The beta subunit of glyceraldehyde 3-phosphate dehydrogenase is an important factor for maintaining photosynthesis and plant development under salt stress-Based on an integrative analysis of the structural, physiological and proteomic changes in chloroplasts in Thellungiella halophila

Sensitivity and responses of chloroplasts to salt stress in plants

Chloroplast, the site for photosynthesis and various biochemical reactions, is subject to many environmental stresses including salt stress, which affects chloroplast structure, photosynthetic processes, osmotic balance, ROS homeostasis, and so on. The maintenance of normal chloroplast function is essential for the survival of plants. Plants have developed different mechanisms to cope with salt-induced toxicity on chloroplasts to ensure the normal function of chloroplasts. The salt tolerance mechanism is complex and varies with plant species, so many aspects of these mechanisms are not entirely clear yet. In this review, we explore the effect of salinity on chloroplast structure and function, and discuss the adaptive mechanisms by which chloroplasts respond to salt stress. Understanding the sensitivity and responses of chloroplasts to salt stress will help us understand the important role of chloroplasts in plant salt stress adaptation and lay the foundation for enhancing plant salt tolerance.

Proximity to Photosystem II is necessary for activation of Plastid Terminal Oxidase (PTOX) for photoprotection

The Plastid Terminal Oxidase (PTOX) is a chloroplast localized plastoquinone oxygen oxidoreductase suggested to have the potential to act as a photoprotective safety valve for photosynthesis. However, PTOX overexpression in plants has been unsuccessful at inducing photoprotection, and the factors that control its activity remain elusive. Here, we show that significant PTOX activity is induced in response to high light in the model species Eutrema salsugineum and Arabidopsis thaliana. This activation correlates with structural reorganization of the thylakoid membrane. Over-expression of PTOX in mutants of Arabidopsis thaliana perturbed in thylakoid stacking also results in such activity, in contrast to wild type plants with normal granal structure. Further, PTOX activation protects against photoinhibition of Photosystem II and reduces reactive oxygen production under stress conditions. We conclude that structural re-arrangements of the thylakoid membranes, bringing Photosystem II and PTOX into proximity, are both required and sufficient for PTOX to act as a Photosystem II sink and play a role in photoprotection.

Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis

BACKGROUND

Quinoa is a highly nutritious and novel crop that is resistant to various abiotic stresses. However, its growth and development is restricted due to its limited utilization of soil phosphorus. Studies on the levels of phosphorus in quinoa seedlings are limited; therefore, we analyzed transcriptome data from quinoa seedlings treated with different concentrations of phosphorus.

RESULTS

To identify core genes involved in responding to various phosphorus levels, the weighted gene co-expression network analysis method was applied. From the 12,085 expressed genes, an analysis of the gene co-expression network was done. dividing the expressed genes into a total of twenty-five different modules out of which two modules were strongly correlated with phosphorus levels. Subsequently we identified five core genes that correlated strongly either positively or negatively with the phosphorus levels. Gene ontology and assessments of the Kyoto Encyclopedia of Genes and Genomes have uncovered important biological processes and metabolic pathways that are involved in the phosphorus level response.

CONCLUSIONS

We discovered crucial new core genes that encode proteins from various transcription factor families, such as MYB, WRKY, and ERF, which are crucial for abiotic stress resistance. This new library of candidate genes associated with the phosphorus level responses in quinoa seedlings will help in breeding varieties that are tolerant to phosphorus levels.

Identification of the GAPDH gene family in Citrullus lanatus and functional characteristics of ClGAPC2 in Arabidopsis thaliana

Members of the GAPDH family play important roles in plant growth and development, as well as in stress responses. Our aim was to identify stress resistance genes through systematic analysis of the GAPDH family in watermelon. This could not only provide genetic resources for stress resistance breeding, but also form a basis for the study of plant stress resistance mechanisms. Eight GAPDHs representing four types of plant GAPDH in watermelon were identified (ClGAPA/B, ClGAPC1-3, ClGAPCp1-2 and ClGAPN). A comprehensive analysis of physicochemical properties, chromosome distribution, evolutionary relationships, exon-intron structure and conserved motifs of watermelon GAPDHs was performed using bioinformatics. Expression characteristics were assessed by RT-qPCR. Based on RT-qPCR results, ClGAPC2 was screened as a candidate for subcellular localization analysis and functional verification in Arabidopsis thaliana. Eight GAPDHs were classified into four subfamilies. GAPDHs in each subgroup were generally conserved and shared similarities in structure and conserved motifs. ClGAPDHs had notable tissue specificity and different expression patterns in response to H₂ O₂ , chilling, salt, osmotic stress, heat, salicylic acid, gibberellin, brassinosterol, ethylene and abscisic acid treatments. Three ClGAPC genes, especially ClGAPC2, were markedly induced by several treatments. ClGAPC2 was located in the nucleus and cytoplasm of tabacum epidermal cells. The ClGAPC2 transgenic Arabidopsis showed enhanced tolerance to salinity at the germination stage. We suggest that ClGAPC2 plays important roles in the adaptation of watermelon to salinity. Our findings provided candidate genes for further improving the salt tolerance of watermelon.

