Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis

Evaluating the phytotoxicological effects of bulk and nano forms of zinc oxide on cellular respiration-related indices and differential gene expression in Hordeum vulgare L

The increasing use of nanoparticles is driving the growth of research on their effects on living organisms. However, studies on the effects of nanoparticles on cellular respiration are still limited. The remodeling of cellular-respiration-related indices in plants induced by zinc oxide nanoparticles (nnZnO) and its bulk form (blZnO) was investigated for the first time. For this purpose, barley (Hordeum vulgare L.) seedlings were grown hydroponically for one week with the addition of test compounds at concentrations of 0, 0.3, 2, and 10 mg mL-1. The results showed that a low concentration (0.3 mg mL-1) of blZnO did not cause significant changes in the respiration efficiency, ATP content, and total reactive oxygen species (ROS) content in leaf tissues. Moreover, a dose of 0.3 mg mL-1 nnZnO increased respiration efficiency in both leaves (17 %) and roots (38 %). Under the influence of blZnO and nnZnO at medium (2 mg mL-1) and high (10 mg mL-1) concentrations, a dose-dependent decrease in respiration efficiency from 28 % to 87 % was observed. Moreover, the negative effect was greater under the influence of nnZnO. The gene transcription of the subunits of the mitochondria electron transport chain (ETC) changed mainly only under the influence of nnZnO in high concentration. Expression of the ATPase subunit gene, atp1, increased slightly (by 36 %) in leaf tissue under the influence of medium and high concentrations of test compounds, whereas in the root tissues, the atp1 mRNA level decreased significantly (1.6-2.9 times) in all treatments. A dramatic decrease (1.5-2.4 times) in ATP content was also detected in the roots. Against the background of overexpression of the AOX1d1 gene, an isoform of alternative oxidase (AOX), the total ROS content in leaves decreased (with the exception of 10 mg mL-1 nnZnO). However, in the roots, where the pressure of the stress factor is higher, there was a significant increase in ROS levels, with a maximum six-fold increase under 10 mg mL-1 nnZnO. A significant decrease in transcript levels of the pentose phosphate pathway and glycolytic enzymes was also shown in the root tissues compared to leaves. Thus, the disruption of oxidative phosphorylation leads to a decrease in ATP synthesis and an increase in ROS production; concomitantly reducing the efficiency of cellular respiration.

Post-synthetic modification of nano-chitosan using gibberellic acid: Foliar application on sorghum under salt stress conditions and estimation of biochemical parameters

The challenge of desert farming with a high salt level has become an ecological task due to salt stress negatively affecting plant growth and reproduction. The current study deals with the cultivation of sorghum under salt stress conditions to counteract the effect of chitosan and gibberellic acid (GA3). Here, the effects of chitosan, GA3 and nano-composite (GA3@chitosan) on biochemical contents, growth and seed yield of sorghum under salinity stress conditions were studied. The results showed that spraying with GA3@chitosan increased sorghum grain yield by 2.07, 1.81 and 1.64 fold higher than salinity stressed plants, chitosan treatment and GA3 treatment, respectively. Additionally, compared to the control of the same variety, the GA3@chitosan spraying treatment improved the concentration of microelements in the grains of the Shandweel-1 and Dorado by 24.51% and 18.39%, respectively for each variety. Furthermore, spraying GA3@chitosan on sorghum varieties increased the accumulation of the macroelements N, P, and K by 34.03%, 47.61%, and 8.67% higher than salt-stressed plants, respectively. On the other hand, the proline and glycinebetaine content in sorghum leaves sprayed with nano-composite were drop by 51.04% and 11.98% less than stressed plants, respectively. The results showed that, in Ras Sudr, the Shandweel-1 variety produced more grain per feddan than the Dorado variety. These findings suggest that GA3@chitosan improves the chemical and biochemical components leading to a decrease in the negative effect of salt stress on the plant which reflects in the high-yield production of cultivated sorghum plants in salt conditions.

GreenPhos, a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility

Protein phosphorylation regulates a variety of important cellular and physiological processes in plants. In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes. This is largely due to the need to improve protein extraction efficiency from plant cells, which have a dense cell wall, and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis. To this end, we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC-MS) runs operated in a data-dependent acquisition (DDA) mode. The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time- and cost-effectiveness. The method, named GreenPhos, combined with single-shot LC-MS, enabled in-depth quantitative identification of Arabidopsis phosphoproteins, including differentially phosphorylated spliceosomal proteins, at multiple time points during salt stress and a number of kinase substrate motifs. GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides, which, if samples are further fractionated and analyzed by multiple LC-MS runs, could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.

COI1 dependent jasmonic acid signalling positively modulates ROS scavenging system in transgenic hairy root culture of tomato

Reactive oxygen species (ROS) production is a routine event in plants. ROS function as signalling molecules in regulating plant development and defence. However, their accumulation beyond threshold leads to toxicity. Hence, plants are evolved with specialized ROS scavenging system involving phytohormones (synthesis and signalling), enzymes and metabolites. To understand the role of phytohormone jasmonic acid (JA) signalling in ROS scavenging, tomato coronatine insensitive 1 (SlCOI1), a key gene in JA signalling, was silenced and overexpressed in tomato transgenic hairy roots (HR) under the constitutive promoter. Targeted metabolomics of transgenic HR revealed accumulation of phenolic acids including ferulic acid, coumaric acid, vanillic acid, and flavonoid catechin in SlCOI1 overexpressed line. Moreover, osmolyte amino acids proline, asparagine, and glutamine showed a positive co-relation with transgenic overexpression of SlCOI1. Ascorbic acid-glutathione, a crucial antioxidant system was found to be influenced by COI1-mediated JA signalling. The expression of genes encoding enzymes superoxide dismutase 1, ascorbate peroxidase 1, and dehydroascorbate reductase 2 was found to be down and upregulated in SlCOI1 silenced and overexpressed lines, respectively. Methyl jasmonate and Fusarium oxysporum f.sp. lycopersici crude extract treatment further confirmed the regulatory role of COI1-mediated JA signalling in regulation of enzymatic components involved in ROS scavenging. The COI1-mediated JA signalling could also elevate the expression of RESPIRATORY BURST OXIDASE HOMOLOG-B gene which is involved in ROS wave signal generation. The present study underscores the role of COI1-mediated JA signalling in modulating enzymatic and non-enzymatic components of ROS scavenging system and pathogen associated molecular pattern triggered immunity.

