Photorespiration: metabolic pathways and their role in stress protection

A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis

Photorespiration functions in part to support photosynthetic performance, especially under stress such as high light, yet the underlying mechanisms are poorly understood. To identify modulators of photorespiration under high light, we have isolated genetic suppressors of the photorespiratory mutant hpr1 (hydroxypyruvate reductase 1) from Arabidopsis. A suppressor that partially rescues hpr1 is mapped to GLYR1, which encodes the cytosolic glyoxylate reductase 1 that converts glyoxylate to glycolate. Independent glyr1 mutants also partially rescue hpr1 and another photorespiratory mutant, catalase 2. Our genetic, transcriptomic and metabolic profiling analyses together reveal a connection between cytosolic glyoxylate and a non-canonical photorespiratory route mediated by HPR2, which we name the photorespiratory glyoxylate shunt. This shunt complements the canonical photorespiratory pathway and is especially critical when high photorespiratory fluxes are required and when the major photorespiratory pathway is deficient. Our findings support the metabolic flexibility of photorespiration and may help to improve crop performance under stress.

Nitrogen source type modulates heat stress response in coral symbiont (Cladocopium goreaui)

Ocean warming due to climate change endangers coral reefs, and regional nitrogen overloading exacerbates the vulnerability of reef-building corals as the dual stress disrupts coral-Symbiodiniaceae mutualism. Different forms of nitrogen may create different interactive effects with thermal stress, but the underlying mechanisms remain elusive. To address the gap, we measured and compared the physiological and transcriptional responses of the Symbiodiniaceae Cladocopium goreaui to heat stress (31°C) when supplied with different types of nitrogen (nitrate, ammonium, or urea). Under heat stress (HS), cell proliferation and photosynthesis of C. goreaui declined, while cell size, lipid storage, and total antioxidant capacity increased, both to varied extents depending on the nitrogen type. Nitrate-cultured cells exhibited the most robust acclimation to HS, as evidenced by the fewest differentially expressed genes (DEGs) and less ROS accumulation, possibly due to activated nitrate reduction and enhanced ascorbate biogenesis. Ammonium-grown cultures exhibited higher algal proliferation and ROS scavenging capacity due to enhanced carotenoid and ascorbate quenching, but potentially reduced host recognizability due to the downregulation of N-glycan biosynthesis genes. Urea utilization led to the greatest ROS accumulation as genes involved in photorespiration, plant respiratory burst oxidase (RBOH), and protein refolding were markedly upregulated, but the greatest cutdown in photosynthate potentially available to corals as evidenced by photoinhibition and selfish lipid storage, indicating detrimental effects of urea overloading. The differential warming nitrogen-type interactive effects documented here has significant implication in coral-Symbiodiniaceae mutualism, which requires further research.IMPORTANCERegional nitrogen pollution exacerbates coral vulnerability to globally rising sea-surface temperature, with different nitrogen types exerting different interactive effects. How this occurs is poorly understood and understudied. This study explored the underlying mechanism by comparing physiological and transcriptional responses of a coral symbiont to heat stress under different nitrogen supplies (nitrate, ammonium, and urea). The results showed some common, significant responses to heat stress as well as some unique, N-source dependent responses. These findings underscore that nitrogen eutrophication is not all the same, the form of nitrogen pollution should be considered in coral conservation, and special attention should be given to urea pollution.

FERONIA regulates salt tolerance in Arabidopsis by controlling photorespiratory flux

Photorespiration is an energetically costly metabolic pathway in plants that responds to environmental stresses. The molecular basis of the regulation of the photorespiratory cycle under stress conditions remains unclear. Here, we discovered that FERONIA (FER) regulates photorespiratory flow under salt stress in Arabidopsis (Arabidopsis thaliana). FER mutation results in hypersensitivity to salt stress, but disruption of ferredoxin-dependent glutamate synthase 1 (GLU1), an enzyme that participates in the photorespiratory pathway by producing glutamate, greatly suppresses fer-4 hypersensitivity to salt stress primarily due to reduced glycine yield. In contrast, disrupting mitochondrial serine hydroxymethyltransferase1 (SHM1), which is supposed to increase glycine levels by hampering the conversion of glycine to serine in the photorespiratory cycle, aggravates fer-4 hypersensitivity to salt stress. Biochemical data show that FER interacts with and phosphorylates SHM1, and this phosphorylation modulates SHM1 stability. Additionally, the production of proline and its intermediate △1-pyrroline-5-carboxylate (P5C), which are both synthesized from glutamate, also contributes to fer-4 hypersensitivity to salt stress. In conclusion, this study elucidates the functional mechanism of FER in regulating salt tolerance by modulating photorespiratory flux, which greatly broadens our understanding of how plants adapt to high salinity.

Expression interplay of genes coding for calcium-binding proteins and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca2+ signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3'-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding for calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding proteins was found to be enriched for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of genes coding for proteins with EF-hand domain, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding proteins, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3' -UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability.

An integrated transcriptome and physiological analysis of nitrogen use efficiency in rice (Oryza sativa L. ssp. indica) under drought stress

Nitrogen is a critical nutrient vital for crop growth. However, our current understanding of nitrogen use efficiency (NUE) under drought remains inadequate. To delve into the molecular mechanisms underlying NUE under drought, a transcriptome and physiological co-expression analysis was performed in rice, which is particularly sensitive to drought. We conducted a pot experiment using rice grown under normal irrigation, mild drought stress, and severe drought stress. Compared to the normal treatment, drought stress led to a significant reduction in NUE across growth stages, with decreases ranging from 2.18% to 31.67%. Totals of 4,424 and 2,452 genes were identified as NUE-related DEGs that showed differential expressions (DEGs) and significantly correlated with NUE (NUE-related) under drought in the vegetative and reproductive stages, respectively. Interestingly, five genes involved in nitrogen metabolism were found in the overlapped genes of these two sets. Furthermore, the two sets of NUE-related DEGs were enriched in glyoxylate and dicarboxylate metabolism, as well as carbon fixation in photosynthetic organisms. Several genes in these two pathways were identified as hub genes in the two sets of NUE-related DEGs. This study offers new insights into the molecular mechanism of rice NUE under drought in agricultural practices and provides potential genes for breeding drought-resistant crops with high NUE.

The genome of Eleocharis vivipara elucidates the genetics of C3-C4 photosynthetic plasticity and karyotype evolution in the Cyperaceae

Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C3 photosynthesis underwater and C4 photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high-quality genome for E. vivipara, representing the first chromosome-level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi-C pattern, chromosome clustering results, and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole-genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross-section studies showed its terrestrial culms developed C4 Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co-expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C4 pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide - malic enzyme and phosphoenolpyruvate carboxykinase type C4 photosynthesis in E. vivipara, and hypothesize that the evolution of C4 photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C3 and C4 photosynthesis, offering promising avenues for crop improvement and breeding.

The mechanisms of photoinhibition and repair in plants under high light conditions and interplay with abiotic stressors

This review comprehensively examines the phenomenon of photoinhibition in plants, focusing mainly on the intricate relationship between photodamage and photosystem II (PSII) repair and the role of PSII extrinsic proteins and protein phosphorylation in these processes. In natural environments, photoinhibition occurs together with a suite of concurrent stress factors, including extreme temperatures, drought and salinization. Photoinhibition, primarily caused by high irradiance, results in a critical imbalance between the rate of PSII photodamage and its repair. Central to this process is the generation of reactive oxygen species (ROS), which not only impair the photosynthetic apparatus first PSII but also play a signalling role in chloroplasts and other cellulular structures. ROS generated under stress conditions inhibit the repair of photodamaged PSII by suppressing D1 protein synthesis and affecting PSII protein phosphorylation. Furthermore, this review considers how environmental stressors exacerbate PSII damage by interfering with PSII repair primarily by reducing de novo protein synthesis. In addition to causing direct damage, these stressors also contribute to ROS production by restricting CO2 fixation, which also reduces the intensity of protein synthesis. This knowledge has significant implications for agricultural practices and crop improvement under stressful conditions.