Integrative transcriptomic and TMT-based proteomic analysis reveals the mechanism by which AtENO2 affects seed germination under salt stress

Seed germination is critical for plant survival and agricultural production and is affected by many cues, including internal factors and external environmental conditions. As a key enzyme in glycolysis, enolase 2 (ENO2) also plays a vital role in plant growth and abiotic stress responses. In our research, we found that the seed germination rate was lower in the AtENO2 mutation (eno2^- ) than in the wild type (WT) under salt stress in Arabidopsis thaliana, while there was no significant difference under normal conditions. However, the mechanisms by which AtENO2 regulates seed germination under salt stress remain limited. In the current study, transcriptome and proteome analyses were used to compare eno2^- and the WT under normal and salt stress conditions at the germination stage. There were 417 and 4442 differentially expressed genes (DEGs) identified by transcriptome, and 302 and 1929 differentially expressed proteins (DEPs) qualified by proteome under normal and salt stress conditions, respectively. The combined analysis found abundant DEGs and DEPs related to stresses and hydrogen peroxide removal were highly down-regulated in eno2^- . In addition, several DEGs and DEPs encoding phytohormone transduction pathways were identified, and the DEGs and DEPs related to ABA signaling were relatively greatly up-regulated in eno2^- . Moreover, we constructed an interactive network and further identified GAPA1 and GAPB that could interact with AtENO2, which may explain the function of AtENO2 under salt stress during seed germination. Together, our results reveal that under salt stress, AtENO2 mainly affects the expression of genes and proteins related to the phytohormone signal transduction pathways, stress response factors, and reactive oxygen species (ROS), and then affects seed germination. Our study lays the foundation for further exploration of the molecular function of AtENO2 under salt stress at the seed germination stage in Arabidopsis thaliana.

Morphological, physiological, and secondary metabolic responses of Taraxacum officinale to salt stress

Salt stress has a major effect on growth and secondary metabolism in medicinal plants, however, the effect of salt stress on Taraxacum officinale F. H. Wigg. is still scarce. In this study, we evaluated the effects of salt stress on the physiology, morphology, phenolic acid accumulation, and expression of genes involved in phenolic acid biosynthesis in T. officinale. We found that plants grew well at 1 g kg^-1 NaCl, and the state of photosystem Ⅱ (PSⅡ) and the organization of the chloroplasts at 0.5 g kg^-1 NaCl showed no significant differences compared with the control. However, 2 g kg^-1 and 4 g kg^-1 NaCl inhibited growth and accelerated leaf senescence. At 4 g kg^-1 NaCl, the fresh and dry weights decreased to 28% and 42% of the control, while chlorosis and necrosis were observed on the leaves. Furthermore, up-regulation of the expression of ToC3'H corresponded with an increase in the levels of caffeoylquinic acids (chlorogenic acid and isochlorogenic acid A) at NaCl concentration ≤ 1 g kg^-1. Expressions of four phenolic acid biosynthesis genes, ToC4H, To4CL, ToHCT, and ToHQT, were down-regulated with increasing NaCl concentrations, consistent with the observed decreases in caftaric and cichoric acids. In summary, cultivation of T. officinale under mild salt stress (NaCl ≤ 1 g kg^-1) is feasible and facilitates the accumulation of caffeoylquinic acids; thus this species may be recommended for saline soils.

A GBS-based genome-wide association study reveals the genetic basis of salinity tolerance at the seedling stage in bread wheat (Triticum aestivum L.)

High salinity levels affect 20% of the cultivated area and 9%–34% of the irrigated agricultural land worldwide, ultimately leading to yield losses of crops. The current study evaluated seven salt tolerance-related traits at the seedling stage in a set of 138 pre-breeding lines (PBLs) and identified 63 highly significant marker-trait associations (MTAs) linked to salt tolerance. Different candidate genes were identified in in silico analysis, many of which were involved in various stress conditions in plants, including glycine-rich cell wall structural protein 1-like, metacaspase-1, glyceraldehyde-3-phosphate dehydrogenase GAPA1, and plastidial GAPA1. Some of these genes coded for structural protein and participated in cell wall structure, some were linked to programmed cell death, and others were reported to show abiotic stress response roles in wheat and other plants. In addition, using the Multi-Trait Genotype-Ideotype Distance Index (MGIDI) protocol, the best-performing lines under salt stress were identified. The SNPs identified in this study and the genotypes with favorable alleles provide an excellent source to impart salt tolerance in wheat.