Plant Life with and without Oxygen: A Metabolomics Approach

Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.

Reversible protein phosphorylation in higher plants: focus on state transitions

Reversible protein phosphorylation is one of the comprehensive mechanisms of cell metabolism regulation in eukaryotic organisms. The review describes the impact of the reversible protein phosphorylation on the regulation of growth and development as well as in adaptation pathways and signaling network in higher plant cells. The main part of the review is devoted to the role of the reversible phosphorylation of light-harvesting proteins of photosystem II and the state transition process in fine-tuning the photosynthetic activity of chloroplasts. A separate section of the review is dedicated to comparing the mechanisms and functional significance of state transitions in higher plants, algae, and cyanobacteria that allows the evolution aspects of state transitions meaning in various organisms to be discussed. Environmental factors affecting the state transitions are also considered. Additionally, we gain insight into the possible influence of STN7-dependent phosphorylation of the target proteins on the global network of reversible protein phosphorylation in plant cells as well as into the probable effect of the STN7 kinase inhibition on long-term acclimation pathways in higher plants.

Analysis of state 1-state 2 transitions by genome editing and complementation reveals a quenching component independent from the formation of PSI-LHCI-LHCII supercomplex in Arabidopsis thaliana

BACKGROUND

The light-harvesting antennae of photosystem (PS) I and PSII are pigment-protein complexes responsible of the initial steps of sunlight conversion into chemical energy. In natural environments plants are constantly confronted with the variability of the photosynthetically active light spectrum. PSII and PSI operate in series but have different optimal excitation wavelengths. The prompt adjustment of light absorption by photosystems is thus crucial to ensure efficient electron flow needed to sustain downstream carbon fixing reactions. Fast structural rearrangements equilibrate the partition of excitation pressure between PSII and PSI following the enrichment in the red (PSII-favoring) or far-red (PSI-favoring) spectra. Redox imbalances trigger state transitions (ST), a photoacclimation mechanism which involves the reversible phosphorylation/dephosphorylation of light harvesting complex II (LHCII) proteins by the antagonistic activities of the State Transition 7 (STN7) kinase/TAP38 phosphatase enzyme pair. During ST, a mobile PSII antenna pool associates with PSI increasing its absorption cross section. LHCII consists of assorted trimeric assemblies of Lhcb1, Lhcb2 and Lhcb3 protein isoforms (LHCII), several being substrates of STN7. However, the precise roles of Lhcb phosphorylation during ST remain largely elusive.

RESULTS

We inactivated the complete Lhcb1 and Lhcb2 gene clades in Arabidopsis thaliana and reintroduced either wild type Lhcb1.3 and Lhcb2.1 isoforms, respectively, or versions lacking N-terminal phosphorylatable residues proposed to mediate state transitions. While the substitution of Lhcb2.1 Thr-40 prevented the formation of the PSI-LHCI-LHCII complex, replacement of Lhcb1.3 Thr-38 did not affect the formation of this supercomplex, nor did influence the amplitude or kinetics of PSII fluorescence quenching upon state 1-state 2 transition.

CONCLUSIONS

Phosphorylation of Lhcb2 Thr-40 by STN7 alone accounts for ≈ 60% of PSII fluorescence quenching during state transitions. Instead, the presence of Thr-38 phosphosite in Lhcb1.3 was not required for the formation of the PSI-LHCI-LHCII supercomplex nor for re-equilibration of the plastoquinone redox state. The Lhcb2 phosphomutant was still capable of ≈ 40% residual fluorescence quenching, implying that a yet uncharacterized, STN7-dependent, component of state transitions, which is unrelated to Lhcb2 Thr-40 phosphorylation and to the formation of the PSI-LHCI-LHCII supercomplex, contributes to the equilibration of the PSI/PSII excitation pressure upon plastoquinone over-reduction.

SnRK2.10 kinase differentially modulates expression of hub WRKY transcription factors genes under salinity and oxidative stress in Arabidopsis thaliana

In nature, all living organisms must continuously sense their surroundings and react to the occurring changes. In the cell, the information about these changes is transmitted to all cellular compartments, including the nucleus, by multiple phosphorylation cascades. Sucrose Non-Fermenting 1 Related Protein Kinases (SnRK2s) are plant-specific enzymes widely distributed across the plant kingdom and key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress and salinity. The main deleterious effects of salinity comprise water deficiency stress, disturbances in ion balance, and the accompanying appearance of oxidative stress. The reactive oxygen species (ROS) generated at the early stages of salt stress are involved in triggering intracellular signaling required for the fast stress response and modulation of gene expression. Here we established in Arabidopsis thaliana that salt stress or induction of ROS accumulation by treatment of plants with H2O2 or methyl viologen (MV) induces the expression of several genes encoding transcription factors (TFs) from the WRKY DNA-Binding Protein (WRKY) family. Their induction by salinity was dependent on SnRK2.10, an ABA non-activated kinase, as it was strongly reduced in snrk2.10 mutants. The effect of ROS was clearly dependent on their source. Following the H2O2 treatment, SnRK2.10 was activated in wild-type (wt) plants and the induction of the WRKY TFs expression was only moderate and was enhanced in snrk2.10 lines. In contrast, MV did not activate SnRK2.10 and the WRKY induction was very strong and was similar in wt and snrk2.10 plants. A bioinformatic analysis indicated that the WRKY33, WRKY40, WRKY46, and WRKY75 transcription factors have a similar target range comprising numerous stress-responsive protein kinases. Our results indicate that the stress-related functioning of SnRK2.10 is fine-tuned by the source and intracellular distribution of ROS and the co-occurrence of other stress factors.

