wild type, the PSI-to-MV electron transfer was abolished by hypoxic atmosphere. A characteristic feature of rcd1 is constitutive expression of mitochondrial dysfunction stimulon (MDS) genes that affect mitochondrial respiration. Similarly to rcd1, in other MDS-overexpressing plants hypoxia also inhibited the PSI-to-MV electron transfer. One possible explanation is that the MDS gene products may affect the Mehler reaction by altering the availability of O₂. In green tissues, this putative effect is masked by photosynthetic O₂ evolution. However, O₂ evolution was rapidly suppressed in MV-treated plants. Transcriptomic meta-analysis indicated that MDS gene expression is linked to hypoxic response not only under MV, but also in standard growth conditions. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Inhibition of endosomal trafficking by brefeldin A interferes with long-distance interaction between chloroplasts and plasma membrane transporters

The huge internodal cells of the characean green algae are a convenient model to study long-range interactions between organelles via cytoplasmic streaming. It has been shown previously that photometabolites and reactive oxygen species released by illuminated chloroplasts are transmitted to remote shaded regions where they interfere with photosynthetic electron transport and the differential activity of plasma membrane transporters, and recent findings indicated the involvement of organelle trafficking pathways. In the present study, we applied pulse amplitude-modulated microscopy and pH-sensitive electrodes to study the effect of brefeldin A (BFA), an inhibitor of vesicle trafficking, on long-distance interactions in Chara australis internodal cells. These data were compared with BFA-induced changes in organelle number, size and distribution using fluorescent dyes and confocal laser scanning microscopy. We found that BFA completely and immediately inhibited endocytosis in internodal cells and induced the aggregation of organelles into BFA compartments within 30-120 min of treatment. The comparison with the physiological data suggests that the early response, the arrest of endocytosis, is related to the attenuation of differences in surface pH, whereas the longer lasting formation of BFA compartments is probably responsible for the acceleration of the cyclosis-mediated interaction between chloroplasts. These data indicate that intracellular turnover of membrane material might be important for the circulation of electric currents between functionally distinct regions in illuminated characean internodes and that translational movement of metabolites is delayed by transient binding of the transported substances to organelles.

Photosynthesis, respiration and growth: A carbon and energy balancing act for alternative oxidase

This review summarizes knowledge of alternative oxidase, a mitochondrial electron transport chain component that lowers the ATP yield of plant respiration. Analysis of mutant and transgenic plants has established that alternative oxidase activity supports leaf photosynthesis. The interaction of alternative oxidase respiration with chloroplast metabolism is important under conditions that challenge energy and/or carbon balance in the photosynthetic cell. Under such conditions, alternative oxidase provides an extra-chloroplastic means to optimize the status of chloroplast energy pools (ATP, NADPH) and to manage cellular carbohydrate pools in response to changing rates of carbon fixation and carbon demand for growth and maintenance. Transcriptional and post-translational mechanisms ensure that alternative oxidase can respond effectively when carbon and energy balance are being challenged. This function appears particularly significant under abiotic stress conditions such as water deficit, high salinity, or temperature extremes. Under such conditions, alternative oxidase respiration positively affects growth and stress tolerance, despite it lowering the energy yield and carbon use efficiency of respiration. In part, this beneficial effect relates to the ability of alternative oxidase respiration to prevent excessive reactive oxygen species generation in both mitochondria and chloroplasts. Recent evidence suggests that alternative oxidase respiration is an interesting target for crop improvement.

Rising atmospheric CO2 concentration inhibits nitrate assimilation in shoots but enhances it in roots of C3 plants

We have proposed that rising atmospheric CO₂ concentrations inhibit malate production in chloroplasts and thus impede assimilation of nitrate into protein in shoots of C₃ plants, a phenomenon that will strongly influence primary productivity and food security under the environmental conditions anticipated during the next few decades. Although hundreds of studies support this proposal, several publications in 2018 and 2019 purport to present counterevidence. The following study evaluates these publications as well as presents new data that elevated CO₂ enhances root nitrate assimilation in wheat and Arabidopsis while it inhibits shoot nitrate assimilation.

