Proteome Analysis of Cold Response in Spring and Winter Wheat (Triticum aestivum) Crowns Reveals Similarities in Stress Adaptation and Differences in Regulatory Processes between the Growth Habits

Deacclimation and reacclimation processes in winter wheat: novel perspectives from time-series transcriptome analysis

Winter wheat achieves freezing tolerance (FT) through cold acclimation (CA) - a process which is induced by low positive temperatures in autumn. The increasing occurrences of temperature fluctuations in winter lead to deacclimation (DEA), causing premature loss of FT, and the cultivars capable of reacclimation (REA) are more likely to survive the subsequent cold spells. The genetic mechanisms of DEA and REA remain poorly understood, necessitating further research to bolster climate resilience in winter wheat. Here, we selected two winter wheat genotypes with contrasting levels of FT and conducted a ten-week-long experiment imitating low-temperature fluctuations after CA under controlled conditions. Crown and leaf tissue samples for RNA-sequencing were collected at CA, DEA, and REA time-points. It is the first transcriptomic study covering both short- and long-term responses to DEA and REA in winter wheat. The study provides novel knowledge regarding CA, DEA, and REA and discusses the gene expression patterns conferring FT under temperature fluctuations. The freezing-tolerant genotype "Lakaja DS" showed elevated photosynthetic activity in leaf tissue and upregulated cryoprotective protein-encoding genes in crowns after CA when compared to the freezing-susceptible "KWS Ferrum". "Lakaja DS" also expressed cold acclimation-associated transcripts at a significantly higher level after 1 week of DEA. Following REA, "Lakaja DS" continued to upregulate dehydrin-related genes in crowns and exhibited significantly higher expression of chitinase transcripts in leaves, when compared to "KWS Ferrum". The findings of this study shed light on the genetic mechanisms governing DEA and REA in winter wheat, thus addressing the gaps in knowledge regarding FT under low-temperature fluctuations. The identified genes should be further examined as potential molecular markers for breeding strategies focused on developing freezing-tolerant winter-type crops. Publicly available datasets generated in this study are valuable resources for further research into DEA and REA, contributing towards the enhancement of winter wheat under global climate change.

TaMAPK3 phosphorylates TaCBF and TaICE and plays a negative role in wheat freezing tolerance

Freezing temperature during overwintering often kills plants; plants have thus, developed a defense mechanism called 'cold acclimation', in which a number of genes are involved in increasing cell protection and gene expression. Mitogen-activated protein kinase (MAPK) controls proteins' activities by phosphorylation and is involved in numerous metabolic pathways. In this study, we identified the protein interaction between TaMAPK3 and the proteins in the cold response pathway, ICE41, ICE87, and CBFIVd-D9. The subcellular localization and bimolecular fluorescence complement (BiFC) assays revealed that these proteins interact in the nucleus or in the plasma membrane. Furthermore, MAPK3-mediated phosphorylation of ICE41, ICE87, and CBFIVd-D9 was verified using an in vitro phosphorylation assay. TaMAPK3-overexpressing transgenic Brachypodium showed a lower survival rate upon freezing stress and lower proline content during cold acclimation, compared to wild-type plants. Furthermore, cold response gene expression analysis revealed that the expression of these genes was suppressed in the transgenic lines under cold treatment. It was further elucidated that MAPK3 mediates the degradation of ICE and CBF proteins, which implies the negative impact of MAPK3 on the freezing tolerance of plants. This study will help to elucidate the molecular mechanisms of cold tolerance and the activity of MAPK3 in wheat.

Adjustments of the Phytochemical Profile of Broccoli to Low and High Growing Temperatures: Implications for the Bioactivity of Its Extracts

Climate change causes shifts in temperature patterns, and plants adapt their chemical content in order to survive. We compared the effect of low (LT) and high (HT) growing temperatures on the phytochemical content of broccoli (Brassica oleracea L. convar. botrytis (L.) Alef. var. cymosa Duch.) microgreens and the bioactivity of their extracts. Using different spectrophotometric, LC-MS/MS, GC-MS, and statistical methods, we found that LT increased the total phenolics and tannins in broccoli. The total glucosinolates were also increased by LT; however, they were decreased by HT. Soluble sugars, known osmoprotectants, were increased by both types of stress, considerably more by HT than LT, suggesting that HT causes a more intense osmotic imbalance. Both temperatures were detrimental for chlorophyll, with HT being more impactful than LT. HT increased hormone indole-3-acetic acid, implying an important role in broccoli's defense. Ferulic and sinapic acid showed a trade-off scheme: HT increased ferulic while LT increased sinapic acid. Both stresses decreased the potential of broccoli to act against H2O2 damage in mouse embryonal fibroblasts (MEF), human keratinocytes, and liver cancer cells. Among the tested cell types treated by H2O2, the most significant reduction in ROS (36.61%) was recorded in MEF cells treated with RT extracts. The potential of broccoli extracts to inhibit α-amylase increased following both temperature stresses; however, the inhibition of pancreatic lipase was increased by LT only. From the perspective of nutritional value, and based on the obtained results, we conclude that LT conditions result in more nutritious broccoli microgreens than HT.

The impact of multiple abiotic stresses on ns-LTP2.8 gene transcript and ns-LTP2.8 protein accumulation in germinating barley (Hordeum vulgare L.) embryos

Abiotic stresses occur more often in combination than alone under regular field conditions limiting in more severe way crop production. Stress recognition in plants primarily occurs in the plasma membrane, modification of which is necessary to maintain homeostasis in response to it. It is known that lipid transport proteins (ns-LTPs) participate in modification of the lipidome of cell membranes. Representative of this group, ns-LTP2.8, may be involved in the reaction to abiotic stress of germinating barley plants by mediating the intracellular transport of hydrophobic particles, such as lipids, helping to maintain homeostasis. The ns-LTP2.8 protein was selected for analysis due to its ability to transport not only linear hydrophobic molecules but also compounds with a more complex spatial structure. Moreover, ns-LTP2.8 has been qualified as a member of pathogenesis-related proteins, which makes it particularly important in relation to its high allergenic potential. This paper demonstrates for the first time the influence of various abiotic stresses acting separately as well as in their combinations on the change in the ns-LTP2.8 transcript, ns-LTP2.8 protein and total soluble protein content in the embryonal axes of germinating spring barley genotypes with different ns-LTP2.8 allelic forms and stress tolerance. Tissue localization of ns-LTP2.8 transcript as well as ns-LTP2.8 protein were also examined. Although the impact of abiotic stresses on the regulation of gene transcription and translation processes remains not fully recognized, in this work we managed to demonstrate different impact on applied stresses on the fundamental cellular processes in very little studied tissue of the embryonal axis of barley.

Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops

Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop productivity. Perception of cold stress by plant cells leads to the activation of cold-responsive transcription factors and downstream genes, which ultimately impart cold tolerance. The response triggered in crops to cold stress includes gene expression/suppression, the accumulation of sugars upon chilling, and signaling molecules, among others. Much of the information on the effects of cold stress on perception, signal transduction, gene expression, and plant metabolism are available in the model plant Arabidopsis but somewhat lacking in major crops. Hence, a complete understanding of the molecular mechanisms by which staple crops respond to cold stress remain largely unknown. Here, we make an effort to elaborate on the molecular mechanisms employed in response to low-temperature stress. We summarize the effects of cold stress on the growth and development of these crops, the mechanism of cold perception, and the role of various sensors and transducers in cold signaling. We discuss the progress in cold tolerance research at the genome, transcriptome, proteome, and metabolome levels and highlight how these findings provide opportunities for designing cold-tolerant crops for the future.

Light-Induced Flavonoid Biosynthesis in Sinopodophyllum hexandrum with High-Altitude Adaptation

Sinopodophyllum hexandrum is a perennial alpine herb producing the anti-cancer metabolite podophyllotoxin (PPT). Although the adaptation of S. hexandrum to high altitudes has been demonstrated and the effects of temperature, precipitation, and UV-B light on plant growth and metabolite accumulation have been studied, knowledge on the role of flavonoid biosynthesis in adapting to high altitudes is limited. In this study, light intensity, amount and type of flavonoids, and differentially expressed proteins (DEPs) and genes (DEGs) at 2300 and 3300 m were analyzed by HPLC, proteomic, transcriptomic, and qRT-PCR analysis. We found that higher light intensity correlated with greater flavonoid, flavonol, and anthocyanin content as well as higher anthocyanin to total flavonoid and flavonol ratios observed at the higher altitude. Based on proteomic and transcriptomic analyses, nine DEPs and 41 DEGs were identified to be involved in flavonoid biosynthesis and light response at 3300 m. The relative expression of nine genes (PAL, CHS1, IFRL, ANS, MYB4, BHLH137, CYP6, PPO1, and ABCB19) involved in flavonoid biosynthesis and seven genes (HSP18.1, HSP70, UBC4, ERF5, ERF9, APX3, and EX2) involved in light stress were observed to be up-regulated at 3300 m compared with 2300 m. These findings indicate that light intensity may play a regulatory role in enhancing flavonoid accumulation that allows S. hexandrum to adapt to elevated-altitude coupled with high light intensity.

Proteomic responses of two spring wheat cultivars to the combined water deficit and aphid (Metopolophium dirhodum) treatments

In the field, plants usually have to face the combined effects of abiotic and biotic stresses. In our study, two spring wheat cultivars-Septima and Quintus-were subjected to three water regimes [70%, 50%, and 40% soil water capacity (SWC)], aphid (Metopolophium dirhodum) infestation, or the combination of both stresses, i.e., water deficit (50%, 40% SWC) and aphids. The study has a 2 × 3 × 2 factorial design with three biological replicates. In the present study, the results of proteomic analysis using 2D-DIGE followed by MALDI-TOF/TOF protein identification are presented. Water deficit but also aphid infestation led to alterations in 113 protein spots including proteins assigned to a variety of biological processes ranging from signaling via energy metabolism, redox regulation, and stress and defense responses to secondary metabolism indicating a long-term adaptation to adverse conditions. The absence of specific proteins involved in plant response to herbivorous insects indicates a loss of resistance to aphids in modern wheat cultivars during the breeding process and is in accordance with the "plant vigor hypothesis." Septima revealed enhanced tolerance with respect to Quintus as indicated by higher values of morphophysiological characteristics (fresh aboveground biomass, leaf length, osmotic potential per full water saturation) and relative abundance of proteins involved in mitochondrial respiration and ATP biosynthesis.

The effect of cold acclimation, deacclimation and reacclimation on metabolite profiles and freezing tolerance in winter wheat

Global climate change will cause longer and warmer autumns, thus negatively affecting the quality of cold acclimation (CA) and reducing the freezing tolerance (FT) of winter wheat. Insufficient FT and fluctuating temperatures during winter can accelerate the deacclimation (DEA) process, whereas reacclimation (REA) is possible only while the vernalization requirement is unfulfilled. Six winter wheat genotypes with different winter hardiness profiles were used to evaluate the impact of constant low-temperature (2°C) and prolonged higher low-temperature (28 days at 10°C followed by 2°C until day 49) on shoot biomass and metabolite accumulation patterns in leaf and crown tissues throughout 49 days of CA, 7 days of DEA, and 14 days of REA. The FT of winter wheat was determined as LT₃₀ values by conducting freezing tests after CA, DEA, and REA. Shoot biomass accumulation, projected as the green leaf area (GLA), was investigated by non-destructive RGB imaging-based phenotyping. Dynamics of carbohydrates, hexose phosphates, organic acids, proteins, and amino acids were assessed in leaf and crown tissues. Results revealed that exposure to higher low-temperature induced higher accumulation of shoot biomass and had a negative impact on FT of winter wheat. Prolonged higher low-temperature negatively affected the accumulation of soluble carbohydrates, protein content and amino acids, and had a positive effect on starch accumulation in leaf and crown tissues after CA, in comparison with the constant low-temperature treatment. DEA resulted in significantly reduced FT. Lower concentrations of glucose-6-phosphate, sucrose and proline, as well as higher concentrations of starch in leaves and crowns were found after DEA. The majority of the genotypes regained FT after REA; higher concentrations of glucose and malate in leaves, and sucrose in crown tissue were observed, whereas starch accumulation was decreased in both tissues. Negative correlations were determined between FT and starch concentration in leaves and crowns, while proline and proteins, accumulated in crowns, showed positive correlations with FT. This study broadens the knowledge regarding the effect of different low-temperature regimes on the dynamics of metabolite accumulation in winter wheat throughout CA, DEA, and REA, and its relationship to biomass accumulation and FT.