Receptor for Activated C Kinase1B (RACK1B) Delays Salinity-Induced Senescence in Rice Leaves by Regulating Chlorophyll Degradation

The widely conserved Receptor for Activated C Kinase1 (RACK1) protein is a WD-40 type scaffold protein that regulates diverse environmental stress signal transduction pathways. Arabidopsis RACK1A has been reported to interact with various proteins in salt stress and Light-Harvesting Complex (LHC) pathways. However, the mechanism of how RACK1 contributes to the photosystem and chlorophyll metabolism in stress conditions remains elusive. In this study, using T-DNA-mediated activation tagging transgenic rice (Oryza sativa L.) lines, we show that leaves from rice RACK1B gene (OsRACK1B) gain-of-function (RACK1B-OX) plants exhibit the stay-green phenotype under salinity stress. In contrast, leaves from down-regulated OsRACK1B (RACK1B-UX) plants display an accelerated yellowing. qRT-PCR analysis revealed that several genes which encode chlorophyll catabolic enzymes (CCEs) are differentially expressed in both RACK1B-OX and RACK1B-UX rice plants. In addition to CCEs, stay-green (SGR) is a key component that forms the SGR-CCE complex in senescing chloroplasts, and which causes LHCII complex instability. Transcript and protein profiling revealed a significant upregulation of OsSGR in RACK1B-UX plants compared to that in RACK1B-OX rice plants during salt treatment. The results imply that senescence-associated transcription factors (TFs) are altered following altered OsRACK1B expression, indicating a transcriptional reprogramming by OsRACK1B and a novel regulatory mechanism involving the OsRACK1B-OsSGR-TFs complex. Our findings suggest that the ectopic expression of OsRACK1B negatively regulates chlorophyll degradation, leads to a steady level of LHC-II isoform Lhcb1, an essential prerequisite for the state transition of photosynthesis for adaptation, and delays salinity-induced senescence. Taken together, these results provide important insights into the molecular mechanisms of salinity-induced senescence, which can be useful in circumventing the effect of salt on photosynthesis and in reducing the yield penalty of important cereal crops, such as rice, in global climate change conditions.

Does temperature favour the spread of Raphidiopsis raciborskii, an invasive bloom-forming cyanobacterium, by altering cellular trade-offs?

As a tropical filamentous cyanobacterium, Raphidiopsis raciborskii has attracted much attention due to its expansion and toxin production. However, the mechanisms of its expansion to temperate regions have not been studied in detail. To address the potential strategies, the physiological and metabolomic profiles of R. raciborskii FACHB 1096 isolated from a temperate lake in China were determined and measured at different temperatures (10 °C, 15 °C, 20 °C, 25 °C, and 32 °C). The results demonstrated that temperature significantly changed cell viability, chlorophyll a content, specific growth rate, Chl a fluorescence, and filamentous shape of R. raciborskii. Low temperature decreased cell viability, specific growth rate, and photosynthetic efficiency, while the proportion of akinete and carbon fixation per unit cell were significantly increased compared with high temperature (32 °C). A constructed unimodal model indicated that filament length, cell volume, and cell length/width of R. raciborskii were significantly reduced in both high and low temperature environments. Under low-temperature conditions, R. raciborskii suffered different degrees of oxidative damage and produced corresponding antioxidant substances to resist oxidative stress, suggesting that low temperature changes the metabolic level of the cells, causing the cells to gradually switch from development to defense. Metabolomic data further confirmed that temperature change induced shifts in metabolic pathways in R. raciborskii, including starch and sucrose metabolic pathways, glutathione metabolic pathways, and the pentose phosphate pathways (PPP), as well as metabolic pathways related to the tricarboxylic acid (TCA) cycle. Our results indicated that the trade-offs of R. raciborskii cells among the growth, cell size, and metabolites can be significantly regulated by temperature, with broad implications for its global expansion in temperate waterbodies.

Mass spectrometric exploration of phytohormone profiles and signaling networks

Phytohormones have crucial roles in plant growth, development, and acclimation to environmental stress; however, measuring phytohormone levels and unraveling their complex signaling networks and interactions remains challenging. Mass spectrometry (MS) has revolutionized the study of complex biological systems, enabling the comprehensive identification and quantification of phytohormones and their related targets. Here, we review recent advances in MS technologies and highlight studies that have used MS to discover and analyze phytohormone-mediated molecular events. In particular, we focus on the application of MS for profiling phytohormones, elucidating phosphorylation signaling, and mapping protein interactions in plants.

Physiological and Transcriptional Responses of Apocynum venetum to Salt Stress at the Seed Germination Stage

Apocynum venetum is a semi-shrubby perennial herb that not only prevents saline-alkaline land degradation but also produces leaves for medicinal uses. Although physiological changes during the seed germination of A. venetum in response to salt stress have been studied, the adaptive mechanism to salt conditions is still limited. Here, the physiological and transcriptional changes during seed germination under different NaCl treatments (0-300 mmol/L) were examined. The results showed that the seed germination rate was promoted at low NaCl concentrations (0-50 mmol/L) and inhibited with increased concentrations (100-300 mmol/L); the activity of antioxidant enzymes exhibited a significant increase from 0 (CK) to 150 mmol/L NaCl and a significant decrease from 150 to 300 mmol/L; and the content of osmolytes exhibited a significant increase with increased concentrations, while the protein content peaked at 100 mmol/L NaCl and then significantly decreased. A total of 1967 differentially expressed genes (DEGs) were generated during seed germination at 300 mmol/L NaCl versus (vs.) CK, with 1487 characterized genes (1293 up-regulated, UR; 194 down-regulated, DR) classified into 11 categories, including salt stress (29), stress response (146), primary metabolism (287), cell morphogenesis (156), transcription factor (TFs, 62), bio-signaling (173), transport (144), photosynthesis and energy (125), secondary metabolism (58), polynucleotide metabolism (21), and translation (286). The relative expression levels (RELs) of selected genes directly involved in salt stress and seed germination were observed to be consistent with the changes in antioxidant enzyme activities and osmolyte contents. These findings will provide useful references to improve seed germination and reveal the adaptive mechanism of A. venetum to saline-alkaline soils.