Does the stromal concentration of Pi control chloroplast ATP synthase protein amount in contrasting growth environments?

Changes in the growth environment can generate imbalances in chloroplast photosynthetic metabolism. Under water deficit, stomatal closure limits CO2 availability such that the production of ATP and NADPH by the thylakoid membrane-localized electron transport chain may not match the consumption of these energy intermediates by the stroma-localized Calvin-Benson cycle, thus challenging energy balance. Alternatively, in an elevated CO2 atmosphere, carbon fixation by the Calvin-Benson cycle may outpace the activity of downstream carbohydrate-utilizing processes, thus challenging carbon balance. Our previous studies have shown that, in both of the above scenarios, a mitochondrial alternative oxidase contributes to maintaining energy or carbon balance, highlighting the importance of photosynthesis-respiration interactions in optimizing photosynthesis in different growth environments. In these previous studies, we observed aberrant amounts of chloroplast ATP synthase protein across the different transgenic plant lines and growth conditions, compared to wild-type. Based on these observations, we develop here the hypothesis that an important determinant of chloroplast ATP synthase protein amount is the stromal concentration of inorganic phosphate. ATP synthase is a master regulator of photosynthesis. Coarse control of ATP synthase protein amount by the stromal inorganic phosphate status could provide a means to coordinate the electron transport and carbon fixation reactions of photosynthesis.

FLOURY ENDOSPERM16 encoding a NAD-dependent cytosolic malate dehydrogenase plays an important role in starch synthesis and seed development in rice

Starch is the most important form of energy storage in cereal crops. Many key enzymes involved in starch biosynthesis have been identified. However, the molecular mechanisms underlying the regulation of starch biosynthesis are largely unknown. In this study, we isolated a novel floury endosperm rice (Oryza sativa) mutant flo16 with defective starch grain (SG) formation. The amylose content and amylopectin structure were both altered in the flo16 mutant. Map-based cloning and complementation tests demonstrated that FLO16 encodes a NAD-dependent cytosolic malate dehydrogenase (CMDH). The ATP contents were decreased in the mutant, resulting in significant reductions in the activity of starch synthesis-related enzymes. Our results indicated that FLO16 plays a critical role in redox homeostasis that is important for compound SG formation and subsequent starch biosynthesis in rice endosperm. Overexpression of FLO16 significantly improved grain weight, suggesting a possible application of FLO16 in rice breeding. These findings provide a novel insight into the regulation of starch synthesis and seed development in rice.

Transcript and metabolic adjustments triggered by drought in Ilex paraguariensis leaves

Abscisic acid is involved in the drought response of Ilex paraguariensis. Acclimation includes root growth stimulation, stomatal closure, osmotic adjustment, photoprotection, and regulation of nonstructural carbohydrates and amino acid metabolisms. Ilex paraguariensis (yerba mate) is cultivated in the subtropical region of South America, where the occurrence of drought episodes limit yield. To explore the mechanisms that allow I. paraguariensis to overcome dehydration, we investigated (1) how gene expression varied between water-stressed and non-stressed plants and (2) in what way the modulation of gene expression was linked to physiological status and metabolite composition. A total of 4920 differentially expressed transcripts were obtained through RNA-Seq after water deprivation. Drought induced the expression of several transcripts involved in the ABA-signalling pathway. Stomatal closure and leaf osmotic adjustments were promoted to minimize water loss, and these responses were accompanied by a high transcriptional remodeling of stress perception, signalling and transcriptional regulation, the photoprotective and antioxidant systems, and other stress-responsive genes. Simultaneously, significant changes in metabolite contents were detected. Glutamine, phenylalanine, isomaltose, fucose, and malate levels were shown to be positively correlated with dehydration. Principal component analysis showed differences in the metabolic profiles of control and stressed leaves. These results provide a comprehensive overview of how I. paraguariensis responds to dehydration at transcriptional and metabolomic levels and provide further characterization of the molecular mechanisms associated with drought response in perennial subtropical species.