Proteomic analysis reveals the molecular mechanism underlying the cold acclimation and freezing tolerance of wheat (Triticum aestivum L.)

Cold acclimation (CA) is an important evolutionary adaptive mechanism for wheat freezing resistence. To clarify the molecular basis of wheat CA and freezing tolerance, the effects of CA (4 °C) and non-CA (20 °C) treatments and freezing stress (-5 °C) on the proteins in the wheat crown were characterized via an iTRAQ-based proteomic analysis. A total of 669 differentially accumulated proteins (DAPs) were identified after the CA, of which seven were also DAPs in the CA plants exposed to freezing stress. Additionally, the 15 DAPs in the CA group and the 23 DAPs in the non-CA group after the freezing treatment differed substantially. Functional analyses indicated that CA enhanced freezing tolerance by regulating proteins involved in signal transduction, carbohydrate metabolism, stress and defense responses, and phenylpropanoid biosynthesis. An integrated transcriptomic, proteomic, and metabolomic analysis revealed significant changes in various components of the glutathione metabolic pathway. The overexpression and silencing of Wdhn13 in Arabidopsis and wheat resulted in increased tolerance and sensitivity to freezing stress, respectively, suggesting Wdhn13 promotes freezing tolerance. Overall, our study offers insights into the regulatory network underlying the CA and freezing tolerance of wheat, which may be useful for elucidating wheat freezing resistance.

High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines

BACKGROUND

High temperature shock is becoming increasingly common in our climate, affecting plant growth and productivity. The ability of a plant to survive stress is a complex phenomenon. One of the essential tissues for plant performance under various environmental stimuli is the crown. However, the molecular characterization of this region remains poorly investigated. Gibberellins play a fundamental role in whole-plant stature formation. This study identified plant stature modifications and crown-specific transcriptome re-modeling in gibberellin-deficient barley sdw1.a (BW827) and sdw1.d (BW828) mutants exposed to increased temperature.

RESULTS

The deletion around the sdw1 gene in BW827 was found to encompass at least 13 genes with primarily regulatory functions. A bigger genetic polymorphism of BW828 than of BW827 in relation to wild type was revealed. Transcriptome-wide sequencing (RNA-seq) revealed several differentially expressed genes involved in gibberellin metabolism and heat response located outside of introgression regions. It was found that HvGA20ox4, a paralogue of the HvGA20ox2 gene, was upregulated in BW828 relative to other genotypes, which manifested as basal internode elongation. The transcriptome response to elevated temperature differed in the crown of sdw1.a and sdw1.d mutants; it was most contrasting for HvHsf genes upregulated under elevated temperature in BW828, whereas those specific to BW827 were downregulated. In-depth examination of sdw1 mutants revealed also some differences in their phenotypes and physiology.

CONCLUSIONS

We concluded that despite the studied sdw1 mutants being genetically related, their heat response seemed to be genotype-specific and observed differences resulted from genetic background diversity rather than single gene mutation, multiple gene deletion, or allele-specific expression of the HvGA20ox2 gene. Differences in the expressional reaction of genes to heat in different sdw1 mutants, found to be independent of the polymorphism, could be further explained by in-depth studies of the regulatory factors acting in the studied system. Our findings are particularly important in genetic research area since molecular response of crown tissue has been marginally investigated, and can be useful for wide genetic research of crops since barley has become a model plant for them.

Climate change regulated abiotic stress mechanisms in plants: a comprehensive review

Global climate change is identified as a major threat to survival of natural ecosystems. Climate change is a dynamic, multifaceted system of alterations in environmental conditions that affect abiotic and biotic components of the world. It results in alteration in environmental conditions such as heat waves, intensity of rainfall, CO₂ concentration and temperature that lead to rise in new pests, weeds and pathogens. Climate change is one of the major constraints limiting plant growth and development worldwide. It impairs growth, disturbs photosynthesis, and reduces physiological responses in plants. The variations in global climate have gained the attention of researchers worldwide, as these changes negatively affect the agriculture by reducing crop productivity and food security. With this background, this review focuses on the effects of elevated atmospheric CO₂ concentration, temperature, drought and salinity on the morphology, physiology and biochemistry of plants. Furthermore, this paper outlines an overview on the reactive oxygen species (ROS) production and their impact on the biochemical and molecular status of plants with increased climatic variations. Also additionally, different tolerance strategies adopted by plants to combat environmental adversities have been discussed.

Comparative physiological and proteomic analyses of mangrove plant Kandelia obovata under cold stress

Cold events had broadly affected the survival and geographic distribution of mangrove plants. Kandelia obovata, has an excellent cold tolerance as a true halophyte and widespread mangrove species. In this study, physiological characters and comparative proteomics of leaves of K. obovata were performed under cold treatment. The physiological analysis showed that K. obovata could alleviate its cold-stress injuries through increasing the levels of antioxidants, the activities of related enzymes, as well as osmotic regulation substances (proline). It was detected 184 differentially expressed protein spots, and of 129 (70.11%) spots were identified. These proteins have been involved in several pathways such as the stress and defense, photosynthesis and photorespiration, signal transduction, transcription factors, protein biosynthesis and degradation, molecular chaperones, ATP synthesis, the tricarboxylic acid (TCA) cycle and primary metabolisms. The protein post-translational modification may be a common phenomenon and plays a key role in cold-response process in K. obovata. According to our precious work, a schematic diagram was drawn for the resistance or adaptation strategy of mangrove plants under cold stress. This study provided valuable information to understand the mechanism of cold tolerance of K. obovata.