Light harvesting regulation: A versatile network of key components operating under various stress conditions in higher plants

Light harvesting is finetuned through two main strategies controlling energy transfer to the reaction centers of photosystems: i) regulating the amount of light energy at the absorption level, ii) regulating the amount of the absorbed energy at the utilization level. The first strategy is ensured by changes in the cross-section, i.e., the size of the photosynthetic antenna. These changes can occur in a short-term (state transitions) or long-term way (changes in antenna protein biosynthesis) depending on the light conditions. The interrelation of these two ways is still underexplored. Regulating light absorption through the long-term modulation of photosystem II antenna size has been mostly considered as an acclimatory mechanism to light conditions. The present review highlights that this mechanism represents one of the most versatile mechanisms of higher plant acclimation to various conditions including drought, salinity, temperature changes, and even biotic factors. We suggest that H₂O₂ is the universal signaling agent providing the switch from the short-term to long-term modulation of photosystem II antenna size under these factors. The second strategy of light harvesting is represented by redirecting energy to waste mainly via thermal energy dissipation in the photosystem II antenna in high light through PsbS protein and xanthophyll cycle. In the latter case, H₂O₂ also plays a considerable role. This circumstance may explain the maintenance of the appropriate level of zeaxanthin not only upon high light but also upon other stress factors. Thus, the review emphasizes the significance of both strategies for ensuring plant sustainability under various environmental conditions.

Application of Magnesium and Calcium Sulfate on Growth and Physiology of Forage Crops under Long-Term Salinity Stress

Soil salinity is major threat to crop growth and reducing cultivated land areas and salt-resistant crops have been required to sustain agriculture in salinized areas. This original research was performed to determine the effectiveness of MgSO₄ (MS) and CaSO₄ (CS) for each species and assess changes in the physiology and growth of fodder crops after short and long-term salt stress. Six treatments (CON (control); NaCl (NaCl 100 mM); 1 MS (1 mM MgSO₄ + 100 mM NaCl); 2 MS (2 mM MgSO₄ + 100 mM NaCl); 7.5 CS (7.5 mM CaSO₄ + 100 mM NaCl); and 10 CS (10 mM CaSO₄ + 100 mM NaCl)) were applied to Red clover (Trifolium pratense) and Tall fescue (Festuca arundinacea) under greenhouse conditions. Cultivars were evaluated based on their dry weights, physiological parameters, forage quality, and ion concentrations. The biomass of both species decreased significantly under NaCl treatments and increased under the MS and CS treatments compared to solely salinity treatments. Salinity caused a decrease in the photosynthetic rate, but compared to CON, the MS and CS treatments yielded superior results. Moreover, the Na⁺/K⁺ ratio increased as Na⁺ concentration increased but crop quality (CP, NDF, ADF) did not show significant differences under salinity. Overall, we concluded that these T. pratense and F. arundinacea species demonstrated various responses to salinity, MS, and CS by different physiological and morphological parameters and it turned out to be efficient under salinity stress.

Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments

During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.

The SnRK2.10 kinase mitigates the adverse effects of salinity by protecting photosynthetic machinery

SNF1-Related protein kinases Type 2 (SnRK2) are plant-specific enzymes widely distributed across the plant kingdom. They are key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress. Here we established that SnRK2.4 and SnRK2.10, ABA-nonactivated kinases, are activated in Arabidopsis thaliana rosettes during the early response to salt stress and contribute to leaf growth retardation under prolonged salinity but act by maintaining different salt-triggered mechanisms. Under salinity, snrk2.10 insertion mutants were impaired in the reconstruction and rearrangement of damaged core and antenna protein complexes in photosystem II (PSII), which led to stronger non-photochemical quenching, lower maximal quantum yield of PSII, and lower adaptation of the photosynthetic apparatus to high light intensity. The observed effects were likely caused by disturbed accumulation and phosphorylation status of the main PSII core and antenna proteins. Finally, we found a higher accumulation of reactive oxygen species (ROS) in the snrk2.10 mutant leaves under a few-day-long exposure to salinity which also could contribute to the stronger damage of the photosynthetic apparatus and cause other deleterious effects affecting plant growth. We found that the snrk2.4 mutant plants did not display substantial changes in photosynthesis. Overall, our results indicate that SnRK2.10 is activated in leaves shortly after plant exposure to salinity and contributes to salt stress tolerance by maintaining efficient photosynthesis and preventing oxidative damage.

Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier

Plant systems science research depends on the dynamic functional maps of the biological substrates of plant phenotypes and host/environment interactions in diverse ecologies. In this context, high-resolution mass spectrometry platforms offer comprehensive insights into the molecular pathways regulated by protein phosphorylation. Reversible protein phosphorylation is a ubiquitous reaction in signal transduction mechanisms in biological systems. In contrast to human and animal biology research, a plethora of experimental options for functional mapping and regulation of plant biology are, however, not currently available. Plant phosphoproteomics is an emerging field of research that aims at addressing this gap in systems science and plant omics, and thus has a large scope to empower fundamental discoveries. To date, large-scale data-intensive identification of phosphorylation events in plants remained technically challenging. In this expert review, we present a critical analysis and overview of phosphoproteomic studies performed in the model plant Arabidopsis thaliana. We discuss the technical strategies used for the enrichment of phosphopeptides and methods used for their quantitative assessment. Various types of mass spectrometry data acquisition and fragmentation methods are also discussed. The insights gathered here can allow plant biology and systems science researchers to design high-throughput function-oriented experimental workflows that elucidate the regulatory signaling mechanisms impacting plant physiology and plant diseases.