The plastidial pentose phosphate pathway is essential for postglobular embryo development in Arabidopsis

Many mutations that affect plastidial metabolism are embryo-lethal, as expected if the disrupted genes encode enzymes with essential housekeeping functions. However, some mutations that disrupt the plastidial oxidative pentose phosphate pathway (OPPP) cause developmental defects, as well as embryo arrest at the globular stage of development. We show that the OPPP provides the substrate for the pathway of purine synthesis, ribose-5-phosphate, and is thus essential for the generation of nucleic acids during the very early stages of embryo development. Inadequate purine synthesis leads to abnormal patterns of cell division in the embryo and blocks development beyond the globular stage. Therefore, defects in primary metabolic pathways can have profound consequences for development as well as simply reducing growth.

Large numbers of genes essential for embryogenesis in Arabidopsis encode enzymes of plastidial metabolism. Disruption of many of these genes results in embryo arrest at the globular stage of development. However, the cause of lethality is obscure. We examined the role of the plastidial oxidative pentose phosphate pathway (OPPP) in embryo development. In nonphotosynthetic plastids the OPPP produces reductant and metabolic intermediates for central biosynthetic processes. Embryos with defects in various steps in the oxidative part of the OPPP had cell division defects and arrested at the globular stage, revealing an absolute requirement for the production via these steps of ribulose-5-phosphate. In the nonoxidative part of the OPPP, ribulose-5-phosphate is converted to ribose-5-phosphate (R5P)—required for purine nucleotide and histidine synthesis—and subsequently to erythrose-4-phosphate, which is required for synthesis of aromatic amino acids. We show that embryo development through the globular stage specifically requires synthesis of R5P rather than erythrose-4-phosphate. Either a failure to convert ribulose-5-phosphate to R5P or a block in purine nucleotide biosynthesis beyond R5P perturbs normal patterning of the embryo, disrupts endosperm development, and causes early developmental arrest. We suggest that seed abortion in mutants unable to synthesize R5P via the oxidative part of the OPPP stems from a lack of substrate for synthesis of purine nucleotides, and hence nucleic acids. Our results show that the plastidial OPPP is essential for normal developmental progression as well as for growth in the embryo.

Interchloroplast communications in Chara are suppressed under the alkaline bands and are relieved after the plasma membrane excitation

Immobile chloroplasts in Chara internodal cells release photometabolites into the streaming cytoplasm that distributes the exported solutes and provides metabolic connectivity between spatially remote plastids. The metabolite transmission by fluid flow is evident from chlorophyll fluorescence changes in shaded chloroplasts upon local illumination applied upstream of the analyzed area. The connectivity correlates with the pH pattern on cell surface: it is strong in cell regions with high H⁺-pump activity and is low in regions featuring large passive H⁺ influx (OH^- efflux). One explanation for low connectivity under the alkaline bands is that H⁺ influx lowers the cytoplasmic pH, thus retarding metabolic conversions of solutes carried by the microfluidic transporter. The cessation of H⁺ influx across the plasma membrane by eliciting the action potential and by adding NH₄Cl into the medium greatly enhanced the amplitude of cyclosis-mediated fluorescence transients. The transition from latent to the transmissive state after the dark pretreatment was paralleled by the temporary increase in chlorophyll fluorescence, reflecting changes in photosynthetic electron transport. It is proposed that the connectivity between distant chloroplasts is controlled by cytoplasmic pH.