Proteome analysis reveals a systematic response of cold-acclimated seedlings of an exotic mangrove plant Sonneratia apetala to chilling stress

Low temperature in winter was the most crucial abiotic stress that limits the mangrove afforestation northward. Previous study demonstrated that Sonneratia apetala initially transplanted to high latitude area exhibited a stronger plasticity of cold tolerance. To clarify the underlying mechanism, the physiological and proteomic responses to chilling stress were investigated in S. apetala leaves. Our results found that cold-acclimated seedlings had lower relative electrolyte leakage and MDA content than non-acclimated seedlings. On the contrary, higher chlorophyll content and photosynthetic capacity were observed in cold-acclimated seedlings. With proteomic analyses, the differentially accumulated proteins (DAPs) involved in ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding were suggested to play important roles in enhancing the cold tolerance of S. apetala. However, the down-regulation DAPs were suggested as a tradeoff between plant growth and chilling response. By the protein-protein interaction analyses, translation elongation factor G, chlorophyll A-B binding protein and ascorbate peroxidase 1 were suggested as the important regulators in cold-acclimated S. apetala seedlings under chilling stress. Based on the above results, a schematic diagram describing the mechanism of cold tolerance of exotic mangrove species S. apetala that was achieved by cold acclimation was presented in this study. SIGNIFICANCE: The major environmental factor limits the mangrove afforestation northward is the low temperature in winter. Previous study reported that Sonneratia apetala grew in high latitude exhibited a higher cold tolerance than that in low latitude, which was suggested as a result of cold acclimation. To further understand "how cold acclimation enhance the cold tolerance in S. apetala", the response of S. apetala subjected to chilling stress with or without cold acclimation was investigated in this study at the physiological and proteomic aspects. Our physiological results showed that S. apetala seedlings treated with cold acclimation exhibited a higher tolerance under chilling stress than that without cold acclimation. By using the comparative proteomic approaches and bioinformatic analyses, various biological processes were suggested to play an important role in enhancing the cold tolerance of S. apetala under chilling stress, such as ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding. Among these differentially accumulated proteins, translation elongation factor G (eEF-G), chlorophyll A-B binding protein (CAB) and ascorbate peroxidase 1 (APX1) were identified as the hub proteins function in coordinated regulating ROS scavenging, photosynthesis and protein biosynthesis in chloroplast and subsequently enhanced the cold tolerance of S. apetala under chilling stress. Our results provided a further understanding of cold acclimation in improving the cold tolerance in exotic mangrove species S. apetala.

Comprehensive Proteome and Lysine Acetylome Analysis Reveals the Widespread Involvement of Acetylation in Cold Resistance of Pepper (Capsicum annuum L.)

Pepper is a typical warmth-loving vegetable that lacks a cold acclimation mechanism and is sensitive to cold stress. Lysine acetylation plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in the resistance of pepper plants to cold stress. In this study, the proteome and acetylome of two pepper varieties with different levels of cold resistance were investigated by subjecting them to cold treatments of varying durations followed by recovery periods. In total, 6,213 proteins and 4,574 lysine acetylation sites were identified, and this resulted in the discovery of 3,008 differentially expressed proteins and 768 differentially expressed acetylated proteins. A total of 1,988 proteins were identified in both the proteome and acetylome, and the functional differences in these co-identified proteins were elucidated through GO enrichment. KEGG analysis showed that 397 identified acetylated proteins were involved in 93 different metabolic pathways. The dynamic changes in the acetylated proteins in photosynthesis and the "carbon fixation in the photosynthetic organisms" pathway in pepper under low-temperature stress were further analyzed. It was found that acetylation of the PsbO and PsbR proteins in photosystem II and the PsaN protein in photosystem I could regulate the response of pepper leaves to cold stress. The acetylation levels of key carbon assimilation enzymes, such as ribulose bisphosphate carboxylase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, glyceraldehyde 3-phosphate dehydrogenase, phosphoribulokinase, and triosephosphate isomerase decreased, leading to decreases in carbon assimilation capacity and photosynthetic efficiency, reducing the cold tolerance of pepper leaves. This study is the first to identify the acetylome in pepper, and it greatly expands the catalog of lysine acetylation substrates and sites in Solanaceae crops, providing new insights for posttranslational modification studies.

Protein kinase and phosphatase control of plant temperature responses

Plants must cope with ever-changing temperature conditions in their environment. Suboptimal high and low temperatures, and stressful extreme temperatures, induce adaptive mechanisms that allow optimal performance and survival, respectively. These processes have been extensively studied at the physiological, transcriptional and (epi)genetic level. Cellular temperature signalling cascades and tolerance mechanisms also involve post-translational modifications (PTMs), particularly protein phosphorylation. Many protein kinases are known to be involved in cold acclimation and heat stress responsiveness but research on the role and importance of kinases and phosphatases in triggering responses to mild changes in temperature such as thermomorphogenesis is inadequately understood. In this review, we summarize the current knowledge on the roles of kinases and phosphatases in plant temperature responses. We discuss how kinases can function over a range of temperatures in different signalling pathways and provide an outlook to the application of PTM-modifying factors for the development of thermotolerant crops.

Tissue-level transcriptomic responses to local and distal chilling reveal potential chilling survival mechanisms in maize

Chilling is a major stress to plants of subtropical and tropical origins including maize (Zea mays L.). To reveal molecular mechanisms underlying chilling tolerance and survival, we investigated transcriptomic responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity in maize. Chilling stress on shoots and roots is found to each contributes to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacities reveals that chilling survival is highly associated with upregulation of abscisic acid biosynthesis and response as well as transcriptional regulators in leaves and crowns. It is also associated with the downregulation of translation in leaves and heat response in crowns. Chilling treatment on whole or part of the plants reveals that response to distal-chilling is very distinct from, and sometimes opposite to, response to local- or whole-plant chilling in both leaves and roots, suggesting a communication between shoots and roots in environmental response. This study thus provides transcriptomic responses in leaves, roots and crowns under differential chilling stresses in maize and reveals potential chilling tolerance and survival mechanisms which lays ground for improving chilling tolerance in crop plants.