Strategies for adaptation to high light in plants

Plants absorb light energy for photosynthesis via photosystem complexes in their chloroplasts. However, excess light can damage the photosystems and decrease photosynthetic output, thereby inhibiting plant growth and development. Plants have developed a series of light acclimation strategies that allow them to withstand high light. In the first line of defense against excess light, leaves and chloroplasts move away from the light and the plant accumulates compounds that filter and reflect the light. In the second line of defense, known as photoprotection, plants dissipate excess light energy through non-photochemical quenching, cyclic electron transport, photorespiration, and scavenging of excess reactive oxygen species. In the third line of defense, which occurs after photodamage, plants initiate a cycle of photosystem (mainly photosystem II) repair. In addition to being the site of photosynthesis, chloroplasts sense stress, especially light stress, and transduce the stress signal to the nucleus, where it modulates the expression of genes involved in the stress response. In this review, we discuss current progress in our understanding of the strategies and mechanisms employed by plants to withstand high light at the whole-plant, cellular, physiological, and molecular levels across the three lines of defense.

Reduced diffusional limitations in carnation stems facilitate higher photosynthetic rates and reduced photorespiratory losses compared with leaves

Green stem photosynthesis has been shown to be relatively inefficient but can occasionally contribute significantly to the carbon budget of desert plants. Although the possession of green photosynthetic stems is a common trait, little is known about their photosynthetic characteristics in non-desert species. Dianthus caryophyllus is a semi-woody species with prominent green stems, which show similar photosynthetic anatomy with leaves. In the present study, we used a combination of gas exchange and chlorophyll fluorescence measurements, some of which were taken under varying O2 and CO2 partial pressures, to investigate whether the apparent anatomical similarities between the species' leaves and stems translate into similar photosynthetic physiology and capacity for CO2 assimilation. Both organs displayed high photosynthetic electron transport rates (ETR) and similar values of steady-state non-photochemical quenching (NPQ), albeit leaves could attain them faster. The analysis of OJIP transients showed that the quantum efficiencies and energy fluxes along the photosynthetic electron transport chain are largely similar between leaves and stems. Stems displayed higher total conductance to CO2 diffusion, similar biochemical properties, significantly higher photosynthetic rates and lower water use efficiency than leaves. Leaf ETR was more sensitive to sub-ambient O2 and super-ambient CO2 partial pressures, while leaves also displayed a higher relative rate of Rubisco oxygenation. We conclude that the highly responsive NPQ and the enhanced photorespiration and WUE in leaves represent photoprotective and water-conserving adaptations to the high incident light intensities they experience naturally, at the expense of higher CO2 assimilation rates, which the vertically orientated stems can readily attain.

Plant responses to co-occurring heat and water deficit stress: A comparative study of tolerance mechanisms in old and modern wheat genotypes

Global climate change increases the likelihood of co-occurrence of hot and dry spells with increased intensity, frequency, and duration. Studying the impact of the two stresses provide a better understanding of tolerance mechanisms in wheat, and our study was focused on revealing plant stress responses to different severities of combined stress at two phenophases in old and modern wheat genotypes. During the stem elongation and anthesis stages, plants were exposed to four treatments: control, deficit irrigation, combined heat, and deficit irrigation at 31 °C (HD31) and 37 °C (HD37). The modern genotypes were less affected by deficit irrigation at stem elongation as they maintained higher photosynthesis, stomatal conductance, and leaf cooling than old genotypes. When the HD37 stress was imposed during anthesis, the modern genotypes exhibited superior performance compared to the old, which was due to their higher photosynthetic rates resulting from improved biochemical regulation and a higher chlorophyll content. The plant responses varied during two phenophases under the combined stress exposure. Genotypes subjected to HD37 stress during stem elongation, photosynthesis was mainly controlled by stomatal regulation, whereas at anthesis it was predominated by biochemical regulation. These findings contribute to a deeper comprehension of plant tolerance mechanisms in response to different intensities of co-occurring hot and dry weather conditions.

Photoprotective mechanisms and higher photorespiration are key points for iron stress tolerance under heatwaves in rice

Considering the current climate change scenario, the development of heat-tolerant rice cultivars (Oryza sativa L.) is paramount for cultivation in waterlogged systems affected by iron (Fe) excess. The objective of this work was to investigate the physiological basis of tolerance to excess Fe in rice cultivars that would maintain photosynthetic efficiency at higher temperatures. In an experimental approach, two rice cultivars (IRGA424 - tolerant and IRGA417- susceptible to Fe toxicity) were exposed to two concentrations of FeSO4-EDTA, control (0.019 mM) and excess Fe (7 mM) and subsequent exposition to heatwaves at different temperatures (25 °C - control, 35, 40, 45, 50, and 55 °C). The increase in temperatures resulted in a higher Fe concentration in shoots accompanied by a lower Rubisco carboxylation rate in both cultivars, but with lower damage in the tolerant one. Stomatal limitation only occurred as a late response to Fe toxicity, especially in the sensitive cultivar. The activation of photorespiration as electron sink under Fe excess with increasing temperature during heatwaves appear as a major mechanism to alleviate oxidative stress in cultivars tolerant to excess Fe. The tolerance to iron toxicity and heat stress is associated with increased photoprotective mechanisms driving non-photochemical dissipation.

Exploration the interaction of cadmium and copper toxic effects in pakchoi (Brassica chinensis L) roots through combinatorial transcriptomic and weighted gene co-expression network analysis

The interaction between cadmium(Cd) and copper(Cu) during combined pollution can lead to more complex toxic effects on humans and plants.However, there is still a lack of sufficient understanding regarding the types of interactions at the plant molecular level and the response strategies of plants to combined pollution. To assess this, we investigated the phenotypic and transcriptomic patterns of pakchoi (Brassica chinensis L) roots in response to individual and combined pollution of Cd and Cu. The results showed that compared to single addition, the translocation factor of heavy metals in roots significantly decreased (p < 0.05) under the combined addition, resulting in higher accumulation of Cd and Cu in the roots. Transcriptomic analysis of pakchoi roots revealed that compared to single pollution, there were 312 and 1926 differentially expressed genes (DEGs) specifically regulated in the Cd2Cu20 and Cd2Cu100 combined treatments, respectively. By comparing the expression of these DEGs among different treatments, we found that the combined pollution of Cd and Cu mainly affected the transcriptome of the roots in an antagonistic manner. Enrichment analysis indicated that pakchoi roots upregulated the expression of genes involved in glucosetransferase activity, phospholipid homeostasis, proton transport, and the biosynthesis of phenylpropanoids and flavonoids to resist Cd and Cu combined pollution. Using weighted gene co-expression network analysis (WGCNA), we identified hub genes related to the accumulation of Cd and Cu in the roots, which mainly belonged to the LBD, thaumatin-like protein, ERF, MYB, WRKY, and TCP transcription factor families. This may reflect a transcription factor-driven trade-off strategy between heavy metal accumulation and growth in pakchoi roots. Additionally, compared to single metal pollution, the expression of genes related to Nramp, cation/H+ antiporters, and some belonging to the ABC transporter family in the pakchoi roots was significantly upregulated under combined pollution. This could lead to increased accumulation of Cd and Cu in the roots. These findings provide new insights into the interactions and toxic mechanisms of multiple metal combined pollution at the molecular level in plants.