Maintaining homeostasis by controlled alternatives for energy distribution in plant cells under changing conditions of supply and demand

Plants depend on light energy for the generation of ATP and reductant as well as on supply of nutrients (inorganic C, N, and S compounds) to successfully produce biomass. Any excess of reducing power or lack of electron acceptors can lead to the formation of reactive oxygen species (ROS). Multiple systems are operating to avoid imbalances and subsequent oxidative stress by efficiently scavenging any formed ROS. Plants can sense an upcoming imbalance and correspondingly adapt to changed conditions not only by an increase of ROS scavengers, but also by using excess incoming light energy productively for assimilatory processes in actively metabolizing cells of growing leaves. CO₂ assimilation in chloroplasts is controlled by various redox-regulated enzymes; their activation state is strictly linked to metabolism due to the effects of small molecules on their actual activation state. Shuttle systems for indirect transfer of reducing equivalents and ATP specifically distribute the energy fluxes between compartments for optimal biomass production. Integration of metabolic and redox signals involves the cytosolic enzyme glyceraldehyde-3-P dehydrogenase (GapC) and some of its many moonlighting functions. Its redox- and metabolite-dependent interactions with the mitochondrial outer membrane, the cytoskeleton, and its occurrence in the nucleus are examples of these additional functions. Induction of the genes required to achieve an optimal response suitable for the respective conditions allows for growth when plants are exposed to different light intensities and nutrient conditions with varying rates of energy input and different assimilatory pathways for its consumption are the required in the long term. A plant-specific respiratory pathway, the alternative oxidase (AOX), functions as a site to convert excess electrons into heat. For acclimation, any imbalance is sensed and elicits signal transduction to induce the required genes. Examples for regulated steps in this sequence of events are given in this review. Continuous adjustment under natural conditions allows for adaptive responses. In contrast, sudden light stress, as employed when analyzing stress responses in lab experiments, frequently results in cell destruction. Knowledge of all the flexible regulatory mechanisms, their responsiveness, and their interdependencies is needed when plant growth is to be engineered to optimize biomass and production of any desired molecules.

Capturing Biochemical Diversity in Cassava ( Manihot esculenta Crantz) through the Application of Metabolite Profiling

Cassava ( Manihot esculenta Crantz) is the predominant staple food in Sub-Saharan Africa (SSA) and an industrial crop in South East Asia. Despite focused breeding efforts for increased yield, resistance, and nutritional value, cassava breeding has not advanced at the same rapidity as other staple crops. In the present study, metabolomic techniques were implemented to characterize the chemotypes of selected cassava accessions and assess potential resources for the breeding program. The metabolite data analyzed was applied to describe the biochemical diversity available in the panel, identifying South American accessions as the most diverse. Genotypes with distinct phenotypic traits showed a representative metabolite profile and could be clearly identified, even if the phenotypic trait was a root characteristic, e.g., high amylose content.

Malate valves: old shuttles with new perspectives

Malate valves act as powerful systems for balancing the ATP/NAD(P)H ratio required in various subcellular compartments in plant cells. As components of malate valves, isoforms of malate dehydrogenases (MDHs) and dicarboxylate translocators catalyse the reversible interconversion of malate and oxaloacetate and their transport. Depending on the co-enzyme specificity of the MDH isoforms, either NADH or NADPH can be transported indirectly. Arabidopsis thaliana possesses nine genes encoding MDH isoenzymes. Activities of NAD-dependent MDHs have been detected in mitochondria, peroxisomes, cytosol and plastids. In addition, chloroplasts possess a NADP-dependent MDH isoform. The NADP-MDH as part of the 'light malate valve' plays an important role as a poising mechanism to adjust the ATP/NADPH ratio in the stroma. Its activity is strictly regulated by post-translational redox-modification mediated via the ferredoxin-thioredoxin system and fine control via the NADP⁺ /NADP(H) ratio, thereby maintaining redox homeostasis under changing conditions. In contrast, the plastid NAD-MDH ('dark malate valve') is constitutively active and its lack leads to failure in early embryo development. While redox regulation of the main cytosolic MDH isoform has been shown, knowledge about regulation of the other two cytosolic MDHs as well as NAD-MDH isoforms from peroxisomes and mitochondria is still lacking. Knockout mutants lacking the isoforms from chloroplasts, mitochondria and peroxisomes have been characterised, but not much is known about cytosolic NAD-MDH isoforms and their role in planta. This review updates the current knowledge on MDH isoforms and the shuttle systems for intercompartmental dicarboxylate exchange, focusing on the various metabolic functions of these valves.