Photosynthesis in response to salinity and submergence in two Rhizophoraceae mangroves adapted to different tidal elevations

Mangrove ecosystems are vulnerable to rising sea levels. When the sea level rises, the plants are exposed to increased salinity and tidal submergence. In Taiwan, the mangrove species Kandelia obovata and Rhizophora stylosa grow in different habitats and at different elevations. To understand the response of photosynthesis to salinity and submergence in mangroves adapted to different tidal elevations, gas exchange and chlorophyll fluorescence parameters were measured in K. obovata and R. stylosa under different salinity (20 and 40‰) and submergence treatments. The period of light induction of photosynthesis for the two mangrove species was >60 min. In the induction process, the increase in photosystem efficiency was faster than the increase in stomatal opening, but CO2 fixation efficiency was restricted by stomatal conductance. The constraint of stomatal opening speed is related to the conservative water-use strategy developed in response to mangrove environments. Submergence increased the photosynthetic rate of K. obovata, but not that of R. stylosa. Although R. stylosa was more salt tolerant than K. obovata, R. stylosa was not submergence tolerant in a high-salinity environment, which may be the reason for the higher intertidal elevations observed for R. stylosa in comparison with K. obovata. The photosynthetic rate and energy-dependent quenching (qE) of the two mangroves presented a negative relationship with photoinhibition, and high-salt treatment simultaneously reduced photosynthetic rate and qE. A decrease in the photosynthetic rate increased excess energy, whereas a decrease in qE decreased photoprotection; both increased photoinhibition. As the degree of photoinhibition can be easily measured in the field, it is a useful ecological monitoring index that provides a suitable reference for mangrove restoration, habitat construction and ecological monitoring.

Meta-Analysis as a Tool to Identify Candidate Genes Involved in the Fagus sylvatica L. Abiotic Stress Response

In this study, we aimed to evaluate whether candidate genes for abiotic stresses in Fagus sylvatica L. are also candidate genes for herbaceous plants, with the purpose of better defining the abiotic stress response model of F. sylvatica. Therefore, a meta-analysis was performed on published papers related to abiotic stress. Firstly, we carried out a systematic review regarding the activity of 24 candidate genes selected for F. sylvatica under abiotic stress reported in 503 articles. After choosing the inclusion criteria, 73 articles out of 503, regarding 12 candidate genes, were included in this analysis. We performed an exploratory meta-analysis based on the random-effect model and the combined effect-size approach (Cohen’s d). The results obtained through Forest and Funnel plots indicate that the candidate genes for F. sylvatica are considered to be candidate genes in other herbaceous species. These results allowed us to set up models of plants’ response to abiotic stresses implementing the stress models in forest species. The results of this study will serve to bridge knowledge gaps regarding the pathways of response to abiotic stresses in trees based on the meta-analysis. The study approach used could be extended to observe larger gene databases and different species.

Proteomics analysis of the effects for different salt ions in leaves of true halophyte Sesuvium portulacastrum

Sesuvium portulacastrum is a true halophyte and shows an optimal development under moderate salinity with large amounts of salt ions in its leaves. However, the specific proteins in response to salt ions are remained unknown. In this study, comparative physiological and proteomic analyses of different leaves subject to NaCl, KCl, NaNO₃ and KNO₃ were performed. Chlorophyll content was decreased under the above four kinds of salt treatments. Starch and soluble sugar contents changed differently under different salt treatments. A total of 53 differentially accumulated proteins (DAPs) were identified by mass spectrometry. Among them, 13, 25, 26 and 25 DAPs were identified after exposure to KCl, NaCl, KNO_3, and NaNO₃, respectively. These DAPs belong to 47 unique genes, and 37 of them are involved in protein-protein interactions. These DAPs displayed different expression patterns after treating with different salt ions. Functional annotation revealed they are mainly involved in photosynthesis, carbohydrate and energy metabolism, lipid metabolism, and biosynthesis of secondary metabolites. Genes and proteins showed different expression profiles under different salt treatments. Enzyme activity analysis indicated P-ATPase was induced by KCl, NaCl and NaNO₃, V-ATPase was induced by KCl and NaCl, whereas V-PPase activity was significantly increased after application of KNO₃, but sharply inhibited by NaCl. These results might deepen our understanding of responsive mechanisms in the leaves of S. portulacastrum upon different salt ions.

Thylakoid proteome variation of Eutrema salsugineum in response to drought and salinity combined stress