Dehydration and rehydration differently affect photosynthesis and volatile monoterpenes in bryophytes with contrasting ecological traits

Bryophytes desiccate rapidly when relative humidity decreases. The capacity to withstand dehydration depends on several ecological and physiological factors. Volatile organic compounds (VOCs) may have a role in enhancing tolerance to desiccating bryophytes. However, the functions of VOCs in bryophytes have received little attention so far. We aimed to investigate the impact of a dehydration-rehydration treatment on primary carbon metabolism and volatile terpenes (VTs) in three bryophytes with contrasting ecological traits: Vessicularia dubyana, Porella platyphylla and Pleurochaete squarrosa. First, we confirmed the desiccation sensitivity gradient of the species. Under fully hydrated conditions, the photosynthetic rate (A) was inversely associated with stress tolerance, with a lower rate in more tolerant species. The partial recovery of A in P. platyphylla and P. squarrosa after rehydration confirmed the desiccation tolerance of these two species. On the other hand, A did not recover after rehydration in V. dubyana. Regarding VT, each species exhibited a distinct VT profile under optimum hydration, with the highest VT pool found in the more desiccation-sensitive species (V. dubyana). However, the observed species-specific VT pattern could be associated with the ecological habitat of each species. P. squarrosa, a moss of dry habitats, may synthesize mainly non-volatile secondary metabolites as stress-defensive compounds. On the other hand, V. dubyana, commonly found submerged, may need to invest photosynthetically assimilated carbon to synthesize a higher amount of VTs to cope with transient water stress occurrence. Further research on the functions of VTs in bryophytes is needed to deepen our understanding of their ecological significance.

How the Ethylene Biosynthesis Pathway of Semi-Halophytes Is Modified with Prolonged Salinity Stress Occurrence?

The mechanism of ethylene (ET)-regulated salinity stress response remains largely unexplained, especially for semi-halophytes and halophytes. Here, we present the results of the multifaceted analysis of the model semi-halophyte Mesembryanthemum crystallinum L. (common ice plant) ET biosynthesis pathway key components' response to prolonged (14 days) salinity stress. Transcriptomic analysis revealed that the expression of 3280 ice plant genes was altered during 14-day long salinity (0.4 M NaCl) stress. A thorough analysis of differentially expressed genes (DEGs) showed that the expression of genes involved in ET biosynthesis and perception (ET receptors), the abscisic acid (ABA) catabolic process, and photosynthetic apparatus was significantly modified with prolonged stressor presence. To some point this result was supported with the expression analysis of the transcript amount (qPCR) of key ET biosynthesis pathway genes, namely ACS6 (1-aminocyclopropane-1-carboxylate synthase) and ACO1 (1-aminocyclopropane-1-carboxylate oxidase) orthologs. However, the pronounced circadian rhythm observed in the expression of both genes in unaffected (control) plants was distorted and an evident downregulation of both orthologs' was induced with prolonged salinity stress. The UPLC-MS analysis of the ET biosynthesis pathway rate-limiting semi-product, namely of 1-aminocyclopropane-1-carboxylic acid (ACC) content, confirmed the results assessed with molecular tools. The circadian rhythm of the ACC production of NaCl-treated semi-halophytes remained largely unaffected by the prolonged salinity stress episode. We speculate that the obtained results represent an image of the steady state established over the past 14 days, while during the first hours of the salinity stress response, the view could be completely different.

Mercury species induce metabolic reprogramming in freshwater diatom Cyclotella meneghiniana

Mercury is a hazardous pollutant of global concern. While advances have been made in identifying the detrimental effects caused by Hg species in phytoplankton, knowledge gaps remain regarding the metabolomic perturbations induced by inorganic mercury (Hg(II)) and monomethylmercury (MeHg) in these organisms. Diatoms represent a major phytoplankton group essential in various global biogeochemical cycles. The current study combined targeted metabolomics, bioaccumulation, and physiological response assays to investigate metabolic perturbations in diatom Cyclotella meneghiniana exposed for 2 h to nanomolar concentrations of Hg(II) and MeHg. Our findings highlight that such exposures induce reprogramming of the metabolism of amino acids, nucleotides, fatty acids, carboxylic acids and antioxidants. These alterations were primarily mercury-species dependent. MeHg exposure induced more pronounced reprogramming of the metabolism of diatoms than Hg(II), which led to less pronounced effects on ROS generation, membrane permeability and chlorophyll concentrations. Hg(II) treatments presented distinct physiological responses, with more robust metabolic perturbations at higher exposures. The present study provides first-time insights into the main metabolic alterations in diatom C. meneghiniana during short-term exposure to Hg species, deepening our understanding of the molecular basis of these perturbations.

Measurement of Photorespiratory Cycle Enzyme Activities in Leaves Exposed to Abiotic Stress

Photorespiration, an essential metabolic component, is a classic example of interactions between the intracellular compartments of a plant cell: the chloroplast, peroxisome, mitochondria, and cytoplasm. The photorespiratory pathway is often modulated by abiotic stress and is considered an adaptive response. Monitoring the patterns of key enzymes located in different subcellular components would be an ideal approach to assessing the modulation of the photorespiratory metabolism under abiotic stress. This chapter describes the procedures for assaying several individual enzyme activities of key photorespiratory enzymes and evaluating their response to oxidative/photooxidative stress. It is essential to ascertain the presence of stress in the experimental material. Therefore, procedures for typical abiotic stress induction in leaves by highlighting without or with menadione (an oxidant that targets mitochondria) are also included.

Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light

Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions. Plants were grown for 5 wk in a low light (LL) regime, and time-resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL. The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism. This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL.

Isotopic clumping in wood as a proxy for photorespiration in trees

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO2]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R-O-CH3) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13CH2D correlates with temperature (18-28 °C) and atmospheric [CO2] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO2] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.

Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses

Glycolate oxidase (GLO) is an FMN-containing enzyme localized in peroxisomes and performs in various molecular and biochemical mechanisms. It is a key player in plant glycolate and glyoxylate accumulation pathways. The role of GLO in disease and stress resistance is well-documented in various plant species. Although studies have been conducted regarding the role of GLO genes from spinach on a microbial level, the direct response of GLO genes to various stresses in short-season and leafy plants like lettuce has not been published yet. The genome of Lactuca sativa cultivar 'Salinas' (v8) was used to identify GLO gene members in lettuce by performing various computational analysis. Dual synteny, protein-protein interactions, and targeted miRNA analyses were conducted to understand the function of GLO genes. The identified GLO genes showed further clustering into two groups i.e., glycolate oxidase (GOX) and hydroxyacid oxidase (HAOX). Genes were observed to be distributed unevenly on three chromosomes, and syntenic analysis revealed that segmental duplication was prevalent. Thus, it might be the main reason for GLO gene diversity in lettuce. Almost all LsGLO genes showed syntenic blocks in respective plant genomes under study. Protein-protein interactions of LsGLO genes revealed various functional enrichments, mainly photorespiration, and lactate oxidation, and among biological processes oxidative photosynthetic carbon pathway was highly significant. Results of in-depth analyses disclosed the interaction of GLO genes with other members of the glycolate pathway and the activity of GLO genes in various organs and developmental stages in lettuce. The extensive genome evaluation of GLO gene family in garden lettuce is believed to be a reference for cloning and studying functional analyses of GLO genes and characterizing other members of glycolate/glyoxylate biosynthesis pathway in various plant species.

Over-activation of cold tolerance in arabidopsis causes carbohydrate shortage compared with Chorispora bungeana

Many plants cope with cold stress by developing acquired freezing tolerance (AFT) through cold acclimation (CA), and some species have strong basal freezing tolerance (BFT) independent of CA. Although CA has been extensively studied, its potential in agricultural applications is still unclear. Here, carbohydrate metabolism and transcriptome in AFT plant Arabidopsis and BFT plant Chorispora bungeana were compared with each other. The results showed that, although both species were able to accumulate soluble sugars during CA, leaf starch accumulation in the daytime was almost blocked in Arabidopsis while it was greatly enhanced in C. bungeana, revealing that Arabidopsis experienced carbohydrate shortage during CA. Transcriptome and pathway enrichment analysis found that genes for photosynthesis antenna proteins were generally repressed by cold stress in both species. However, cold-up-regulated genes were enriched in protein translation in Arabidopsis, whilst they were enriched in carotenoid biosynthesis, flavonoid biosynthesis, and beta-amylases in C. bungeana. Furthermore, weighted gene co-expression network analysis (WGCNA) showed that the inhibition of starch accumulation was associated with down-regulation of genes for photosynthesis antenna proteins and up-regulation of genes for protein translation, DNA repair, and proteasome in Arabidopsis but not in C. bungeana. Taken together, our results revealed that over-activation of common tolerant mechanisms resulted in insufficient carbohydrate supplies in Arabidopsis during CA, and photoprotective mechanisms played important roles in cold adaptation of C. bungeana. These findings uncovered the drawback of CA in improving freezing tolerance and highlighted photoprotection as a possible solution for agricultural applications.