Long-range interactions of Chara chloroplasts are sensitive to plasma-membrane H+ flows and comprise separate photo- and dark-operated pathways

Local illumination of the characean internode with a 30-s pulse of white light was found to induce the delayed transient increase of modulated chlorophyll fluorescence in shaded cell parts, provided the analyzed region is located downstream in the cytoplasmic flow at millimeter distances from the light spot. The fluorescence response to photostimulation of a remote cell region indicates that the metabolites produced by source chloroplasts in an illuminated region are carried downstream with the cytoplasmic flow, thus ensuring long-distance communications between anchored plastids in giant internodal cells. The properties of individual stages of metabolite signaling are not yet well known. We show here that the export of assimilates and/or reducing equivalents from the source chloroplasts into the flowing cytoplasm is largely insensitive to the direction of plasma-membrane H⁺ flows, whereas the events in sink regions where these metabolites are delivered to the acceptor chloroplasts under dim light are controlled by H⁺ fluxes across the plasma membrane. The fluorescence response to local illumination of remote cell regions was best pronounced under weak background light and was also observed in a modified form within 1-2 min after the transfer of cell to darkness. The fluorescence transients in darkened cells were suppressed by antimycin A, an inhibitor of electron transfer from ferredoxin to plastoquinone, whereas the fluorescence response under background light was insensitive to this inhibitor. We conclude that the accumulation of reduced metabolites in the stroma leads to the reduction of photosystem II primary quinone acceptor (Q_A) via two separate (photochemical and non-photochemical) pathways.

Identification of key genes involved in the phenotypic alterations of res (restored cell structure by salinity) tomato mutant and its recovery induced by salt stress through transcriptomic analysis

BACKGROUND

The res (restored cell structure by salinity) mutant, recently identified as the first tomato mutant accumulating jasmonate in roots under non-stressful conditions, exhibits a remarkable growth inhibition and morphological alterations in roots and leaves, which are suppressed when the mutant plants are exposed to salinity. In order to understand the molecular basis of the phenotype recovery induced by salt stress in the res mutant, we carried out a comparative transcriptomic analysis in roots and leaves of wild-type and res plants in absence of stress (control) and when the phenotypic recovery of res mutant began to be observed upon salt stress (5 days of 200 mM NaCl).

RESULTS

The number of differentially expressed genes was three times greater in roots than in leaves of res vs WT plants grown in control, and included the down-regulation of growth-promoting genes and the up-regulation of genes involved in Ca²⁺ signalling, transcription factors and others related to stress responses. However, these expression differences were attenuated under salt stress, coinciding with the phenotypic normalisation of the mutant. Contrarily to the attenuated response observed in roots, an enhanced response was found in leaves under salt stress. This included drastic expression changes in several circadian clock genes, such as GIGANTEA1, which was down-regulated in res vs WT plants. Moreover, the higher photosynthetic efficiency of res leaves under salt stress was accompanied by specific salt-upregulation of the genes RUBISCO ACTIVASE1 and ALTERNATIVE OXIDASE1A. Very few genes were found to be differentially expressed in both tissues (root and leaf) and conditions (control and salt), but this group included SlWRKY39 and SlMYB14 transcription factors, as well as genes related to protein homeostasis, especially protease inhibitors such as METALLOCARBOXYPEPTIDASE INHIBITOR, which also seem to play a role in the phenotype recovery and salt tolerance of res mutant.