The Resistance of Oilseed Rape Microspore-Derived Embryos to Osmotic Stress Is Associated With the Accumulation of Energy Metabolism Proteins, Redox Homeostasis, Higher Abscisic Acid, and Cytokinin Contents

The present study aims to investigate the response of rapeseed microspore-derived embryos (MDE) to osmotic stress at the proteome level. The PEG-induced osmotic stress was studied in the cotyledonary stage of MDE of two genotypes: Cadeli (D) and Viking (V), previously reported to exhibit contrasting leaf proteome responses under drought. Two-dimensional difference gel electrophoresis (2D-DIGE) revealed 156 representative protein spots that have been selected for MALDI-TOF/TOF analysis. Sixty-three proteins have been successfully identified and divided into eight functional groups. Data are available via ProteomeXchange with identifier PXD024552. Eight selected protein accumulation trends were compared with real-time quantitative PCR (RT-qPCR). Biomass accumulation in treated D was significantly higher (3-fold) than in V, which indicates D is resistant to osmotic stress. Cultivar D displayed resistance strategy by the accumulation of proteins in energy metabolism, redox homeostasis, protein destination, and signaling functional groups, high ABA, and active cytokinins (CKs) contents. In contrast, the V protein profile displayed high requirements of energy and nutrients with a significant number of stress-related proteins and cell structure changes accompanied by quick downregulation of active CKs, as well as salicylic and jasmonic acids. Genes that were suitable for gene-targeting showed significantly higher expression in treated samples and were identified as phospholipase D alpha, peroxiredoxin antioxidant, and lactoylglutathione lyase. The MDE proteome profile has been compared with the leaf proteome evaluated in our previous study. Different mechanisms to cope with osmotic stress were revealed between the genotypes studied. This proteomic study is the first step to validate MDE as a suitable model for follow-up research on the characterization of new crossings and can be used for preselection of resistant genotypes.

Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.

Abscisic Acid-Enemy or Savior in the Response of Cereals to Abiotic and Biotic Stresses?

Abscisic acid (ABA) is well-known phytohormone involved in the control of plant natural developmental processes, as well as the stress response. Although in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) its role in mechanism of the tolerance to most common abiotic stresses, such as drought, salinity, or extreme temperatures seems to be fairly well recognized, not many authors considered that changes in ABA content may also influence the sensitivity of cereals to adverse environmental factors, e.g., by accelerating senescence, lowering pollen fertility, and inducing seed dormancy. Moreover, recently, ABA has also been regarded as an element of the biotic stress response; however, its role is still highly unclear. Many studies connect the susceptibility to various diseases with increased concentration of this phytohormone. Therefore, in contrast to the original assumptions, the role of ABA in response to biotic and abiotic stress does not always have to be associated with survival mechanisms; on the contrary, in some cases, abscisic acid can be one of the factors that increases the susceptibility of plants to adverse biotic and abiotic environmental factors.

Physiological and Anatomical Mechanisms in Wheat to Cope with Salt Stress Induced by Seawater

Two pot experiments were conducted in a greenhouse to examine ¹⁴C fixation and its distribution in biochemical leaf components, as well as the physiological and anatomical adaptability responses of wheat (Triticum aestivum L.) grown with seawater diluted to 0.2, 3.0, 6.0, and 12.0 dS m^-1. The results showed significant reductions in chlorophyll content, ¹⁴C fixation (photosynthesis), plant height, main stem diameter, total leaf area per plant, and total dry weight at 3.0, 6.0, and 12.0 dS m^-1 seawater salt stress. The ¹⁴C loss was very high at 12.0 ds m^-1 after 120 h. ¹⁴C in lipids (ether extract) showed significant changes at 12.0 dS m^-1 at 96 and 120 h. The findings indicated the leaf and stem anatomical feature change of wheat plants resulting from adaptation to salinity stress. A reduction in the anatomical traits of stem and leaf diameter, wall thickness, diameter of the hollow pith cavity, total number of vascular bundles, number of large and small vascular bundles, bundle length and width, thickness of phloem tissue, and diameter of the metaxylem vessel of wheat plants was found. In conclusion, salt stress induces both anatomical and physiological changes in the stem and leaf cells of wheat, as well as the tissues and organs, and these changes in turn make it possible for the plants to adapt successfully to a saline environment.

Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley

Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.

Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses

Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.

Impact assessment of major abiotic stresses on the proteome profiling of some important crop plants: a current update

Abiotic stresses adversely affect the plant's growth and development leading to loss of crop plants and plant products in terms of both the quality and quantity. Two main strategies are adopted by plants to acclimatize to stresses; avoidance and tolerance. These adaptive strategies of plants at the cellular and metabolic level enable them to withstand such detrimental conditions. Acclimatization is associated with intensive changes in the proteome of plants and these changes are directly involved in plants response to stress. Proteome studies can be used to screen for these proteins and their involvement in plants response to various abiotic stresses evaluated. In this review, proteomic studies of different plants species under different abiotic stresses, particularly drought, salinity, heat, cold, and waterlogging, are discussed. From different proteomic studies, the stress response can be determined by an interaction between proteomic and physiological changes which occur in plants during such stress conditions. These identified proteins from different processes under different abiotic stress conditions definitely add to our understanding for exploiting them in various biotechnological applications in crop improvement.

Apoplast proteomic analysis reveals drought stress-responsive protein datasets in chilli (Capsicum annuum L.)

Drought is one of the major environmental constrains that limit plant performance worldwide. Plant apoplast which acts as connecting link between environment and plant protoplast carries multiple functions in plant metabolism and signalling. To investigate the drought induced changes in apoplast, proteome analysis in conjunction with antioxidant enzyme activity changes were studied in chilli (Capsicum annuum L). Drought induced apoplast proteome revealed augmented phenyl alanine ammonia lyase, peroxidase activities and reduced catalase activity. LC-MS analysis of apoplast proteome revealed differential expression of proteins under water stress conditions. Up-regulation of 43 protein species which encompass stress related proteins such as defensins, peroxidises, polygalaturonase inhibitor proteins, superoxide dismutase proteins were observed. Unlike control, twenty unique protein species were identified to be present in proteome of drought treated plants. Qualitative and quantitative changes in apoplast proteome emphasize the dynamics of plant apoplast and its role in drought stress. This work would provide insights into drought induced proteomic changes in apoplast and also would prove to be useful for protein phenotyping.

iTRAQ-Based Quantitative Proteome Revealed Metabolic Changes in Winter Turnip Rape (Brassica rapa L.) under Cold Stress