Photosynthesis and biochemical characterization of the green alga Chlamydopodium fusiforme (Chlorophyta) grown in a thin-layer cascade

Photosynthesis, growth and biochemical composition of the biomass of the freshwater microalga Chlamydopodium fusiforme cultures outdoors in a thin-layer cascade were investigated. Gross oxygen production measured off-line in samples taken from the outdoor cultures was correlated with the electron transport rate estimated from chlorophyll a fluorescence measurements. According to photosynthesis measurements, a mean of 38.9  ±  10.3 mol of photons were required to release one mole of O2, which is 4.86 times higher than the theoretical value (8 photons per 1 O2). In contrast, according to the fluorescence measurements, a mean of 11.7  ±  0.74 mol of photons were required to release 1 mol of O2. These findings indicate that fluorescence-based photosynthesis rates may not be fully replace oxygen measurements to evaluate the performance of an outdoor culture. Daily gross biomass productivity was 0.3 g DW L-1 day-1 consistently for 4 days. Biomass productivity was strongly affected by the suboptimal concentration at which the culture was operated and by the respiration rate, as the substantial volume of culture was kept in the dark (about 45% of the total volume). As the cells were exposed to excessive light, the photosynthetic activity was mainly directed to the synthesis of carbohydrates in the biomass. In the morning, carbohydrate content decreased because of the dark respiration. Per contra, protein content in the biomass was lower at the end of the day and higher in the morning due to carbohydrate consumption by respiration. The data gathered in these trials are important for the future exploitation of Chlamydopodium fusiforme as a potential novel species in the field of microalgae for the production of bio-based compounds.

High light-induced changes in whole-cell proteomic profile and its correlation with the organization of thylakoid super-complex in cyclic electron transport mutants of Chlamydomonas reinhardtii

Light and nutrients are essential components of photosynthesis. Activating the signaling cascades is critical in starting adaptive processes in response to high light. In this study, we have used wild-type (WT), cyclic electron transport (CET) mutants like Proton Gradient Regulation (PGR) (PGRL1), and PGR5 to elucidate the actual role in regulation and assembly of photosynthetic pigment-protein complexes under high light. Here, we have correlated the biophysical, biochemical, and proteomic approaches to understand the targeted proteins and the organization of thylakoid pigment-protein complexes in the photoacclimation. The proteomic analysis showed that 320 proteins were significantly affected under high light compared to the control and are mainly involved in the photosynthetic electron transport chain, protein synthesis, metabolic process, glycolysis, and proteins involved in cytoskeleton assembly. Additionally, we observed that the cytochrome (Cyt) b₆ expression is increased in the pgr5 mutant to regulate proton motive force and ATPase across the thylakoid membrane. The increased Cyt b₆ function in pgr5 could be due to the compromised function of chloroplast (cp) ATP synthase subunits for energy generation and photoprotection under high light. Moreover, our proteome data show that the photosystem subunit II (PSBS) protein isoforms (PSBS1 and PSBS2) expressed more than the Light-Harvesting Complex Stress-Related (LHCSR) protein in pgr5 compared to WT and pgrl1 under high light. The immunoblot data shows the photosystem II proteins D1 and D2 accumulated more in pgrl1 and pgr5 than WT under high light. In high light, CP43 and CP47 showed a reduced amount in pgr5 under high light due to changes in chlorophyll and carotenoid content around the PSII protein, which coordinates as a cofactor for efficient energy transfer from the light-harvesting antenna to the photosystem core. BN-PAGE and circular dichroism studies indicate changes in macromolecular assembly and thylakoid super-complexes destacking in pgrl1 and pgr5 due to changes in the pigment-protein complexes under high light. Based on this study, we emphasize that this is an excellent aid in understanding the role of CET mutants in thylakoid protein abundances and super-complex organization under high light.

Plant NADPH-dependent thioredoxin reductases are crucial for the metabolism of sink leaves and plant acclimation to elevated CO2

Plants contain three NADPH-thioredoxin reductases (NTR) located in the cytosol/mitochondria (NTRA/B) and the plastid (NTRC) with important metabolic functions. However, mutants deficient in all NTRs remained to be investigated. Here, we generated and characterised the triple Arabidopsis ntrabc mutant alongside with ntrc single and ntrab double mutants under different environmental conditions. Both ntrc and ntrabc mutants showed reduced growth and substantial metabolic alterations, especially in sink leaves and under high CO₂ (HC), as compared to the wild type. However, ntrabc showed higher effective quantum yield of PSII under both constant and fluctuating light conditions, altered redox states of NADH/NAD⁺ and glutathione (GSH/GSSG) and lower potential quantum yield of PSII in sink leaves in ambient but not high CO₂ concentrations, as compared to ntrc, suggesting a functional interaction between chloroplastic and extra-chloroplastic NTRs in photosynthesis regulation depending on leaf development and environmental conditions. Our results unveil a previously unknown role of the NTR system in regulating sink leaf metabolism and plant acclimation to HC, while it is not affecting full plant development, indicating that the lack of the NTR system can be compensated, at least to some extent, by other redox mechanisms.

Glycine differentially improved the growth and biochemical composition of Synechocystis sp. PAK13 and Chlorella variabilis DT025

The potential of microalgae to produce valuable compounds has garnered considerable attention. However, there are various challenges that hinder their large-scale industrial utilization, such as high production costs and the complexities associated with achieving optimal growth conditions. Therefore, we investigated the effects of glycine at different concentrations on the growth and bioactive compounds production of Synechocystis sp. PAK13 and Chlorella variabilis cultivated under nitrogen availability. Glycine supplementation resulted in increased biomass and bioactive primary metabolites accumulation in both species. Sugar production, particularly glucose content, significantly improved in Synechocystis at 3.33 mM glycine (1.4 mg/g). This led to enhanced organic acid, particularly malic acid, and amino acids production. Glycine stress also influenced the concentration of indole-3-acetic acid, which was significantly higher in both species compared to the control. Furthermore, fatty acids content increased by 2.5-fold in Synechocystis and by 1.36-fold in Chlorella. Overall, the exogenous application of glycine is a cheap, safe, and effective approach to enhancing sustainable microalgal biomass and bioproducts production.

Deciphering the toxicity mechanism of haloquinolines on Chlorella pyrenoidosa using QSAR and metabolomics approaches

The hazardous potential of haloquinolines (HQLs) is becoming an issue of great concern due to its wide and long-term usage in many personal care products. We examined the growth inhibition, structure-activity relationship, and toxicity mechanism of 33 HQLs on Chlorella pyrenoidosa using the 72-h algal growth inhibition assay, three-dimensional quantitative structure-activity relationship (3D-QSAR), and metabolomics. We found that the IC₅₀ (half maximal inhibitory concentration) values for 33 compounds ranged from 4.52 to > 150 mg·L^-1, most tested compounds were toxic (1 mg·L^-1 < IC₅₀ < 10 mg·L^-1) or harmful (10 mg·L^-1 < IC₅₀ < 100 mg·L^-1) for the aquatic ecosystem. Hydrophobic properties of HQLs dominate their toxicity. Halogen atoms with large volume appear at the 2, 3, 4, 5, 6, and 7-positions of the quinoline ring to significantly increase the toxicity. In algal cells, HQLs can block diverse carbohydrates, lipids, and amino acid metabolism pathways, thereby resulting in energy usage, osmotic pressure regulation, membrane integrity, oxidative stress disorder, thus fatally damaging algal cells. Therefore, our results provide insight into the toxicity mechanism and ecological risk of HQLs.