It is well known that plant responses to stress involve different events occurring at different places of the cell/leaf and at different time scales in relation with the plant development. In fact, the organelles proteomes include a wide range of proteins that could include a wide range of proteins showing a considerable change in cellular functions and metabolism process. On this basis, a comparative proteomics analysis and fluorescence induction measurements were performed to investigate the photosynthetic performance and the relative thylakoid proteome variation in Eutrema salsugineum cultivated under salt stress (200 mM NaCl), water deficit stress (PEG) and combined treatment (PEG + NaCl) as a hyperosmotic stress. The obtained results showed a significant decrease of plant growth under drought stress conditions, with the appearance of some toxicity symptoms, especially in plants subjected to combined treatment. Application of salt or water stress alone showed no apparent change in the chlorophyll a fluorescence transients, primary photochemistry (fluorescence kinetics of the O-J phase), the PQ pool state (J-I phase changes), (Fv/Fm) and (Fk/Fj) ratios. However, a considerable decrease of all these parameters was observed under severe osmotic stress (PEG + NaCl). The thylakoid proteome analysis revealed 58 proteins showing a significant variation in their abundance between treatments (up or down regulation). The combined treatment (PEG + NaCl) induced a decrease in the expression of the whole PSII core subunit (D1, D2, CP43, CP47, PsbE and PsbH), whereas the OEC subunits proteins remained constant. An increase in the amount of PsaD, PsaE, PsaF, PsaH, PsaK and PsaN was detected under drought stress (PEG5%). No significant change in the accumulation of Cyt b6 and Cyt f was observed. Some regulated proteins involved in cellular redox homeostasis were detected (glutamine synthetase, phosphoglycerate kinase, transketolase), and showed a significant decrease under the combined treatment. Some oxidative stress related proteins were significantly up-regulated under salt or drought stress and could play a crucial role in the PSI photoprotection and the control of ROS production level.

Differential expression gene/protein contribute to heat stress-responsive in Tetraena propinqua in Saudi Arabia

Within their natural habitat, plants are subjected to abiotic stresses that include heat stress. In the current study, the effect of 4 h, 24 h, and 48 h of heat stress on Tetraena propinqua ssp. migahidii seedling's protein profile and proteomic analyses were investigated. Total soluble protein SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis) profile showed 18-protein bands, the newly synthesized protein band (with molecular weights 86.5, 30.2 and 31.4 KD) at 24 h of heat stress and 48 of normal conditions. Proteomic analysis showed that 81 and 930 targets are involved in gene and protein expression respectively. At 4 h, 57 genes and 110 proteins in C4 reached 56 genes and 173 proteins in T4. At 24 h, 63 genes and 180 proteins in C24 decreased to 54 genes and 151 protein in T24. After 48 h, 56 genes and 136 proteins in C48 increased to 64 genes and 180 proteins in T48. The genes and proteins involved in transcription, translation, photosynthesis, transport, and other unknown metabolic processes, were differentially expressed under treatments of heat stress. These findings provide insights into the molecular mechanisms related to heat stress, in addition to its influence on the physiological traits of T. propinqua seedlings. Heat stress-mediated differential regulation genes indicate a role in the development and stress response of T. propinqua. The candidate dual-specificity genes and proteins identified in this study paves way for more molecular analysis of up-and-down-regulation.

Stability of thylakoid protein complexes and preserving photosynthetic efficiency are crucial for the successful recovery of the halophyte Cakile maritima from high salinity

Plants native to extreme habitats often face changes in environmental conditions such as salinity level and water availability. In response, plants have evolved efficient mechanisms allowing them to survive or recover. In the present work, effects of high salinity and salt-stress release were studied on the halophyte Cakile maritima. Four week-old plants were either cultivated at 0 mM NaCl or 200 mM NaCl. After one month of treatment, plants were further irrigated at either 0 mM NaCl, 200 mM NaCl, or rewatered to 0 mM NaCl (stress release). Upon salt stress, C. maritima plants exhibited reduced biomass production and shoot hydration which were associated with a decrease in the amount of chlorophyll a and b. However, under the same stressful conditions a significant increase of anthocyanin and malonyldialdehyde concentrations was noticed. Salt-stressed plants were able to maintain stable protein complexes of thylakoid membranes. Measurement of chlorophyll fluorescence and P700 redox state showed that PSI was more susceptible for damage by salinity than PSII. PSII machinery was significantly enhanced under saline conditions. All measured parameters were partially restored under salt-stress release conditions. Photoinhibition of PSI was also reversible and C. maritima was able to successfully re-establish PSI machinery indicating the high contribution of chloroplasts in salt tolerance mechanisms of C. maritima. Overall, to overcome high salinity stress, C. maritima sets a cascade of physio-biochemical and molecular pathways. Chloroplasts seem to act as metabolic centers as part of this adaptive process enabling growth restoration in this halophyte following salt stress release.

Effects of Salinity Stress on Chloroplast Structure and Function

Salinity is a growing problem affecting soils and agriculture in many parts of the world. The presence of salt in plant cells disrupts many basic metabolic processes, contributing to severe negative effects on plant development and growth. This review focuses on the effects of salinity on chloroplasts, including the structures and function of these organelles. Chloroplasts house various important biochemical reactions, including photosynthesis, most of which are considered essential for plant survival. Salinity can affect these reactions in a number of ways, for example, by changing the chloroplast size, number, lamellar organization, lipid and starch accumulation, and interfering with cross-membrane transportation. Research has shown that maintenance of the normal chloroplast physiology is necessary for the survival of the entire plant. Many plant species have evolved different mechanisms to withstand the harmful effects of salt-induced toxicity on their chloroplasts and its machinery. The differences depend on the plant species and growth stage and can be quite different between salt-sensitive (glycophyte) and salt-tolerant (halophyte) plants. Salt stress tolerance is a complex trait, and many aspects of salt tolerance in plants are not entirely clear yet. In this review, we discuss the different mechanisms of salt stress tolerance in plants with a special focus on chloroplast structure and its functions, including the underlying differences between glycophytes and halophytes.