Winter turnip rape (Brassica rapa L.) is a large-scale winter-only oil crop cultivated in Northwest China. However, its cold-resistant molecular mechanism remains inadequate. Studying the cold adaptation mechanisms of winter turnip rape based on the proteomic technique of isobaric tags for relative and absolute quantification (iTRAQ) offers a solution to this problem. Under cold stress (−4 °C for eight hours), 51 and 94 differently accumulated proteins (DAPs) in Longyou 7 (cold-tolerant) and Tianyou 4 (cold-sensitive) were identified, respectively. These DAPs were classified into 38 gene ontology (GO) term categories, such as metabolic process, cellular process, catalytic activity, and binding. The 142 DAPs identified between the two cold-stressed cultivars were classified into 40 GO terms, including cellular process, metabolic process, cell, catalytic activity, and binding. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DAPs participated in 10 pathways. The abundance of most protein functions in ribosomes, carbon metabolism, photosynthesis, and energy metabolism including the citrate cycle, pentose phosphate pathway, and glyoxylate and dicarboxylate metabolism decreased, and the proteins that participate in photosynthesis–antenna and isoflavonoid biosynthesis increased in cold-stressed Longyou 7 compared with those in cold-stressed Tianyou 4. The expression pattern of genes encoding the 10 significant DAPs was consistent with the iTRAQ data. This study provides new information on the proteomic differences between the leaves of Longyou 7 and Tianyou 4 plants and explains the possible molecular mechanisms of cold-stress adaptation in B. rapa.

Insight into cellular proteome of Lolium multiflorum/Festuca arundinacea introgression forms to decipher crucial mechanisms of cold acclimation in forage grasses

Frost tolerance is the main component of winter-hardiness. To express this trait, plants sense low temperature, and respond by activating the process of cold acclimation. The molecular mechanisms of this acclimation have not been fully understood in the agronomically important group of forage grasses, including Lolium-Festuca species. Herein, the introgression forms of L. multiflorum/F. arundinacea distinct with respect to their frost tolerance, were used as models for the comprehensive, proteomic and physiological, research to recognize the crucial components of cold acclimation in forage grasses. The obtained results stressed the importance of photosynthetic performance under acclimation to low temperature. The stable level of photochemical processes after three weeks of cold acclimation in the introgression form with a higher level of frost tolerance, combined simultaneously with only slightly (but not significantly) decreased level of CO₂ assimilation after that period, despite significantly lower stomatal conductance, indicated the capacity for that form to acclimate its photosynthesis to low temperature. This phenomenon was driven by the Calvin cycle efficiency, associated with revealed here accumulation profiles and activities of chloroplastic aldolase. The capacity to acclimate the photosynthetic machinery to cold could be one of the most crucial components of forage grass metabolism to improve frost tolerance.

Abiotic Stress Signaling in Wheat - An Inclusive Overview of Hormonal Interactions During Abiotic Stress Responses in Wheat

Rapid global warming directly impacts agricultural productivity and poses a major challenge to the present-day agriculture. Recent climate change models predict severe losses in crop production worldwide due to the changing environment, and in wheat, this can be as large as 42 Mt/°C rise in temperature. Although wheat occupies the largest total harvested area (38.8%) among the cereals including rice and maize, its total productivity remains the lowest. The major production losses in wheat are caused more by abiotic stresses such as drought, salinity, and high temperature than by biotic insults. Thus, understanding the effects of these stresses becomes indispensable for wheat improvement programs which have depended mainly on the genetic variations present in the wheat genome through conventional breeding. Notably, recent biotechnological breakthroughs in the understanding of gene functions and access to whole genome sequences have opened new avenues for crop improvement. Despite the availability of such resources in wheat, progress is still limited to the understanding of the stress signaling mechanisms using model plants such as Arabidopsis, rice and Brachypodium and not directly using wheat as the model organism. This review presents an inclusive overview of the phenotypic and physiological changes in wheat due to various abiotic stresses followed by the current state of knowledge on the identified mechanisms of perception and signal transduction in wheat. Specifically, this review provides an in-depth analysis of different hormonal interactions and signaling observed during abiotic stress signaling in wheat.

Purine salvage in plants

Purine bases and nucleosides are produced by turnover of nucleotides and nucleic acids as well as from some cellular metabolic pathways. Adenosine released from the S-adenosyl-L-methionine cycle is linked to many methyltransferase reactions, such as the biosynthesis of caffeine and glycine betaine. Adenine is produced by the methionine cycles, which is related to other biosynthesis pathways, such those for the production of ethylene, nicotianamine and polyamines. These purine compounds are recycled for nucleotide biosynthesis by so-called "salvage pathways". However, the salvage pathways are not merely supplementary routes for nucleotide biosynthesis, but have essential functions in many plant processes. In plants, the major salvage enzymes are adenine phosphoribosyltransferase (EC 2.4.2.7) and adenosine kinase (EC 2.7.1.20). AMP produced by these enzymes is converted to ATP and utilised as an energy source as well as for nucleic acid synthesis. Hypoxanthine, guanine, inosine and guanosine are salvaged to IMP and GMP by hypoxanthine/guanine phosphoribosyltransferase (EC 2.4.2.8) and inosine/guanosine kinase (EC 2.7.1.73). In contrast to de novo purine nucleotide biosynthesis, synthesis by the salvage pathways is extremely favourable, energetically, for cells. In addition, operation of the salvage pathway reduces the intracellular levels of purine bases and nucleosides which inhibit other metabolic reactions. The purine salvage enzymes also catalyse the respective formation of cytokinin ribotides, from cytokinin bases, and cytokinin ribosides. Since cytokinin bases are the active form of cytokinin hormones, these enzymes act to maintain homeostasis of cellular cytokinin bioactivity. This article summarises current knowledge of purine salvage pathways and their possible function in plants and purine salvage activities associated with various physiological phenomena are reviewed.

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.

Hydrogen Peroxide and Abscisic Acid Mediate Salicylic Acid-Induced Freezing Tolerance in Wheat

Salicylic acid (SA) can induce plant resistance to biotic and abiotic stresses through cross talk with other signaling molecules, whereas the interaction between hydrogen peroxide (H₂O₂) and abscisic acid (ABA) in response to SA signal is far from clear. Here, we focused on the roles and interactions of H₂O₂ and ABA in SA-induced freezing tolerance in wheat plants. Exogenous SA pretreatment significantly induced freezing tolerance of wheat via maintaining relatively higher dark-adapted maximum photosystem II quantum yield, electron transport rates, less cell membrane damage. Exogenous SA induced the accumulation of endogenous H₂O₂ and ABA. Endogenous H₂O₂ accumulation in the apoplast was triggered by both cell wall peroxidase and membrane-linked NADPH oxidase. The pharmacological study indicated that pretreatment with dimethylthiourea (H₂O₂ scavenger) completely abolished SA-induced freezing tolerance and ABA synthesis, while pretreatment with fluridone (ABA biosynthesis inhibitor) reduced H₂O₂ accumulation by inhibiting NADPH oxidase encoding genes expression and partially counteracted SA-induced freezing tolerance. These findings demonstrate that endogenous H₂O₂ and ABA signaling may form a positive feedback loop to mediate SA-induced freezing tolerance in wheat.