Effects of instantaneous changes in temperature, light, and salinity on the dynamics of dissolved organic carbon release by Sargassum thunbergii

Although macroalgae are regarded as the emerging fourth category of "blue carbon", few studies are available on the dynamics of dissolved organic carbon (DOC) release. Sargassum thunbergii is a typical intertidal macroalgae; and tidal action usually triggers instantaneous changes in temperature, light and salinity. Therefore, we investigated the mechanism of short-term changes in temperature, light and salinity on DOC release by S. thunbergii. As well as these factors coupled with desiccation, the combined effect of DOC release was revealed. The results showed the DOC release rate of S. thunbergii was from 0.028 to 0.037 mg C g -1(FW) h-1 under different photosynthetically active radiation (PAR, 0-1500 μmol photons m-2 s-1). The DOC release rate of S. thunbergii was from 0.008 to 0.208 mg C g -1(FW) h-1 under different salinity (5-40). The DOC release rate of S. thunbergii was from 0.031 to 0.034 mg C g -1(FW) h-1 under different temperature (10-30 °C). Either the increase in intracellular organic matter concentration due to increased photosynthesis (change in PAR and temperature, active), cell dehydration due to dry-out process (passive) or the decrease in extracellular salt concentration (passive) would lead to an increase in the difference in osmotic pressure and promote DOC release.

How Central Carbon Metabolites of Mexican Mint (Plectranthus amboinicus) Plants Are Impacted under Different Watering Regimes

Plants are sessile, and their ability to reprogram their metabolism to adapt to fluctuations in soil water level is crucial but not clearly understood. A study was performed to determine alterations in intermediate metabolites involved in central carbon metabolism (CCM) following exposure of Mexican mint (Plectranthus amboinicus) to varying watering regimes. The water treatments were regular watering (RW), drought (DR), flooding (FL), and resumption of regular watering after flooding (DHFL) or after drought (RH). Leaf cluster formation and leaf greening were swift following the resumption of regular watering. A total of 68 key metabolites from the CCM routes were found to be significantly (p < 0.01) impacted by water stress. Calvin cycle metabolites in FL plants, glycolytic metabolites in DR plants, total tricarboxylic acid (TCA) cycle metabolites in DR and DHFL plants, and nucleotide biosynthetic molecules in FL and RH plants were significantly (p < 0.05) increased. Pentose phosphate pathway (PPP) metabolites were equally high in all the plants except DR plants. Total Calvin cycle metabolites had a significantly (p < 0.001) strong positive association with TCA cycle (r = 0.81) and PPP (r = 0.75) metabolites. Total PPP metabolites had a moderately positive association with total TCA cycle metabolites (r = 0.68; p < 0.01) and a negative correlation with total glycolytic metabolites (r = -0.70; p < 0.005). In conclusion, the metabolic alterations of Mexican mint plants under different watering regimes were revealed. Future studies will use transcriptomic and proteomic approaches to identify genes and proteins that regulate the CCM route.

Proteomics for abiotic stresses in legumes: present status and future directions

Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.

Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus

Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.

Strategies for manipulating Rubisco and creating photorespiratory bypass to boost C3 photosynthesis: Prospects on modern crop improvement

Photosynthesis is a process that uses solar energy to fix CO₂ in the air and converts it into sugar, and ultimately powers almost all life activities on the earth. C₃ photosynthesis is the most common form of photosynthesis in crops. Current efforts of increasing crop yields in response to growing global food requirement are mostly focused on improving C₃ photosynthesis. In this review, we summarized the strategies of C₃ photosynthesis improvement in terms of Rubisco properties and photorespiratory limitation. Potential engineered targets include Rubisco subunits and their catalytic sites, Rubisco assembly chaperones, and Rubisco activase. In addition, we reviewed multiple photorespiratory bypasses built by strategies of synthetic biology to reduce the release of CO₂ and ammonia and minimize energy consumption by photorespiration. The potential strategies are suggested to enhance C₃ photosynthesis and boost crop production.

Memory or acclimation of water stress in pea rely on root system's plasticity and plant's ionome modulation

INTRODUCTION

Peas, as legume crops, could play a major role in the future of food security in the context of worldwide human nutrient deficiencies coupled with the growing need to reduce consumption of animal products. However, pea yields, in terms of quantity and quality (i.e. grain content), are both susceptible to climate change, and more specifically to water deficits, which nowadays occur more frequently during crop growth cycles and tend to last longer. The impact of soil water stress on plant development and plant growth is complex, as its impact varies depending on soil water availability (through the modulation of elements available in the soil), and by the plant's ability to acclimate to continuous stress or to memorize previous stress events.

METHOD

To identify the strategies underlying these plant responses to water stress events, pea plants were grown in controlled conditions under optimal water treatment and different types of water stress; transient (during vegetative or reproductive periods), recurrent, and continuous (throughout the plant growth cycle). Traits related to water, carbon, and ionome uptake and uses were measured and allowed the identification typical plant strategies to cope with water stress.

CONCLUSION

Our results highlighted (i) the common responses to the three types of water stress in shoots, involving manganese (Mn) in particular, (ii) the potential implications of boron (B) for root architecture modification under continuous stress, and (iii) the establishment of an "ecophysiological imprint" in the root system via an increase in nodule numbers during the recovery period.

Nitrogen assimilation and photorespiration become more efficient under chloride nutrition as a beneficial macronutrient

Chloride (Cl^-) and nitrate ( NO 3 - ) are closely related anions involved in plant growth. Their similar physical and chemical properties make them to interact in cellular processes like electrical balance and osmoregulation. Since both anions share transport mechanisms, Cl^- has been considered to antagonize NO 3 - uptake and accumulation in plants. However, we have recently demonstrated that Cl^- provided at beneficial macronutrient levels improves nitrogen (N) use efficiency (NUE). Biochemical mechanisms by which beneficial Cl^- nutrition improves NUE in plants are poorly understood. First, we determined that Cl^- nutrition at beneficial macronutrient levels did not impair the NO 3 - uptake efficiency, maintaining similar NO 3 - content in the root and in the xylem sap. Second, leaf NO 3 - content was significantly reduced by the treatment of 6 mM Cl^- in parallel with an increase in NO 3 - utilization and NUE. To verify whether Cl^- nutrition reduces leaf NO 3 - accumulation by inducing its assimilation, we analysed the content of N forms and the activity of different enzymes and genes involved in N metabolism. Chloride supply increased transcript accumulation and activity of most enzymes involved in NO 3 - assimilation into amino acids, along with a greater accumulation of organic N (mostly proteins). A reduced glycine/serine ratio and a greater ammonium accumulation pointed to a higher activity of the photorespiration pathway in leaves of Cl^--treated plants. Chloride, in turn, promoted higher transcript levels of genes encoding enzymes of the photorespiration pathway. Accordingly, microscopy observations suggested strong interactions between different cellular organelles involved in photorespiration. Therefore, in this work we demonstrate for the first time that the greater NO 3 - utilization and NUE induced by beneficial Cl^- nutrition is mainly due to the stimulation of NO 3 - assimilation and photorespiration, possibly favouring the production of ammonia, reductants and intermediates that optimize C-N re-utilization and plant growth. This work demonstrates new Cl^- functions and remarks on its relevance as a potential tool to manipulate NUE in plants.