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.

Genome-wide analysis and phosphorylation sites identification of the 14-3-3 gene family and functional characterization of MeGRF3 in cassava

The biological functionality of many members of the 14-3-3 gene family is regulated via phosphorylation at multiple amino acid residues. The specific phosphorylation-mediated regulation of these proteins during cassava root tuberization, however, is not well understood. In this study, 15 different 14-3-3 genes (designated MeGRF1 - 15) were identified within the cassava genome. Based upon evolutionary conservation and structural analyses, these cassava 14-3-3 proteins were grouped into ε and non-ε clusters. We found these 15 MeGRF genes to be unevenly distributed across the eight cassava chromosomes. When comparing the expression of these genes during different developmental stages, we found that three of these genes (MeGRF9, 12 and 15) were overexpressed at all developmental stages at 75, 104, 135, 182 and 267 days post-planting relative to the fibrous root stage, whereas two (MeGRF5 and 7) were downregulated during these same points. In addition, the expression of most MeGRF genes changed significantly in the early and middle stages of root tuberization. This suggests that these different MeGRF genes likely play distinct regulatory roles during cassava root tuberization. Subsequently, 18 phosphorylated amino acid residues were detected on nine of these MeGRF proteins. A phosphomimetic mutation at serine-65 in MeGRF3 in Arabidopsis thaliana (Arabidopsis) slightly influenced starch metabolism in these plants, and significantly affected the role of MeGRF3 in salt stress responses. Together these results indicate that 14-3-3 genes play key roles in responses to abiotic stress and the regulation of starch metabolism, offering valuable insights into the functions of these genes in cassava.

Proteomic Analysis of Rice Subjected to Low Light Stress and Overexpression of OsGAPB Increases the Stress Tolerance

BACKGROUND

Light provides the energy for photosynthesis and determines plant morphogenesis and development. Low light compromises photosynthetic efficiency and leads to crop yield loss. It remains unknown how rice responds to low light stress at a proteomic level.

RESULTS

In this study, the quantitative proteomic analysis with isobaric tags for relative and absolute quantitation (iTRAQ) was used and 1221 differentially expressed proteins (DEPs) were identified from wild type rice plants grown in control or low light condition (17% light intensity of control), respectively. Bioinformatic analysis of DEPs indicated low light remarkably affects the abundance of chloroplastic proteins. Specifically, the proteins involved in carbon fixation (Calvin cycle), electron transport, and ATPase complex are severely downregulated under low light. Furthermore, overexpression of the downregulated gene encoding rice β subunit of glyceraldehyde-3-phosphate dehydrogenase (OsGAPB), an enzyme in Calvin cycle, significantly increased the CO₂ assimilation rate, chlorophyll content and fresh weight under low light conditions but have no obvious effect on rice growth and development under control light.

CONCLUSION

Our results revealed that low light stress on vegetative stage of rice inhibits photosynthesis possibly by decreasing the photosynthetic proteins and OsGAPB gene is a good candidate for manipulating rice tolerance to low light stress.

Silicon and Gibberellins: Synergistic Function in Harnessing ABA Signaling and Heat Stress Tolerance in Date Palm (Phoenix dactylifera L.)

Date palm is one of the most economically vital fruit crops in North African and Middle East countries, including Oman. A controlled experiment was conducted to investigate the integrative effects of silicon (Si) and gibberellic acid (GA₃) on date palm growth and heat stress. The exogenous application of Si and GA₃ significantly promoted plant growth attributes under heat stress (44 ± 1 °C). The hormonal modulation (abscisic acid [ABA] and salicylic acid [SA]), antioxidant accumulation, and the expression of abiotic stress-related genes were evaluated. Interestingly, heat-induced oxidative stress was markedly reduced by the integrative effects of Si and GA₃ when compared to their sole application, with significant reductions in superoxide anions and lipid peroxidation. The reduction of oxidative stress was attributed to the enhancement of polyphenol oxidase, catalase, peroxidase, and ascorbate peroxidase activities as well as the upregulation of their synthesis related genes expression viz. GPX2, CAT, Cyt-Cu/Zn SOD, and glyceraldehyde3-phosphate dehydrogenase gene (GAPDH). The results showed the activation of heat shock factor related genes (especially HsfA3) during exogenous Si and GA₃ as compared to the control. Furthermore, the transcript accumulation of ABA signaling-related genes (PYL4, PYL8, and PYR1) were significantly reduced with the combined treatment of Si and GA₃, leading to reduced production of ABA and, subsequently, SA antagonism via its increased accumulation. These findings suggest that the combined application of Si and GA₃ facilitate plant growth and metabolic regulation, impart tolerance against stress, and offers novel stress alleviating strategies for a green revolution in sustainable food security.