Unraveling physiological, biochemical and molecular mechanisms involved in olive (Olea europaea L. cv. Chétoui) tolerance to drought and salt stresses

Olive (Olea europaea L.) is an economically important crop for the Mediterranean basin, where prolonged drought and soil salinization may occur. This plant has developed a series of mechanisms to tolerate and grow under these adverse conditions. By using an integrated approach, we described in Chétoui olive cultivar the changes in plant growth, oxidative damage and osmolyte accumulation in leaves, in combination with corresponding changes in physiological parameters and proteome. Our results showed, under both stress conditions, a greater growth reduction of the aboveground plant organs than of the underground counterparts. This was associated with a reduction of all photosynthetic parameters, the integrity of photosystem II and leaf nitrogen content, and corresponding representation of photosynthetic apparatus proteins, Calvin-Benson cycle and nitrogen metabolism. The most significant changes were observed under the salinity stress condition. Oxidative stress was also observed, in particular, lipid peroxidation, which could be tentatively balanced by a concomitant photoprotective/antioxidative increase of carotenoid levels. At the same time, various compensative mechanisms to cope with nitrogen source demands and to control plant cell osmolarity were also shown by olive plants under these stresses. Taken together, these findings suggest that the Chétoui variety is moderately sensitive to both drought and salt stress, although it has greater ability to tolerate water depletion.

Hydrogen Peroxide and Abscisic Acid Mediate Salicylic Acid-Induced Freezing Tolerance in Wheat

Salicylic acid (SA) can induce plant resistance to biotic and abiotic stresses through cross talk with other signaling molecules, whereas the interaction between hydrogen peroxide (H₂O₂) and abscisic acid (ABA) in response to SA signal is far from clear. Here, we focused on the roles and interactions of H₂O₂ and ABA in SA-induced freezing tolerance in wheat plants. Exogenous SA pretreatment significantly induced freezing tolerance of wheat via maintaining relatively higher dark-adapted maximum photosystem II quantum yield, electron transport rates, less cell membrane damage. Exogenous SA induced the accumulation of endogenous H₂O₂ and ABA. Endogenous H₂O₂ accumulation in the apoplast was triggered by both cell wall peroxidase and membrane-linked NADPH oxidase. The pharmacological study indicated that pretreatment with dimethylthiourea (H₂O₂ scavenger) completely abolished SA-induced freezing tolerance and ABA synthesis, while pretreatment with fluridone (ABA biosynthesis inhibitor) reduced H₂O₂ accumulation by inhibiting NADPH oxidase encoding genes expression and partially counteracted SA-induced freezing tolerance. These findings demonstrate that endogenous H₂O₂ and ABA signaling may form a positive feedback loop to mediate SA-induced freezing tolerance in wheat.

Comparative proteomic analysis provides novel insights into chlorophyll biosynthesis in celery under temperature stress

Chlorophyll (Chl) is essential for light harvesting and energy transduction in photosynthesis. A proper amount of Chl within plant cells is important to celery (Apium graveolens) yield and quality. Temperature stress is an influential abiotic stress affecting Chl biosynthesis and plant growth. There are limited proteomic studies regarding Chl accumulation under temperature stress in celery leaves. Here, the proteins from celery leaves under different temperature treatments (4, 25 and 38°C) were analyzed using a proteomic approach. There were 71 proteins identified through MALDI-TOF-TOF analysis. The relative abundance of proteins involved in carbohydrate and energy metabolism, protein metabolism, amino acid metabolism, antioxidant and polyamine biosynthesis were enhanced under cold stress. These temperature stress-responsive proteins may establish a new homeostasis to enhance temperature tolerance. Magnesium chelatase (Mg-chelatase) and glutamate-1-semialdehyde aminotransferase (GSAT), related to Chl biosynthesis, showed increased abundances under cold stress. Meanwhile, the Chl contents were decreased in heat- and cold-stressed celery leaves. The inhibition of Chl biosynthesis may be due to the downregulated mRNA levels of 15 genes involved in Chl biosynthesis. The study will expand our knowledge on Chl biosynthesis and the temperature tolerance mechanisms in celery leaves.

Effect of the Winter Wheat Cheyenne 5A Substituted Chromosome on Dynamics of Abscisic Acid and Cytokinins in Freezing-Sensitive Chinese Spring Genetic Background

The effect of short- and long-term cold treatment on the abscisic acid (ABA) and cytokinin (CK) metabolism, and their main biosynthesis- and signaling-related genes were investigated in freezing-sensitive and freezing-tolerant wheat genotypes. Varieties Cheyenne and Chinese Spring substituted with the 5A Cheyenne chromosome, which represented freezing-tolerant genotypes, were compared with the freezing-sensitive Chinese Spring. Hormone levels and gene expression data indicated that the short- and long-term cold treatments are associated with specific regulation of the accumulation of cold-protective proteins and phytohormone levels, as well as the expression profiles of the hormone-related genes. The significant differences were observed between the genotypes, and between their leaf and crown tissues, too. The level of dehydrins, including WCS120 protein, and expression of WCS120 gene were considerably higher in the freezing-tolerant genotypes after 21 days of cold treatment. Expression of Cor14b and CBF14, cold-responsive regulator genes, was increased by cold treatment in all genotypes, to higher extent in freezing-tolerant genotypes. Cluster analysis revealed that the tolerant genotypes had a similar response to cold treatment, regarding expression of the ABA and CK metabolic genes, as well as hormone levels in leaves. As far as hormone levels in crowns are concerned, however, the strongly freezing-tolerant Cheyenne variety clustered separately from the Chinese Spring and the substitution line, which were more similar to each other after both 1 and 21 days of cold treatment than to Cheyenne. Based on these results we concluded that the 5A chromosome of wheat might have both a direct and an indirect impact on the phytohormone-dependent cold-induced freezing tolerance. Based on the gene expression data, novel genetic markers could be developed, which may be used to determine the freezing tolerance level in a wide range of wheat varieties.