Elevated inorganic carbon and salinity enhances photosynthesis and ATP synthesis in picoalga Picocystis salinarum as revealed by label free quantitative proteomics

Saline soda lakes are of immense ecological value as they niche some of the most exclusive haloalkaliphilic communities dominated by bacterial and archaeal domains, with few eukaryotic algal representatives. A handful reports describe Picocystis as a key primary producer with great production rates in extremely saline alkaline habitats. An extremely haloalkaliphilic picoalgal strain, Picocystis salinarum SLJS6 isolated from hypersaline soda lake Sambhar, Rajasthan, India, grew robustly in an enriched soda lake medium containing mainly Na₂CO₃, 50 g/l; NaHCO_3, 50 g/l, NaCl, 50 g/l (salinity ≈150‰) at pH 10. To elucidate the molecular basis of such adaptation to high inorganic carbon and NaCl concentrations, a high-throughput label-free quantitation based quantitative proteomics approach was applied. Out of the total 383 proteins identified in treated samples, 225 were differentially abundant proteins (DAPs), of which 150 were statistically significant (p < 0.05) including 70 upregulated and 64 downregulated proteins after 3 days of growth in highly saline-alkaline medium. Most DAPs were involved in photosynthesis, oxidative phosphorylation, glucose metabolism and ribosomal structural components envisaging that photosynthesis and ATP synthesis were central to the salinity-alkalinity response. Key components of photosynthetic machinery like photosystem reaction centres, adenosine triphosphate (ATP) synthase ATP, Rubisco, Fructose-1,6-bisphosphatase, Fructose-bisphosphate aldolase were highly upregulated. Enzymes peptidylprolyl isomerases (PPIase), important for correct protein folding showed remarkable marked-up regulation along with other chaperon proteins indicating their role in osmotic adaptation. Enhanced photosynthetic activity exhibited by P. salinarum in highly saline-alkaline condition is noteworthy as photosynthesis is suppressed under hyperosmotic conditions in most photosynthetic organisms. The study provided the first insights into the proteome of extremophilic alga P. salinarum exhibiting extraordinary osmotic adaptation and proliferation in polyextreme conditions prevailing in saline sodic ecosystems, potentially unraveling the basis of resilience in this not so known organism and paves the way for a promising future candidate for biotechnological applications and model organism for deciphering the molecular mechanisms of osmotic adaptation. The mass spectrometry proteomics data is available at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD037170.

Unique features of regulation of sulfate assimilation in monocots

Sulfate assimilation is an essential pathway of plant primary metabolism, regulated by the demand for reduced sulfur (S). The S-containing tripeptide glutathione (GSH) is the key signal for such regulation in Arabidopsis, but little is known about the conservation of these regulatory mechanisms beyond this model species. Using two model monocot species, C3 rice (Oryza sativa) and C4Setaria viridis, and feeding of cysteine or GSH, we aimed to find out how conserved are the regulatory mechanisms described for Arabidopsis in these species. We showed that while in principle the regulation is similar, there are many species-specific differences. For example, thiols supplied by the roots are translocated to the shoots in rice but remain in the roots of Setaria. Cysteine and GSH concentrations are highly correlated in Setaria, but not in rice. In both rice and Setaria, GSH seems to be the signal for demand-driven regulation of sulfate assimilation. Unexpectedly, we observed cysteine oxidation to sulfate in both species, a reaction that does not occur in Arabidopsis. This reaction is dependent on sulfite oxidase, but the enzyme(s) releasing sulfite from cysteine still need to be identified. Altogether our data reveal a number of unique features in the regulation of S metabolism in the monocot species and indicate the need for using multiple taxonomically distinct models to better understand the control of nutrient homeostasis, which is important for generating low-input crop varieties.

Core metabolism plasticity in phytoplankton: Response of Dunaliella tertiolecta to oil exposure

Human alterations to the marine environment such as an oil spill can induce oxidative stress in phytoplankton. Exposure to oil has been shown to be lethal to most phytoplankton species, but some are able to survive and grow at unaffected or reduced growth rates, which appears to be independent of the class and phylum of the phytoplankton and their ability to consume components of oil heterotrophically. The goal of this article is to test the role of core metabolism plasticity in the oil-resisting ability of phytoplankton. Experiments were performed on the oil- resistant chlorophyte, Dunaliella tertiolecta, in control and water accommodated fractions of oil, with and without metabolic inhibitors targeting the core metabolic pathways. We observed that inhibiting pathways such as photosynthetic electron transport (PET) and pentose-phosphate pathway were lethal; however, inhibition of pathways such as mitochondrial electron transport and cyclic electron transport caused growth to be arrested. Pathways such as photorespiration and Kreb's cycle appear to play a critical role in the oil-tolerating ability of D. tertiolecta. Analysis of photo-physiology revealed reduced PET under inhibition of photorespiration but not Kreb's cycle. Further studies showed enhanced flux through Kreb's cycle suggesting increased energy production and photorespiration counteract oxidative stress. Lastly, reduced extracellular carbohydrate secretion under oil exposure indicated carbon and energy conservation, which together with enhanced flux through Kreb's cycle played a major role in the survival of D. tertiolecta under oil exposure by meeting the additional energy demands. Overall, we present data that suggest the role of phenotypic plasticity of multiple core metabolic pathways in accounting for the oxidative stress tolerating ability of certain phytoplankton species.

Improvement in the photoprotective capability benefits the productivity of a yellow-green wheat mutant in N-deficient conditions

Wheat yellow-green mutant Jimai5265yg has a more efficient photosynthetic system and higher productivity than its wild type under N-deficient conditions. To understand the relationship between photosynthetic properties and the grain yield, we conducted a field experiment under different N application levels. Compared to wild type, the Jimai5265yg flag leaves had higher mesophyll conductance, photosynthetic N-use efficiency, and photorespiration in the field without N application. Chlorophyll a fluorescence analysis showed that PSII was more sensitive to photoinhibition due to lower nonphotochemical quenching (NPQ) and higher nonregulated heat dissipation. In N-deficient condition, the PSI acceptor side of Jimai5265yg was less reduced. We proposed that the photoinhibited PSII protected PSI from over-reduction through downregulation of electron transport. PCA analysis also indicated that PSI photoprotection and electron transport regulation were closely associated with grain yield. Our results suggested that the photoprotection mechanism of PSI independent of NPQ was critical for crop productivity.

Physiological and metabolomics responses of Hydrangea macrophylla (Thunb.) Ser. and Hydrangea strigosa Rehd. to lead exposure

Hydrangea is a potential remediation plant for lead (Pb) pollution. Plant roots communicate with soil through the release of root exudates. It is crucial to study rhizoremediation mechanisms to understand the response of root exudates to contamination stress. Here, we investigated the physiological responses and metabolomic profiling of two Hydrangea species, a horticultural cultivar (Hydrangea macrophylla (Thunb.) Ser.) and a wild type (Hydrangea strigosa Rehd.), under Pb-free and Pb-stressed conditions for 50 days. The results showed that Pb treatment adversely affected the biomass and root growth of the two species. H. strigosa was a Pb-tolerant species with higher superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and more ascorbic acid (AsA) content in roots. Metabolomic profiling showed that 181 and 169 compounds were identified in H. macrophylla and H. strigosa root exudates, respectively, among which 18 showed significant differences between H. macrophylla and H. strigosa under Pb exposure. H. strigosa showed significantly (P < 0.05) higher secretion of sucrose, glycolic acid, and nonanoic acid than H. macrophylla after Pb treatment. Pb stress promoted fatty acid metabolism in H. strigosa, suppressed amino acid metabolism in H. macrophylla, and promoted a higher carbohydrate metabolism in H. strigosa compared with H. macrophylla. This study provides a possible mechanism for the high Pb absorption potential of Hydrangea.

Physiological and proteomic responses of Chlamydomonas reinhardtii to arsenate and lead mixtures

Arsenic (As) and lead (Pb) are frequently emitted from various sources into environment, but microbial responses to their combined toxicity have not been systematically investigated. In this study, Chlamydomonas reinhardtii was exposed to two levels of arsenate (As (V), 50, 500 μg/L), Pb (II) (500, 5000 μg/L) and their mixture (50 μg/L As (V) + 500 μg/L Pb (II); 500 μg/L As (V) + 5000 μg/L Pb (II)). The growth of C. reinhardtii was inhibited more remarkably by As (V) than by Pb (II). The As stress was alleviated by Pb in the 50 μg/L As (V) + 500 μg/L Pb (II) treatment, but was enhanced upon the 500 μg/L As (V) + 5000 μg/L Pb (II) exposure, with more pronounced changes in a number of physiological parameters of the algal cells. Proteomic results showed that 71 differently expressed proteins (DEPs) in the treatment of 50 μg/L As (V) + 500 μg/L Pb (II), and 167 DEPs were identified in that of 500 μg/L As (V) + 5000 μg/L Pb (II). These proteins were involved in energy metabolism, photosynthetic carbon fixation, reactive oxygen scavenging and defense, and amino acid synthesis. Taken together, these physiological and proteomic data demonstrated that C. reinhardtii could resist the As (V) and Pb (II) combined treatments through extracellular complexation and intracellular pathways.