Exploring the diversity of plant proteome

The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.

Regulation of Plant Responses to Salt Stress

Salt stress is a major environmental stress that affects plant growth and development. Plants are sessile and thus have to develop suitable mechanisms to adapt to high-salt environments. Salt stress increases the intracellular osmotic pressure and can cause the accumulation of sodium to toxic levels. Thus, in response to salt stress signals, plants adapt via various mechanisms, including regulating ion homeostasis, activating the osmotic stress pathway, mediating plant hormone signaling, and regulating cytoskeleton dynamics and the cell wall composition. Unraveling the mechanisms underlying these physiological and biochemical responses to salt stress could provide valuable strategies to improve agricultural crop yields. In this review, we summarize recent developments in our understanding of the regulation of plant salt stress.

Oxidative Stress-Induced Alteration of Plant Central Metabolism

Oxidative stress is an integral component of various stress conditions in plants, and this fact largely determines the substantial overlap in physiological and molecular responses to biotic and abiotic environmental challenges. In this review, we discuss the alterations in central metabolism occurring in plants experiencing oxidative stress. To focus on the changes in metabolite profile associated with oxidative stress per se, we primarily analyzed the information generated in the studies based on the exogenous application of agents, inducing oxidative stress, and the analysis of mutants displaying altered oxidative stress response. Despite of the significant variation in oxidative stress responses among different plant species and tissues, the dynamic and transient character of stress-induced changes in metabolites, and the strong dependence of metabolic responses on the intensity of stress, specific characteristic changes in sugars, sugar derivatives, tricarboxylic acid cycle metabolites, and amino acids, associated with adaptation to oxidative stress have been detected. The presented analysis of the available data demonstrates the oxidative stress-induced redistribution of metabolic fluxes targeted at the enhancement of plant stress tolerance through the prevention of ROS accumulation, maintenance of the biosynthesis of indispensable metabolites, and production of protective compounds. This analysis provides a theoretical basis for the selection/generation of plants with improved tolerance to oxidative stress and the development of metabolic markers applicable in research and routine agricultural practice.

Mapping Plant Phosphoproteome with Improved Tandem MOAC and Label-Free Quantification

Protein phosphorylation represents a fundamental and evolutionarily conserved type of posttranslational modification that regulates protein functions and cellular signal transmission. Due to the dynamic nature of protein phosphorylation processes in plant cells, large-scale studies of phosphoproteins face several challenges such as low stoichiometry in the modified peptides in a proteome, as well as heterogeneity of the phosphopeptides of a given protein. Here we describe an updated tandem MOAC combined phosphoprotein and phosphopeptide enrichment strategy, a scalable phosphoproteomics approach that allows identification of thousands of phophopeptides in plant materials in one LC-MS analysis. We implemented modifications to several steps of the original tandem MOAC procedure to increase the identification and quantification of phosphopeptides in a sample beginning with less amount of tissue and a smaller amount of extracted protein.

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action

The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remain largely elusive. Our discovery driven comparative proteomics analysis revealed unique early signaling response of the yeast Saccharomyces cerevisiae on the proteome level to oxidants with a different mechanism of action as early as 3 min after treatment with four oxidants, namely H₂O₂, cumene hydroperoxide (CHP), and menadione and diamide, when protein abundances were compared using label-free quantification relying on a high-resolution mass analyzer (Orbitrap). We identified significant regulation of 196 proteins in response to H₂O₂, 569 proteins in response to CHP, 369 proteins in response to menadione and 207 proteins in response to diamide. Only 17 proteins were common across all treatments, but several more proteins were shared between two or three oxidants. Pathway analyses revealed that each oxidant triggered a unique signaling mechanism associated with cell survival and repair. Signaling pathways mostly regulated by oxidants were Ran, TOR, Rho, and eIF2. Furthermore, each oxidant regulated these pathways in a unique way indicating specificity of response to oxidants having different modes of action. We hypothesize that interplay of these signaling pathways may be important in recognizing different oxidants to trigger different downstream MAPK signaling cascades and to induce specific responses.

Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold

Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.

Mass Spectrometry Untangles Plant Membrane Protein Signaling Networks

Plasma membranes (PMs) act as primary cellular checkpoints for sensing signals and controlling solute transport. Membrane proteins communicate with intracellular processes through protein interaction networks. Deciphering these signaling networks provides crucial information for elucidating in vivo cellular regulation. Large-scale proteomics enables system-wide characterization of the membrane proteome, identification of ligand-receptor pairs, and elucidation of signals originating at membranes. In this review we assess recent progress in the development of mass spectrometry (MS)-based proteomic pipelines for determining membrane signaling pathways. We focus in particular on current techniques for the analysis of membrane protein phosphorylation and interaction, and how these proteins may be connected to downstream changes in gene expression, metabolism, and physiology.

Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na₂CO₃ stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na₂CO₃-responsive proteins. A total of 104 and 102 Na₂CO₃-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na₂CO₃-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction, and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na₂CO₃ tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na₂CO₃ stress, which help to improve our understanding of the Na₂CO₃-responsive mechanisms in halophytes.