The chloroplast proteome response to drought stress in cassava leaves

Cassava is an important tropical crop with strong resistance to drought stress. The chloroplast, the site of photosynthesis, is sensitive to stress, and the drought-response proteins in cassava chloroplasts are worthy of investigation. In this study, cassava leaves were collected for ultra-structure observation from plants subjected to different drought stress conditions. Our results showed that drought stress can promote starch accumulation in cassava chloroplasts. To evaluate changes in chloroplast proteins under different drought conditions, two-dimensional electrophoresis was performed using purified chloroplasts, which resulted in the identification of 26 unique chloroplast proteins responsive to drought stress. These drought-responsive proteins are predominantly related to photosynthesis, carbon and nitrogen metabolism, and amino acid metabolism. Among them, most photosynthesis-related proteins are downregulated, with decreases in photosynthetic parameters upon drought stress. Several proteins associated with carbon and nitrogen metabolism, including rubisco and carbonic anhydrase, were upregulated, which might promote drought tolerance in cassava by enhancing the carbohydrate conversion efficiency and protecting the plant from oxidative stress. Our proteomic data not only provide insight into the complement of proteins in cassava chloroplasts but also further our overall understanding of drought-responsive proteins in cassava chloroplasts.

Molecular Evolution and Functional Analysis of Rubredoxin-Like Proteins in Plants

Rubredoxins are a class of iron-containing proteins that play an important role in the reduction of superoxide in some anaerobic bacteria and also act as electron carriers in many biochemical processes. Unlike the more widely studied about rubredoxin proteins in anaerobic bacteria, very few researches about the function of rubredoxins have been proceeded in plants. Previous studies indicated that rubredoxins in A. thaliana may play a critical role in responding to oxidative stress. In order to identify more rubredoxins in plants that maybe have similar functions as the rubredoxin-like protein of A. thaliana, we identified and analyzed plant rubredoxin proteins using bioinformatics-based methods. Totally, 66 candidate rubredoxin proteins were identified based on public databases, exhibiting lengths of 187-360 amino acids with molecular weights of 19.856-37.117 kDa. The results of subcellular localization showed that these candidate rubredoxins were localized to the chloroplast, which might be consistent with the fact that rubredoxins were predominantly expressed in leaves. Analyses of conserved motifs indicated that these candidate rubredoxins contained rubredoxin and PDZ domains. The expression patterns of rubredoxins in glycophyte and halophytic plant under salt/drought stress revealed that rubredoxin is one of the important stress response proteins. Finally, the coexpression network of rubredoxin in Arabidopsis thaliana under abiotic was extracted from ATTED-II to explore the function and regulation relationship of rubredoxin in Arabidopsis thaliana. Our results showed that putative rubredoxin proteins containing PDZ and rubredoxin domains, localized to the chloroplast, may act with other proteins in chloroplast to responses to abiotic stress in higher plants. These findings might provide value inference to promote the development of plant tolerance to some abiotic stresses and other economically important crops.

Comparative physiological and proteomic analyses of the chloroplasts in halophyte Sesuvium portulacastrum under differential salt conditions

Sesuvium portulacastrum, an important mangrove-associated true halophyte belongs to the family Aizoaceae, has excellent salt tolerance. Chloroplasts are the most sensitive organelles involved in the response to salinity. However, the regulation mechanism of chloroplasts of S. portulacastrum under salinity stress has not been reported. In this study, morphological and physiological analyses of leaves and comparative proteomics of chloroplasts isolated from the leaves of S. portulacastrum under different NaCl treatments were performed. Our results showed that the thickness of the palisade tissue, the leaf area, the maximum photochemical efficiency of photosystem II, and the electron transport rate increased remarkably after the plants were subjected to differential saline environments, indicating that salinity can increase photosynthetic efficiency and improve the growth of S. portulacastrum. Subsequently, 55 differentially expressed protein species (DEPs) from the chloroplasts of S. portulacastrum under differential salt conditions were positively identified by mass spectrometry. These DEPs were involved in multiple metabolic pathways, such as photosynthesis, carbon metabolism, ATP synthesis and the cell structure. Among these DEPs, the abundance of most proteins was induced by salt stress. Based on a combination of the morphological and physiological data, as well as the chloroplast proteome results, we speculated that S. portulacastrum can maintain photosynthetic efficiency and growth by maintaining the stability of the photosystem II complex, promoting the photochemical reaction rate, enhancing carbon fixation, developing plastoglobules, and preserving the biomembrane system of chloroplasts under salt stress.

Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

Comparative proteomic analysis of Chlamydomonas reinhardtii control and a salinity-tolerant strain revealed a differential protein expression pattern

Proteins involved in membrane transport and trafficking, stress and defense, iron uptake and metabolism, as well as proteolytic enzymes, were remarkably up-regulated in the salinity-tolerant strain of Chlamydomonas reinhardtii. Excessive concentration of NaCl in the environment can cause adverse effects on plants and microalgae. Successful adaptation of plants to long-term salinity stress requires complex cellular adjustments at different levels from molecular, biochemical and physiological processes. In this study, we developed a salinity-tolerant strain (ST) of the model unicellular green alga, Chlamydomonas reinhardtii, capable of growing in medium containing 300 mM NaCl. Comparative proteomic analyses were performed to assess differential protein expression pattern between the ST and the control progenitor cells. Proteins involved in membrane transport and trafficking, stress and defense, iron uptake and metabolism, as well as protein degradation, were remarkably up-regulated in the ST cells, suggesting the importance of these processes in acclimation mechanisms to salinity stress. Moreover, 2-DE-based proteomic also revealed putative salinity-specific post-translational modifications (PTMs) on several important housekeeping proteins. Discussions were made regarding the roles of these differentially expressed proteins and the putative PTMs in cellular adaptation to long-term salinity stress.

Heat-Responsive Photosynthetic and Signaling Pathways in Plants: Insight from Proteomics

Heat stress is a major abiotic stress posing a serious threat to plants. Heat-responsive mechanisms in plants are complicated and fine-tuned. Heat signaling transduction and photosynthesis are highly sensitive. Therefore, a thorough understanding of the molecular mechanism in heat stressed-signaling transduction and photosynthesis is necessary to protect crop yield. Current high-throughput proteomics investigations provide more useful information for underlying heat-responsive signaling pathways and photosynthesis modulation in plants. Several signaling components, such as guanosine triphosphate (GTP)-binding protein, nucleoside diphosphate kinase, annexin, and brassinosteroid-insensitive I-kinase domain interacting protein 114, were proposed to be important in heat signaling transduction. Moreover, diverse protein patterns of photosynthetic proteins imply that the modulations of stomatal CO₂ exchange, photosystem II, Calvin cycle, ATP synthesis, and chlorophyll biosynthesis are crucial for plant heat tolerance.

Salinity Response in Chloroplasts: Insights from Gene Characterization

Salinity is a severe abiotic stress limiting agricultural yield and productivity. Plants have evolved various strategies to cope with salt stress. Chloroplasts are important photosynthesis organelles, which are sensitive to salinity. An understanding of molecular mechanisms in chloroplast tolerance to salinity is of great importance for genetic modification and plant breeding. Previous studies have characterized more than 53 salt-responsive genes encoding important chloroplast-localized proteins, which imply multiple vital pathways in chloroplasts in response to salt stress, such as thylakoid membrane organization, the modulation of photosystem II (PS II) activity, carbon dioxide (CO₂) assimilation, photorespiration, reactive oxygen species (ROS) scavenging, osmotic and ion homeostasis, abscisic acid (ABA) biosynthesis and signaling, and gene expression regulation, as well as protein synthesis and turnover. This review presents an overview of salt response in chloroplasts revealed by gene characterization efforts.

Salt stress induces changes in the proteomic profile of micropropagated sugarcane shoots

Salt stress is one of the most common stresses in agricultural regions worldwide. In particular, sugarcane is affected by salt stress conditions, and no sugarcane cultivar presently show high productivity accompanied by a tolerance to salt stress. Proteomic analysis allows elucidation of the important pathways involved in responses to various abiotic stresses at the biochemical and molecular levels. Thus, this study aimed to analyse the proteomic effects of salt stress in micropropagated shoots of two sugarcane cultivars (CB38-22 and RB855536) using a label-free proteomic approach. The mass spectrometry proteomics data are available via ProteomeXchange with identifier PXD006075. The RB855536 cultivar is more tolerant to salt stress than CB38-22. A quantitative label-free shotgun proteomic analysis identified 1172 non-redundant proteins, and 1160 of these were observed in both cultivars in the presence or absence of NaCl. Compared with CB38-22, the RB855536 cultivar showed a greater abundance of proteins involved in non-enzymatic antioxidant mechanisms, ion transport, and photosynthesis. Some proteins, such as calcium-dependent protein kinase, photosystem I, phospholipase D, and glyceraldehyde-3-phosphate dehydrogenase, were more abundant in the RB855536 cultivar under salt stress. Our results provide new insights into the response of sugarcane to salt stress, and the changes in the abundance of these proteins might be important for the acquisition of ionic and osmotic homeostasis during exposure to salt stress.

Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO2 concentrations: A proteomics perspective

Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO₂ concentrations. Growth under a high concentration of CO₂ could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO₂. Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species. Among the 816 isolated proteins, those involved in carbon fixation were found to be the most abundant ones. An increase in the abundance of six key enzymes out of the eleven core enzymes involved in carbon fixation was detected in plants grown at a high CO₂ concentration. Proteome changes were corroborated by the detection of a decrease in the stomatal aperture and in the vascular bundle area in Eucalyptus urophylla plantlets grown in an environment of high atmospheric CO₂. Our proteomics approach indicates a positive metabolic response regarding carbon fixation in a CO₂-enriched atmosphere. The slight but significant increase in the abundance of the Calvin enzymes suggests that stomatal closure did not prevent an increase in the carbon assimilation rates.

BIOLOGICAL SIGNIFICANCE

The sample enrichment strategy and data analysis used here enabled the identification of all enzymes and most protein isoforms involved in the Calvin-Benson-Bessham cycle in Eucalyptus urophylla. Upon growth in CO₂-enriched chambers, Eucalyptus urophylla plantlets responded by reducing the vascular bundle area and stomatal aperture size and by increasing the abundance of six of the eleven core enzymes involved in carbon fixation. Our proteome approach provides an estimate on how a commercially important C3-type plant would respond to an increase in CO₂ concentrations. Additionally, confirmation at the protein level of the predicted genes involved in carbon assimilation may be used in plant transformation strategies aiming to increase plant adaptability to climate changes or to increase plant productivity.

Comparative Proteomic Analysis of Cultured Suspension Cells of the Halophyte Halogeton glomeratus by iTRAQ Provides Insights into Response Mechanisms to Salt Stress

Soil salinity severely threatens land use capability and crop yields worldwide. An analysis of the molecular mechanisms of salt tolerance in halophytes will contribute to the development of salt-tolerant crops. In this study, a combination of physiological characteristics and iTRAQ-based proteomic approaches was conducted to investigate the molecular mechanisms underlying the salt response of suspension cell cultures of halophytic Halogeton glomeratus. These cells showed halophytic growth responses comparable to those of the whole plant. In total, 97 up-regulated proteins and 192 down-regulated proteins were identified as common to both 200 and 400 mM NaCl concentration treatments. Such salinity responsive proteins were mainly involved in energy, carbohydrate metabolism, stress defense, protein metabolism, signal transduction, cell growth, and cytoskeleton metabolism. Effective regulatory protein expression related to energy, stress defense, and carbohydrate metabolism play important roles in the salt-tolerance of H. glomeratus suspension cell cultures. However, known proteins regulating Na(+) efflux from the cytoplasm and its compartmentalization into the vacuole did not change significantly under salinity stress suggesting our existing knowledge concerning Na(+) extrusion and compartmentalization in halophytes needs to be evaluated further. Such data are discussed in the context of our current understandings of the mechanisms involved in the salinity response of the halophyte, H. glomeratus.

A Different Pattern of Production and Scavenging of Reactive Oxygen Species in Halophytic Eutrema salsugineum (Thellungiella salsuginea) Plants in Comparison to Arabidopsis thaliana and Its Relation to Salt Stress Signaling

Isolated thylakoids from halophytic Eutrema salsugineum (Thellungiella salsuginea) produces more H2O2 in comparison to glycophytic Arabidopsis thaliana. The first objective of this study was to verify whether this feature is relevant also to the intact chloroplasts and leaves. Enhanced H2O2 levels in chloroplasts and leaves of E. salsugineum were positively verified with several methods (electron microscopy, staining with Amplex Red and with diaminobenzidine). This effect was associated with a decreased ratio of [Formula: see text]/H2O2 in E. salsugineum in comparison to A. thaliana as detected by electron paramagnetic resonance method. As a next step, we tested how this specific ROS signature of halophytic species affects the antioxidant status and down-stream components of ROS signaling. Comparison of enzymatic antioxidants revealed a decreased activity of ascorbate peroxidase (APX), enhanced activity of glutathione peroxidase, and the presence of thylakoid-bound forms of iron superoxide dismutase (FeSOD) and APX in E. salsugineum. These cues were, however, independent from application of salt stress. The typical H2O2-dependent cellular responses, namely the levels of glucosinolates and stress-related hormones were determined. The total glucosinolate content in E. salsugineum water-treated leaves was higher than in A. thaliana and increased after salinity treatment. Treatment with salinity up-regulated all of tested stress hormones, their precursors and catabolites [abscisic acid (ABA), dihydrophaseic acid, phaseic acid, 1-aminocyclopropane-1-carboxylic acid, salicylic acid, jasmonic acid, cis-(+)-12-oxo-phytodienoic acid and jasmonoyl-L-isoleucine] in A. thaliana, whereas in E. salsugineum only a stimulation in ethylene synthesis and ABA catabolism was noted. Obtained results suggest that constitutively enhanced H2O2 generation in chloroplasts of E. salsugineum might be a crucial component of stress-prepardeness of this halophytic species. It shapes a very efficient antioxidant protection (in which glucosinolates might play a specific role) and a fine tuning of hormonal signaling to suppress the cell death program directed by jasmonate pathway.