Plants and water in a changing world: a physiological and ecological perspective

The reduction of greenhouse gases (GHGs) emission by replacing fossil energy stocks with carbon–neutral fuels is a major topic of the political and scientific debate on environmental sustainability. Such shift in energy sources is expected to curtail the accumulation rate of atmospheric CO₂, which is a strong infrared absorber and thus contributes to the global warming effect. Although such change would produce desirable outputs, the consequences of a drastic decrease in atmospheric CO₂ (the substrate of photosynthesis) should be carefully considered in the light of its potential impact on ecosystems stability and agricultural productivity. Indeed, plants regulate CO₂ uptake and water loss through the same anatomical structure: the leaf stomata. A reduced CO₂ availability is thus expected to enhance transpiration rate in plants decreasing their water use efficiency and imposing an increased water demand for both agricultural and wild ecosystems. We suggest that this largely underestimated issue should be duly considered when implementing policies that aim at the mitigation of global environmental changes and, at the same time, promote sustainable agricultural practices, include the preservation of biodiversity. Also, we underlie the important role(s) that modern biotechnology could play to tackle these global challenges by introducing new traits aimed at creating crop varieties with enhanced CO₂ capture and water- and light-use efficiency.

Active metabolism and biomass dynamics of biocrusts are shaped by variation in their successional state and seasonal energy sources

Seasonal growth and changes in biomass within communities are the core of ecosystem dynamics. Biocrusts play a prominent role as pioneers in dryland soils. However, the seasonal dynamics of biocrusts remain poorly resolved. In this study, we collected biocrusts across a successional gradient (cyanobacteria, cyanolichen, chlorolichen, and moss-dominated) from southeastern Tengger Desert (China) during the summer and autumn seasons, and explored seasonal changes in metabolism and biomass using multi-omics approaches. We found that Cyanobacteria and Ascomycota were the dominant active taxa and both exhibited higher abundances in autumn. We also found that the dominant primary producers in biocrusts strongly affected community-wide characteristics of metabolism. Along with seasonal differences in light energy utilization, utilization of inorganic energy sources exhibited higher expression in the summer while for organic sources, in the autumn. We found that overall metabolism was significantly regulated by the ratio of intracellular to extracellular polymer degradation, and affected by NO₃^-, PO₄^3- and EC (in the summer)/NO₂^- (in the autumn). In summary, biocrust growth varied with seasonal variation in light energy utilization and complementary chemical energy sources, with the most suitable season varying with biocrust successional type.

Biogenic Volatile Organic Compounds and Protein Expressions of Chamaecyparis formosensis and Chamaecyparis obtusa var. formosana Leaves under Different Light Intensities and Temperatures

Both Chamaecyparis formosensis and C. obtusa var. formosana are representative cypresses of high economic value in Taiwan, the southernmost subtropical region where cypresses are found. Both species show differences of their habitats. To find out the effects of environmental factors on the CO₂ assimilation rate and the biogenic volatile organic compound (BVOC) emission of both species, saplings from both species were grown under different light intensity and temperature regimes. The results indicated that the net CO₂ assimilation rates and total BVOC emission rates of both species increased with increasing light intensity. C. formosensis showed a higher magnitude of change, but C. obtusa var. formosana had considerably increased sesquiterpenoid and diterpenoid emission in BVOC under high light intensity. Both species grown under higher temperatures had significantly lower BVOC emission rates. Proteomic analyses revealed that compared to C. formosensis saplings, C. obtusa var. formosana saplings had less differentially expressed proteins in terms of protein species and fold changes in response to the growth conditions. These proteins participated mainly in photosynthesis, carbon metabolism, amino acid and protein processing, signal transduction, and stress mechanisms. These proteins might be the major regulatory factors affecting BVOC emission of these two species under different environments.

Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis

In the area of climate change, nanotechnology provides handy tools for improving crop production and assuring sustainability in global agricultural system. Due to excellent physiological and biochemical properties, silver nanoparticles (AgNPs) have been widely studied for potential use in agriculture. However, there are concerns about the mechanism of the toxic effects of the accumulation of AgNPs on crop growth and development. In this study, the impacts of AgNPs on cotton (Gossypium hirsutum) seedlings were evaluated by integrating physiological and comprehensive metabolomic analyses. Potting-soil-grown, two-week-old cotton seedlings were foliar-exposed to 5 mg/plant AgNP or 0.02 mg/plant Ag⁺ (equivalent to the free Ag⁺ released from AgNPs). Primary metabolites and volatile organic compounds (VOCs) were identified by gas chromatography-mass spectrometry (GC-MS) and solid-phase microextraction (SPME) GC-MS, respectively. AgNPs inhibited the photosynthetic capacity of the cotton leaves. The metabolic spectrum analysis identified and quantified 73 primary metabolites and 45 VOCs in cotton leaves. Both treatments significantly changed the metabolite profiles of plant leaves. Among the primary metabolites, AgNPs induced marked changes in amino acids, sugars and sugar alcohols. Among the VOCs, 13 volatiles, mainly aldehydes, alkanes and terpenoids, were specifically altered only in response to AgNPs. In summary, our study showed that the comprehensive influence of AgNPs on primary metabolites and VOCs was not merely attributed to the released Ag⁺ but was caused by AgNP-specific effects on cotton leaves. These results provide important knowledge about the physiological and chemical changes in cotton leaves upon exposure to AgNPs and offer a new insight for supporting the sustainable use of AgNPs in agriculture.

Photosynthetic Carbon Fixation and Sucrose Metabolism Supplemented by Weighted Gene Co-expression Network Analysis in Response to Water Stress in Rice With Overlapping Growth Stages

Drought stress at jointing and booting phases of plant development directly affects plant growth and productivity in rice. Limited by natural factors, the jointing and booting stages in rice varieties are known to overlap in high-latitude areas that are more sensitive to water deficit. However, the regulation of photosynthetic carbon fixation and sucrose metabolism in rice leaves under different degrees of drought stress remains unclear. In this study, rice plants were subjected to three degrees of drought stress (-10, -25, -and 40 kPa) for 15 days during the jointing-booting stage, we investigated photosynthetic carbon sequestration and sucrose metabolism pathways in rice leaves and analyzed key genes and regulatory networks using transcriptome sequencing in 2016. And we investigated the effects of drought stress on the growth periods of rice with overlapping growth periods in 2016 and 2017. The results showed that short-term drought stress promoted photosynthetic carbon fixation. However, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) activity significantly decreased, resulting in a significant decrease in photosynthetic rate. Drought stress increased the maximum activity of fructose-1,6-bisphosphate aldolase (FBA). FBA maintains the necessary photosynthetic rate during drought stress and provides a material base after the resumption of irrigation in the form of controlling the content of its reaction product triose phosphate. Drought stress significantly affected the activities of sucrose synthase (SuSase) and sucrose phosphate synthase (SPS). Vacuoles invertase (VIN) activity increased significantly, and the more severe the drought, the higher the VIN activity. Severe drought stress at the jointing-booting stage severely restricted the growth process of rice with overlapping growth stages and significantly delayed heading and anthesis stages. Transcriptome analysis showed that the number of differentially expressed genes was highest at 6-9 days after drought stress. Two invertase and four β-amylase genes with time-specific expression were involved in sucrose-starch metabolism in rice under drought stress. Combined with weighted gene co-expression network analysis, VIN and β-amylase genes up-regulated throughout drought stress were regulated by OsbZIP04 and OsWRKY62 transcription factors under drought stress. This study showed that any water deficit at the jointing-booting stage would have a serious effect on sucrose metabolism in leaves of rice with overlapping growth stages.