Salt Stress Signals on Demand: Cellular Events in the Right Context

Plant stress is a real dilemma; it puzzles plant biologists and is a global problem that negatively affects people’s daily lives. Of particular interest is salinity, because it represents one of the major water-related stress types. We aimed to determine the signals that guide the cellular-related events where various adaptation mechanisms cross-talk to cope with salinity-related water stress in plants. In an attempt to unravel these mechanisms and introduce cellular events in the right context, we expansively discussed how salt-related signals are sensed, with particular emphasis on aquaporins, nonselective cation channels (NSCCs), and glycosyl inositol phosphorylceramide (GIPC). We also elaborated on the critical role Ca2⁺, H⁺, and ROS in mediating signal transduction pathways associated with the response and tolerance to salt stress. In addition, the fragmentary results from the literature were compiled to develop a harmonized, informational, and contemplative model that is intended to improve our perception of these adaptative mechanisms and set a common platform for plant biologists to identify intriguing research questions in this area.

Two Chloroplast Proteins Negatively Regulate Plant Drought Resistance Through Separate Pathways

Drought is one of the most deleterious environmental conditions affecting crop growth and productivity. Here we report the important roles of a nuclear-encoded chloroplast protein, PsbP Domain Protein 5 (PPD5), in drought resistance in Arabidopsis (Arabidopsis thaliana). From a forward genetic screen, a drought-resistant mutant named ppd5-2 was identified, which has a knockout mutation in PPD5 The ppd5 mutants showed increased H₂O₂ accumulation in guard cells and enhanced stomatal closure in response to drought stress. Further analysis revealed that the chloroplast-localized PPD5 protein interacts with and is phosphorylated by OST1, and phosphorylation of PPD5 increases its protein stability. Double mutant ppd5-2ost1-3 exhibited phenotypes resembling the ost1-3 single mutant with decreased stomatal closure, increased water loss, reduced H₂O₂ accumulation in guard cells, and hypersensitivity to drought stress. These results indicate that the chloroplast protein PPD5 negatively regulates drought resistance by modulating guard cell H₂O₂ accumulation via an OST1-dependent pathway. Interestingly, the thf1-1 mutant defective in the chloroplast protein THF1 displayed drought-resistance and H₂O₂ accumulation similar to the ppd5 mutants, but the thf1-1ost1-3 double mutant resembled the phenotypes of the thf1-1 single mutant. These results indicate that both OST1-dependent and OST1-independent pathways exist in the regulation of H₂O₂ production in chloroplasts of guard cells under drought stress conditions. Additionally, our findings suggest a strategy to improve plant drought resistance through manipulation of chloroplast proteins.

Functional analysis tools for post-translational modification: a post-translational modification database for analysis of proteins and metabolic pathways

Post-translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high-resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post-Translational Modifications (FAT-PTM) database (https://bioinformatics.cse.unr.edu/fat-ptm/), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large-scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT-PTM database currently supports tools to visualize protein-centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein-centric metabolic pathways and groups of proteins that are co-modified by multiple PTMs. Overall, the FAT-PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.

Quantitative Phosphoproteomic and Physiological Analyses Provide Insights into the Formation of the Variegated Leaf in Catalpa fargesii

Variegated plants are valuable materials for investigating leaf color regulated mechanisms. To unveil the role of posttranslational modification in the variegated phenotype, we conducted global quantitative phosphoproteomic analysis on different leaf color sectors of Maiyuanjinqiu and the corresponding of Catalpa fargesii using Ti⁴⁺-IMAC phosphopeptide enrichment. A total of 3778 phosphorylated sites assigned to 1646 phosphoproteins were identified, and 3221 in 1434 proteins were quantified. Differential phosphoproteins (above 1.5 or below 1/1.5) in various leaf color sectors were selected for functional enrichment analyses. Gene ontology (GO) enrichment revealed that processes of photosynthesis, regulation of the generation of precursor metabolites, response to stress, homeostasis, amino acid metabolism, transport–related processes, and most of the energy metabolisms might contribute to leaf color. KEGG pathway enrichment analysis was performed based on differential phosphoproteins (DPs) in different organelles. The result showed that most enriched pathways were located in the chloroplasts and cytosol. The phosphorylation levels of glycometabolism enzymes might greatly affect leaf variegation. Measurements of fluorescence parameters and enzyme activities confirmed that protein phosphorylation could affect plant physiology by regulating enzyme activity. These results provide new clues for further study the formation mechanisms of naturally variegated phenotype.

Rapid and reproducible phosphopeptide enrichment by tandem metal oxide affinity chromatography: application to boron deficiency induced phosphoproteomics

Mass spectrometry has been instrumental in enabling the study of molecular signaling on a cellular scale by way of site-specific quantification of protein post-translational modifications, in particular phosphorylation. Here we describe an updated tandem metal oxide affinity chromatography (MOAC) combined phosphoprotein/phosphopeptide enrichment strategy, a scalable phosphoproteomics approach that allows rapid identification of thousands of phosphopeptides in plant materials. We implemented modifications to several steps of the original tandem MOAC procedure to increase the amount of quantified phosphopeptides and hence site-specific phosphorylation of proteins in a sample beginning with the less amounts of tissue and a substantially smaller amount of extracted protein. We applied this technology to generate time-resolved maps of boron signaling in Arabidopsis roots. We show that the successive enrichment of phosphoproteins in a first and phosphopeptide extraction in a second step using our optimized procedure strongly enriched the root phosphoproteome. Our results reveal that boron deficiency affects over 20% of the measured root phosphoproteome and that many phosphorylation sites with known biological function, and an even larger number of previously undescribed sites, are modified during the time course of boron deficiency. We identify transcription factors as key regulators of hormone signaling pathways that modulate gene expression in boron deprived plants. Furthermore, our phosphorylation kinetics data demonstrate that mitogen-activated protein kinase (MAPK) cascades mediate polarized transport of boron in Arabidopsis roots. Taken together, we establish and validate a robust approach for proteome-wide phosphorylation analysis in plant biology research.