CONCLUSIONS

In summary, in this study we have identified genes which seem to have a prominent role in salt tolerance. Moreover, we think this work could contribute to future breeding of tomato crops with increased stress tolerance.

Ferredoxin/thioredoxin system plays an important role in the chloroplastic NADP status of Arabidopsis

NADP is a key electron carrier for a broad spectrum of redox reactions, including photosynthesis. Hence, chloroplastic NADP status, as represented by redox status (ratio of NADPH to NADP⁺ ) and pool size (sum of NADPH and NADP⁺ ), is critical for homeostasis in photosynthetic cells. However, the mechanisms and molecules that regulate NADP status in chloroplasts remain largely unknown. We have now characterized an Arabidopsis mutant with imbalanced NADP status (inap1), which exhibits a high NADPH/NADP⁺ ratio and large NADP pool size. inap1 is a point mutation in At2g04700, which encodes the catalytic subunit of ferredoxin/thioredoxin reductase. Upon illumination, inap1 demonstrated earlier increases in NADP pool size than the wild type did. The mutated enzyme was also found in vitro to inefficiently reduce m-type thioredoxin, which activates Calvin cycle enzymes, and NADP-dependent malate dehydrogenase to export reducing power to the cytosol. Accordingly, Calvin cycle metabolites and amino acids diminished in inap1 plants. In addition, inap1 plants barely activate NADP-malate dehydrogenase, and have an altered redox balance between the chloroplast and cytosol, resulting in inefficient nitrate reduction. Finally, mutants deficient in m-type thioredoxin exhibited similar light-dependent NADP dynamics as inap1. Collectively, the data suggest that defects in ferredoxin/thioredoxin reductase and m-type thioredoxin decrease the consumption of NADPH, leading to a high NADPH/NADP⁺ ratio and large NADP pool size. The data also suggest that the fate of NADPH is an important influence on NADP pool size.

Manganese binding to Rubisco could drive a photorespiratory pathway that increases the energy efficiency of photosynthesis

Most plants, contrary to popular belief, do not waste over 30% of their photosynthate in a futile cycle called photorespiration. Rather, the photorespiratory pathway generates additional malate in the chloroplast that empowers many energy-intensive chemical reactions, such as those involved in nitrate assimilation. Thus, the balance between carbon fixation and photorespiration determines the plant carbon-nitrogen balance and protein concentrations. Plant protein concentrations, in turn, depend not only on the relative concentrations of carbon dioxide and oxygen in the chloroplast but also on the relative activities of magnesium and manganese, which are metals that associate with several key enzymes in the photorespiratory pathway and alter their function. Understanding the regulation of these processes is critical for sustaining food quality under rising CO2 atmospheres.

Malate transported from chloroplast to mitochondrion triggers production of ROS and PCD in Arabidopsis thaliana

Programmed cell death (PCD) is a fundamental biological process. Deficiency in MOSAIC DEATH 1 (MOD1), a plastid-localized enoyl-ACP reductase, leads to the accumulation of reactive oxygen species (ROS) and PCD, which can be suppressed by mitochondrial complex I mutations, indicating a signal from chloroplasts to mitochondria. However, this signal remains to be elucidated. In this study, through cloning and analyzing a series of mod1 suppressors, we reveal a comprehensive organelle communication pathway that regulates the generation of mitochondrial ROS and triggers PCD. We show that mutations in PLASTIDIAL NAD-DEPENDENT MALATE DEHYDROGENASE (plNAD-MDH), chloroplastic DICARBOXYLATE TRANSPORTER 1 (DiT1) and MITOCHONDRIAL MALATE DEHYDROGENASE 1 (mMDH1) can each rescue the ROS accumulation and PCD phenotypes in mod1, demonstrating a direct communication from chloroplasts to mitochondria via the malate shuttle. Further studies demonstrate that these elements play critical roles in the redox homeostasis and plant growth under different photoperiod conditions. Moreover, we reveal that the ROS level and PCD are significantly increased in malate-treated HeLa cells, which can be dramatically attenuated by knockdown of the human gene MDH2, an ortholog of Arabidopsis mMDH1. These results uncover a conserved malate-induced PCD pathway in plant and animal systems, revolutionizing our understanding of the communication between organelles.