HPR1 Is Required for High Light Intensity Induced Photorespiration in Arabidopsis thaliana

High light intensity as one of the stresses could lead to generation of large amounts of reactive oxygen species (ROS) in plants, resulting in severe plant growth retardation. The photorespiration metabolism plays an important role in producing and removing a variety of ROS, maintaining the dynamic balance of the redox reaction, and preventing photoinhibition. Arabidopsis hydroxypyruvate reductase 1 (HPR1) is a primary metabolic enzyme in the photorespiration cycle. However, the role of HPR1 in plants response to high light is not clear. Here, we found that the expression of HPR1 could be induced by high light intensity. The growth and photosynthetic capacity of hpr1 mutants are seriously affected under high light intensity. The absence of HPR1 suppresses the rates of photorepair of Photosystem II (PSII), aggravates the production of ROS, and accelerates photorespiration rates. Moreover, the activity of ROS scavenging enzymes in the hpr1 mutants is significantly higher. These results indicate that HPR1 is involved in plant response to high light intensity and is essential for maintaining the dynamic balance of ROS and photorespiration.

Comparative transcriptome analysis of heat stress responses of Clematis lanuginosa and Clematis crassifolia

BACKGROUND

Clematis species are attractive ornamental plants with a variety of flower colors and patterns. Heat stress is one of the main factors restricting the growth, development, and ornamental value of Clematis. Clematis lanuginosa and Clematis crassifolia are large-flowered and evergreen Clematis species, respectively, that show different tolerance to heat stress. We compared and analyzed the transcriptome of C. lanuginose and C. crassifolia under heat stress to determine the regulatory mechanism(s) of resistance.

RESULTS

A total of 1720 and 6178 differentially expressed genes were identified from C. lanuginose and C. crassifolia, respectively. The photosynthesis and oxidation-reduction processes of C. crassifolia were more sensitive than C. lanuginose under heat stress. Glycine/serine/threonine metabolism, glyoxylic metabolism, and thiamine metabolism were important pathways in response to heat stress in C. lanuginose, and flavonoid biosynthesis, phenylalanine metabolism, and arginine/proline metabolism were the key pathways in C. crassifolia. Six sHSPs (c176964_g1, c200771_g1, c204924_g1, c199407_g2, c201522_g2, c192936_g1), POD1 (c200317_g1), POD3 (c210145_g2), DREB2 (c182557_g1), and HSFA2 (c206233_g2) may be key genes in the response to heat stress in C. lanuginose and C. crassifolia.

CONCLUSIONS

We compared important metabolic pathways and differentially expressed genes in response to heat stress between C. lanuginose and C. crassifolia. The results increase our understanding of the response mechanism and candidate genes of Clematis under heat stress. These data may contribute to the development of new Clematis varieties with greater heat tolerance.

Lanthanum and cerium disrupt similar biological pathways and interact synergistically in Triticum aestivum as revealed by metabolomic profiling and quantitative modeling

The industrial and agricultural applications of rare earth elements (REEs) lead to considerable REE emissions into environment. Yet, little is known about the molecular-level effects and interactions of REEs in terrestrial plants. Herein, the individual and joint effects of La and Ce in Triticum aestivum were investigated using mass spectrometry-based metabolomics. Metabolic effect level index (MELI) was utilized as a readable endpoint for quantifying mixture interactions. Exposure to single La/Ce at environmentally relevant levels induced significant dose-dependent metabolic changes. The highly overlap of differential metabolites and perturbed pathways of La and Ce suggested their similar mode of action. Exposure to La-Ce mixtures did not induce additional metabolic pathway perturbation. Specifically, metabolism of amino sugar and nucleotide sugar, starch and sucrose, fructose and mannose, glycerophospholipid and purine were disrupted for both single and binary exposures. These results, together with physiological indicators, point to REE-induced oxidative stress, energy expenditure, DNA damage and membrane disturbance. The MELI calculations showed that La and Ce interacted synergistically at the overall metabolic level, which could be causally linked to synergistic interaction at the individual level (root elongation). This work proved metabolomics could be an important and effective strategy for interpreting toxicity and interactions of REE mixtures.

Phytotoxic effect and molecular mechanism induced by graphene towards alfalfa (Medicago sativa L.) by integrating transcriptomic and metabolomics analysis

Although the widespread use of nanoparticles has been reported in various fields, the toxic mechanisms of molecular regulation involved in the alfalfa treated by nanomaterials is still in the preliminary research stage. In this study, Bara 310 SC (Bara, tolerant genotype) and Gold Empress (Gold, susceptible genotype) were used to investigate how the leaves of alfalfa interpret the physiological responses to graphene stress based on metabolome and transcriptome characterizations. Herein, graphene at different concentrations (0, 1% and 2%, w/w) were selected as the analytes. Physiological results showed antioxidant defence system and photosynthesis was significantly disturbed under high environmental concentration of graphene. With Ultra high performance liquid chromatography electrospray tandem mass spectrometry (UPLC-ESI-MS/MS), 406 metabolites were detected and 62/13 and 110/58 metabolites significantly changed in the leaves of Gold/Bara under the 1% and 2%-graphene treatments (w/w), respectively. The most important metabolites which were accumulated under graphene stress includes amino acids, flavonoids, organic acids and sugars. Transcriptomic analysis reveals 1125 of core graphene-responsive genes in alfalfa that was robustly differently expressed in both genotypes. And differential expression genes (DEGs) potentially related to photosynthetic enzymes, antioxidant enzymes, amino acids metabolism, and sucrose and starch metabolic which finding was supported by the metabolome study. Gold was more disturbed by graphene stress at both transcriptional and metabolic levels, since more stress-responsive genes/metabolites were identified in Gold. A comprehensive analysis of transcriptomic and metabolomic data highlights the important role of amino acid metabolism and nicotinate and nicotinamide metabolism pathways for graphene tolerance in alfalfa. Our study provide necessary information for better understanding the phytotoxicity molecular mechanism underlying nanomaterials tolerance of plant.

Effects of Light Spectral Quality on Photosynthetic Activity, Biomass Production, and Carbon Isotope Fractionation in Lettuce, Lactuca sativa L., Plants

The optimization of plant-specific LED lighting protocols for indoor plant growing systems needs both basic and applied research. Experiments with lettuce, Lactuca sativa L., plants using artificial lighting based on narrow-band LEDs were carried out in a controlled environment. We investigated plant responses to the exclusion of certain spectral ranges of light in the region of photosynthetically active radiation (PAR); in comparison, the responses to quasimonochromatic radiation in the red and blue regions were studied separately. The data on plant phenotyping, photosynthetic activity determination, and PAM fluorometry, indicating plant functional activity and stress responses to anomalous light environments, are presented. The study on carbon isotopic composition of photoassimilates in the diel cycle made it possible to characterize the balance of carboxylation and photorespiration processes in the leaves, using a previously developed oscillatory model of photosynthesis. Thus, the share of plant photorespiration (related to plant biomass enrichment with ¹³C) increased in response to red-light action, while blue light accelerated carboxylation (related to ¹²C enrichment). Blue light also reduced water use efficiency. These data are supported by the observations from the light environments missing distinct PAR spectrum regions. The fact that light of different wavelengths affects the isotopic composition of total carbon allowed us to elucidate the nature of its action on the organization of plant metabolism.

Salt tolerance mechanisms in the Lycopersicon clade and their trade-offs

Salt stress impairs growth and yield in tomato, which is mostly cultivated in arid and semi-arid areas of the world. A number of wild tomato relatives (Solanum pimpinellifolium, S. pennellii, S. cheesmaniae and S. peruvianum) are endemic to arid coastal areas and able to withstand higher concentration of soil salt concentrations, making them a good genetic resource for breeding efforts aimed at improving salt tolerance and overall crop improvement. However, the complexity of salt stress response makes it difficult to introgress tolerance traits from wild relatives that could effectively increase tomato productivity under high soil salt concentrations. Under commercial production, biomass accumulation is key for high fruit yields, and salt tolerance management strategies should aim to maintain a favourable plant water and nutrient status. In this review, we first compare the effects of salt stress on the physiology of the domesticated tomato and its wild relatives. We then discuss physiological and energetic trade-offs for the different salt tolerance mechanisms found within the Lycopersicon clade, with a focus on the importance of root traits to sustain crop productivity.