The Phosphoproteomic Response of Okra (Abelmoschus esculentus L.) Seedlings to Salt Stress

Soil salinization is a major environmental stresses that seriously threatens land use efficiency and crop yields worldwide. Although the overall response of plants to NaCl has been well studied, the contribution of protein phosphorylation to the detoxification and tolerance of NaCl in okra (Abelmoschus esculentus L.) seedlings is unclear. The molecular bases of okra seedlings’ responses to 300 mM NaCl stress are discussed in this study. Using a combination of affinity enrichment, tandem mass tag (TMT) labeling and high-performance liquid chromatography–tandem mass spectrometry analysis, a large-scale phosphoproteome analysis was performed in okra. A total of 4341 phosphorylation sites were identified on 2550 proteins, of which 3453 sites of 2268 proteins provided quantitative information. We found that 91 sites were upregulated and 307 sites were downregulated in the NaCl/control comparison group. Subsequently, we performed a systematic bioinformatics analysis including gene ontology annotation, domain annotation, subcellular localization, and Kyoto Encyclopedia of Genes and Genomes pathway annotation. The latter revealed that the differentially expressed proteins were most strongly associated with ‘photosynthesis antenna proteins’ and ‘RNA degradation’. These differentially expressed proteins probably play important roles in salt stress responses in okra. The results should help to increase our understanding of the molecular mechanisms of plant post-translational modifications in response to salt stress.

Local and Systemic Metabolic Responses during Light-Induced Rapid Systemic Signaling

Plants evolved multiple signaling pathways that transduce light-related signals between leaves. These are thought to improve light stress acclimation in a process termed systemic acquired acclimation. Although responses to light stress have been studied extensively in local leaves, and to a lesser degree in systemic leaves, little is known about the responses that occur in the different tissues that connect the local to the systemic leaves. These could be important in defining the specificity of the systemic response as well as in supporting the generation of different systemic signals. Here, we report that local application of light stress to one rosette leaf of bolting Arabidopsis (Arabidopsis thaliana) plants resulted in a metabolic response that encompassed local, systemic and transport tissues (stem tissues that connect the local to the systemic tissues), demonstrating a high degree of physical and metabolic continuity between different tissues throughout the plant. Our results further indicate that the response of many of the systemically altered metabolites is associated with the function of the reactive oxygen species wave and that the levels of eight different metabolites are altered in a similar manner in all tissues tested (local, systemic, and transport). These compounds could define a core metabolic signature for light stress that propagates from the local to the systemic leaves. Our findings suggest that metabolic changes occurring in cells that connect the local and systemic tissues play an important role in systemic acquired acclimation and could convey specificity to the rapid systemic response of plants to light stress.

Post-transcriptional regulation of the oxidative stress response in plants

Due to their sessile lifestyle, plants can be exposed to several kinds of stresses that will increase the production of reactive oxygen species (ROS), such as hydrogen peroxide, singlet oxygen, and hydroxyl radicals, in the plant cells and activate several signaling pathways that cause alterations in the cellular metabolism. Nevertheless, when ROS production outreaches a certain level, oxidative damage to nucleic acids, lipids, metabolites, and proteins will occur, finally leading to cell death. Until now, the most comprehensive and detailed readout of oxidative stress responses is undoubtedly obtained at the transcriptome level. However, transcript levels often do not correlate with the corresponding protein levels. Indeed, together with transcriptional regulations, post-transcriptional, translational, and/or post-translational regulations will shape the active proteome. Here, we review the current knowledge on the post-transcriptional gene regulation during the oxidative stress responses in planta.

GBS Mapping and Analysis of Genes Conserved between Gossypium tomentosum and Gossypium hirsutum Cotton Cultivars that Respond to Drought Stress at the Seedling Stage of the BC₂F₂ Generation

Cotton production is on the decline due to ever-changing environmental conditions. Drought and salinity stress contribute to over 30% of total loss in cotton production, the situation has worsened more due to the narrow genetic base of the cultivated upland cotton. The genetic diversity of upland cotton has been eroded over the years due to intense selection and inbreeding. To break the bottleneck, the wild cotton progenitors offer unique traits which can be introgressed into the cultivated cotton, thereby improving their performance. In this research, we developed a BC₂F₂ population between wild male parent, G. tomentosum as the donor, known for its high tolerance to drought and the elite female parent, G. hirsutum as the recurrent parent, which is high yielding but sensitive to drought stress. The population was genotyped through the genotyping by sequencing (GBS) method, in which 10,888 single-nucleotide polymorphism (SNP) s were generated and used to construct a genetic map. The map spanned 4191.3 cM, with average marker distance of 0.3849 cM. The map size of the two sub genomes had a narrow range, 2149 cM and 2042.3 cM for At and Dt_sub genomes respectively. A total of 66,434 genes were mined, with 32,032 (48.2%) and 34,402 (51.8%) genes being obtained within the At and Dt_sub genomes respectively. Pkinase (PF00069) was found to be the dominant domain, with 1069 genes. Analysis of the main sub family, serine threonine protein kinases through gene ontology (GO), cis element and miRNA targets analysis revealed that most of the genes were involved in various functions aimed at enhancing abiotic stress tolerance. Further analysis of the RNA sequence data and qRT-PCR validation revealed 16 putative genes, which were highly up regulated under drought stress condition, and were found to be targeted by ghr-miR169a and ghr-miR164, previously associated with NAC(NAM, ATAF1/2 and CUC2) and myeloblastosis (MYB), the top rank drought stress tolerance genes. These genes can be exploited further to aid in development of more drought tolerant cotton genotypes.

Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.)

Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.

Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.)

Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F₁ hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress.