Overexpression of plastidic maize NADP-malate dehydrogenase (ZmNADP-MDH) in Arabidopsis thaliana confers tolerance to salt stress

The plastidic C4 Zea mays NADP-malate dehydrogenase (ZmNADP-MDH), responsible for catalysis of oxaloacetate to malate, was overexpressed in Arabidopsis thaliana to assess its impact on photosynthesis and tolerance to salinity stress. Different transgenic lines were produced having ~3-6-fold higher MDH protein abundance and NADP-MDH enzyme activity than vector control. The overexpressors had similar chlorophyll, carotenoid, and protein content as that of vector control. Their photosynthetic electron transport rates, carbon assimilation rate, and consequently fresh weight and dry weight were almost similar. However, these overexpressors were tolerant to salt stress (150 mM NaCl). In saline environment, the Fv/Fm ratio, yield of photosystem II, chlorophyll, and protein content were higher in ZmNADP-MDH overexpressor than vector control. Under identical conditions, the generation of reactive oxygen species (H₂O₂) and production of malondialdehyde, a membrane lipid peroxidation product, were lower in overexpressors. In stress environment, the structural distortion of granal organization and swelling of thylakoids were less pronounced in ZmNADP-MDH overexpressing plants as compared to the vector control. Chloroplastic NADP-MDH in consort with cytosolic and mitochondrial NAD-MDH plays an important role in exporting reducing power (NADPH) and exchange of metabolites between different cellular compartments that maintain the redox homeostasis of the cell via malate valve present in chloroplast envelope membrane. The tolerance of NADP-MDH overexpressors to salt stress could be due to operation of an efficient malate valve that plays a major role in maintaining the cellular redox environment.

Improved chloroplast energy balance during water deficit enhances plant growth: more crop per drop

The non-energy-conserving alternative oxidase (AOX) respiration of plant mitochondria is known to interact with chloroplast photosynthesis. This may have consequences for growth, particularly under sub-optimal conditions when energy imbalances can impede photosynthesis. This hypothesis was tested by comparing the metabolism and growth of wild-type Nicotiana tabacum with that of AOX knockdown and overexpression lines during a prolonged steady-state mild to moderate water deficit. Under moderate water deficit, the AOX amount was an important determinant of the rate of both mitochondrial respiration in the light and net photosynthetic CO2 assimilation (A) at the growth irradiance. In particular, AOX respiration was necessary to maintain optimal proton and electron fluxes at the chloroplast thylakoid membrane, which in turn prevented a water-deficit-induced biochemical limitation of photosynthesis. As a result of differences in A, AOX overexpressors gained more biomass and knockdowns gained less biomass than wild-type during moderate water deficit. Biomass partitioning also differed, with the overexpressors having a higher percentage, and the knockdowns having a lower percentage, of total above-ground biomass in reproductive tissue than wild-type. The results establish that improving chloroplast energy balance by using a non-energy-conserving respiratory electron sink can increase photosynthesis and growth during prolonged water deficit.

Effects of free air carbon dioxide enrichment (FACE) on nitrogen assimilation and growth of winter wheat under nitrate and ammonium fertilization

A 2-year Free Air CO₂ Enrichment (FACE) experiment was conducted with winter wheat. It was investigated whether elevated atmospheric CO₂ concentration (e[CO₂ ]) inhibit nitrate assimilation and whether better growth and nitrogen acquisition under e[CO₂ ] can be achieved with an ammonium-based fertilization as it was observed in hydroponic culture with wheat. Under e[CO₂ ] a decrease in nitrate assimilation has been discussed as the cause for observed declines in protein concentration in C₃ cereals. Wheat was grown under ambient [CO₂ ] and e[CO₂ ] (600 ppm) with three levels (deficiency, optimal, and excessive) of nitrate-based fertilization (calcium ammonium nitrate; CAN) or with optimal ammonium-based fertilization. Ammonium fertilization was applied via injection of an ammonium solution into the soil in the 1st year and by surface application of urea combined with nitrification inhibitors (UNI) in the 2nd year. Results showed that ammonium-based fertilization was successfully achieved in the 2nd year with respect to nitrification control, as soil ammonium concentration was considerably higher over the growing season for UNI fertilized plots compared to optimal CAN plots. Also, stem nitrate concentration, flag leaf nitrate reductase activity, and transcript levels were lower in UNI fertilized plants compared to optimal CAN. Regarding the e[CO₂ ] effect on nitrate reductase activity and transcript levels, no alteration could be observed for any nitrogen fertilizer treatment. Flag leaf growth was stimulated under e[CO₂ ] leading to an enhanced nitrate reductase activity referred to m² ground area at late flowering being in line with a higher nitrogen acquisition under e[CO₂ ]. Moreover, nitrogen acquisition was considerably higher in nitrate fertilized plants compared to ammonium fertilized plants under e[CO₂ ]. Our results obtained under field conditions show that a change from nitrate- to ammonium-based fertilization will not lead to a better growth and nitrogen acquisition of winter wheat under future e[CO₂ ].

Cyclosis-mediated long distance communications of chloroplasts in giant cells of Characeae

Long-distance communications in giant characean internodal cells involve cytoplasmic streaming as an effective means for transportation of regulatory substances. The local illumination of Chara corallina Klein ex C.L.Willdenow internodal cells with an intense 30s pulse of white light caused a transient increase of modulated chlorophyll fluorescence in cell regions positioned downstream the cytoplasmic flow after a delay whose duration increased with the axial distance from the light source. No changes in fluorescence were observed in cell regions residing upstream of the light spot. The transient increase in actual fluorescence F' in cell areas exposed to constant dim illumination at large distances from the brightly lit area indicates the transmission of photosynthetically active metabolite between chloroplasts separated by 1-5mm distances. The shapes of fluorescence transients were sensitive to retardation of cytoplasmic streaming by cytochalasin D and to variations in cyclosis velocity during gradual recovery of streaming after an instant arrest of cyclosis by elicitation of the action potential. Furthermore, the analysed fluorescence transients were skewed on the ascending or descending fronts depending on the position of light-modulated cytoplasmic package at the moment of streaming cessation with respect to the point of measurements. The observations are simulated in qualitative terms with a simplified streaming-diffusion model.

Plants increase CO2 uptake by assimilating nitrogen via the photorespiratory pathway

Photorespiration is a major bioengineering target for increasing crop yields as it is often considered a wasteful process. Photorespiratory metabolism is integrated into leaf metabolism and thus may have certain benefits. Here, we show that plants can increase their rate of photosynthetic CO₂ uptake when assimilating nitrogen de novo via the photorespiratory pathway by fixing carbon as amino acids in addition to carbohydrates. Plants fed NO₃^- had higher rates of CO₂ assimilation under photorespiratory than low-photorespiratory conditions, while plants lacking NO₃^- nutrition exhibited lower stimulation of CO₂ uptake. We modified the widely used Farquhar, von Caemmerer and Berry photosynthesis model to include the carbon and electron requirements for nitrogen assimilation via the photorespiratory pathway. Our modified model improves predictions of photosynthetic CO₂ uptake and of rates of photosynthetic electron transport. The results highlight how photorespiration can improve photosynthetic performance despite reducing the efficiency of Rubisco carboxylation.