GABA accretion reduces Lsi-1 and Lsi-2 gene expressions and modulates physiological responses in Oryza sativa to provide tolerance towards arsenic

GABA counteracts wide range of stresses through regulation of GABA shunt pathway in plants. Although, GABA assisted tolerance against As toxicity in plants is still unexplored. We have examined GABA induced tolerance in rice seedlings with two exposure periods of GABA i.e., short term and long term. Results showed that accumulation of GABA reduced the expressions of Lsi-1 and Lsi-2 transporter genes, which ultimately decreased the accumulation of As in rice seedlings. The accumulation of GABA also modulated the gene expression of GABA shunt pathway and activity of antioxidant enzymes, which strongly induced the tolerance in plants. Antioxidant enzymes such as CAT, POD, GPX and SOD showed maximum alteration in activity with GABA accretion. In both exposure periods, long term accumulation of GABA was highly efficient to provide tolerance to plants against As(III), while higher level of GABA at short term was toxic. Tolerance responses of GABA towards As(III) was reflected by minimal changes in various physiological (WUE, A, gs, PhiPS2, qp, NPQ, ETR and Trmmol) and growth parameters with concomitant accumulation. Oxidative stress marker such as TBARS and H2O2 contents were reduced with GABA accumulation. These results suggested that GABA sturdily inhibits As accumulation and provides tolerance towards As(III).

Flux control through protein phosphorylation in yeast

Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast Saccharomyces cerevisiae, a widely used cell factory and model organism, is reported to show frequent phosphorylation events in metabolism. Studying protein phosphorylation in S. cerevisiae allows for gaining new insight into the function of regulatory networks, which may enable improved metabolic engineering as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies and computational approaches are imperative to expand the current knowledge of protein phosphorylation in S. cerevisiae.

Metabolomics, a Powerful Tool for Agricultural Research

Metabolomics, which is based mainly on nuclear magnetic resonance (NMR), gas-chromatography (GC) or liquid-chromatography (LC) coupled to mass spectrometry (MS) analytical technologies to systematically acquire the qualitative and quantitative information of low-molecular-mass endogenous metabolites, provides a direct snapshot of the physiological condition in biological samples. As complements to transcriptomics and proteomics, it has played pivotal roles in agricultural and food science research. In this review, we discuss the capacities of NMR, GC/LC-MS in the acquisition of plant metabolome, and address the potential promise and diverse applications of metabolomics, particularly lipidomics, to investigate the responses of Arabidopsis thaliana, a primary plant model for agricultural research, to environmental stressors including heat, freezing, drought, and salinity.

A Tale of Two Sugars: Trehalose 6-Phosphate and Sucrose

Trehalose 6-phosphate (Tre6P), the intermediate of trehalose biosynthesis, is an essential signal metabolite in plants, linking growth and development to carbon status. The Suc-Tre6P nexus model postulates that Tre6P is both a signal and negative feedback regulator of Suc levels, forming part of a mechanism to maintain Suc levels within an optimal range and functionally comparable to the insulin-glucagon system for regulating blood Glc levels in animals. The target range and sensitivity of the Tre6P-Suc feedback control circuit can be adjusted according to the cell type, developmental stage, and environmental conditions. In source leaves, Tre6P modulates Suc levels by affecting Suc synthesis, whereas in sink organs it regulates Suc consumption. In illuminated leaves, Tre6P influences the partitioning of photoassimilates between Suc, organic acids, and amino acids via posttranslational regulation of phosphoenolpyruvate carboxylase and nitrate reductase. At night, Tre6P regulates the remobilization of leaf starch reserves to Suc, potentially linking starch turnover in source leaves to carbon demand from developing sink organs. Use of Suc for growth in developing tissues is strongly influenced by the antagonistic activities of two protein kinases: SUC-NON-FERMENTING-1-RELATED KINASE1 (SnRK1) and TARGET OF RAPAMYCIN (TOR). The relationship between Tre6P and SnRK1 in developing tissues is complex and not yet fully resolved, involving both direct and indirect mechanisms, and positive and negative effects. No direct connection between Tre6P and TOR has yet been described. The roles of Tre6P in abiotic stress tolerance and stomatal regulation are also discussed.

An evolutionary view on thylakoid protein phosphorylation uncovers novel phosphorylation hotspots with potential functional implications

The regulation of photosynthetic light reactions by reversible protein phosphorylation is well established today, but functional studies have so far mostly been restricted to processes affecting light-harvesting complex II and the core proteins of photosystem II. Virtually no functional data are available on regulatory effects at the other photosynthetic complexes despite the identification of multiple phosphorylation sites. Therefore we summarize the available data from 50 published phospho-proteomics studies covering the main complexes involved in photosynthetic light reactions in the 'green lineage' (i.e. green algae and land plants) as well as its cyanobacterial counterparts. In addition, we performed an extensive orthologue search for the major photosynthetic thylakoid proteins in 41 sequenced genomes and generated sequence alignments to survey the phylogenetic distribution of phosphorylation sites and their evolutionary conservation from green algae to higher plants. We observed a number of uncharacterized phosphorylation hotspots at photosystem I and the ATP synthase with potential functional relevance as well as an unexpected divergence of phosphosites. Although technical limitations might account for a number of those differences, we think that many of these phosphosites have important functions. This is particularly important for mono- and dicot plants, where these sites might be involved in regulatory processes such as stress acclimation.

Novel connections in plant organellar signalling link different stress responses and signalling pathways

To coordinate growth, development and responses to environmental stimuli, plant cells need to communicate the metabolic state between different sub-compartments of the cell. This requires signalling pathways, including protein kinases, secondary messengers such as Ca(2+) ions or reactive oxygen species (ROS) as well as metabolites and plant hormones. The signalling networks involved have been intensively studied over recent decades and have been elaborated more or less in detail. However, it has become evident that these signalling networks are also tightly interconnected and often merge at common targets such as a distinct group of transcription factors, most prominently ABI4, which are amenable to regulation by phosphorylation, potentially also in a Ca(2+)- or ROS-dependent fashion. Moreover, the signalling pathways connect several organelles or subcellular compartments, not only in functional but also in physical terms, linking for example chloroplasts to the nucleus or peroxisomes to chloroplasts thereby enabling physical routes for signalling by metabolite exchange or even protein translocation. Here we briefly discuss these novel findings and try to connect them in order to point out the remaining questions and emerging developments in plant organellar signalling.