The effect of Fusarium culmorum infection and deoxynivalenol (DON) application on proteome response in barley cultivars Chevron and Pedant

Fusarium head blight (FHB) disease adversely affects grain quality and final yield in small-grain cereals including barley. In the present study, the effect of an artificial infection with Fusarium culmorum and an application of deoxynivalenol (DON) on barley spikes of cultivars Chevron and Pedant during flowering was investigated at grain mid-dough stage (BBCH 73) 10days after pathogen inoculation (10 dai). Proteomic analysis using a two-dimensional differential gel electrophoresis (2D-DIGE) technique coupled with LC-MS/MS investigated 98 protein spots revealing quantitative or qualitative differences between the experimental variants. Protein functional annotation of 93 identified protein spots revealed that most affected functional groups represent storage proteins (globulins, hordeins), followed by proteins involved in carbohydrate metabolism (α-amylase inhibitor, β-amylase, glycolytic enzymes), amino acid metabolism (aminotransferases), defence response (chitinase, xylanase inhibitor, serpins, SGT1, universal stress protein USP), protein folding (chaperones, chaperonins), redox metabolism (ascorbate-glutathione cycle), and proteasome-dependent protein degradation. The obtained results indicate adverse effects of infection on plant proteome as well as an active plant response to pathogen as shown by enhanced levels of several inhibitors of pathogen-produced degradation enzymes (α-amylase inhibitor, xylanase inhibitor, serpins), chaperones, and other stress-related proteins (SGT1, USP). Genotypic differences were found in hordein abundance between Chevron and Pedant.

Comparative Proteomic Analysis of Paulownia fortunei Response to Phytoplasma Infection with Dimethyl Sulfate Treatment

Paulownia fortunei is a widely cultivated economic forest tree species that is susceptible to infection with phytoplasma, resulting in Paulownia witches' broom (PaWB) disease. Diseased P. fortunei is characterized by stunted growth, witches' broom, shortened internodes, and etiolated and smaller leaves. To understand the molecular mechanism of its pathogenesis, we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography coupled with tandem mass spectrometry approaches to study changes in the proteomes of healthy P. fortunei, PaWB-infected P. fortunei, and PaWB-infected P. fortunei treated with 15 mg·L⁻¹ or 75 mg·L⁻¹ dimethyl sulfate. We identified 2969 proteins and 104 and 32 differentially abundant proteins that were phytoplasma infection responsive and dimethyl sulfate responsive, respectively. Based on our analysis of the different proteomes, 27 PaWB-related proteins were identified. The protein-protein interactions of these 27 proteins were analyzed and classified into four groups (photosynthesis-related, energy-related, ribosome-related, and individual proteins). These PaWB-related proteins may help in developing a deeper understanding of how PaWB affects the morphological characteristics of P. fortunei and further establish the mechanisms involved in the response of P. fortunei to phytoplasma.

Changes in protein abundance and activity involved in freezing tolerance acquisition in winter barley (Hordeum vulgare L.)

The changes in protein abundance induced by cold hardening were analysed by 2 DE in ten doubled haploid (DH) lines of winter barley, highly differentiated with respect to freezing tolerance level. Among 45 differential proteins identified by MALDI-TOF/TOF, the majority was classified as related to photosynthesis, carbohydrate metabolism, oxidation-reduction reactions and stress response. Among the detected proteins, higher abundance of RuBisCO large and small subunits, RuBisCO activase, two Oxygen-evolving enhancer proteins, Ferredoxin-NADP reductase, Cytochrome P450-dependent fatty acid hydroxylase and 14-3-3 protein was associated with higher freezing tolerance level. Lower relative level of hypothetical ATP synthase beta subunit, uncharacterized mitochondrial protein AtMg00810 and ribosomal RNA small subunit methyltransferase G also seems to be important. The results of proteomic studies were complemented by the evaluation of photosynthetic apparatus acclimation, showing distinctive differences between the studied genotypes in the number of active PSII reaction centres (RC/CS_m). Additionally, the analysis of antioxidative enzyme activities suggests the importance of H₂O₂ as a signalling molecule possibly involved in the initiation of cold-induced plant acclimation. However, in DH lines with high freezing tolerance, H₂O₂ generation during cold hardening treatment was accompanied by more stable activity of catalase, H₂O₂-decomposing enzyme.

SIGNIFICANCE

In the study, the changes in protein abundance induced by cold hardening treatment were analysed by two-dimensional gel electrophoresis in ten doubled haploid (DH) lines of winter barley. Harnessing DH technology resulted in distinctive widening of genetic variation with respect to freezing tolerance level. Both the cold-hardening effect on the protein pattern in an individual winter barley DH line as well as the variation among the selected DH lines were investigated, which resulted in the identification of 45 differentiated proteins classified as involved in 14 metabolic pathways and cellular processes. Among them, eight proteins: (1) the precursor of RuBisCO large subunit, (2) RuBisCO small subunit (partial), (3) RuBisCO activase small isoform, (4) the precursor of Oxygen-evolving enhancer protein 1-like (predicted protein), (5) Oxygen-evolving enhancer protein 2, (6) the leaf isozyme of Ferredoxin-NADP reductase, (7) hypothetical protein M569_12509 Cytochrome P450-dependent fatty acid hydroxylase-like and (8) hypothetical protein BRADI_1g11290 (14-3-3 protein A-like) were accumulated to a higher level in leaves of cold-hardened seedlings of freezing tolerant winter barley DH lines in comparison with susceptible ones. Three others: (9) hypothetical protein BRADI_5g05668 F1 ATP synthase beta subunit-like, (10) predicted protein uncharacterized mitochondrial protein AtMg00810-like and (11) BnaA02g08010D Ribosomal RNA small subunit methyltransferase G-like were detected at lower level in freezing tolerant seedlings in comparison with susceptible genotypes. The last two were for the first time linked to cold acclimation. The results of complementary analyses indicate that PSII activity and stability of antioxidative enzymes under low temperature are also very important for freezing tolerance acquisition.

iTRAQ and virus-induced gene silencing revealed three proteins involved in cold response in bread wheat

By comparing the differentially accumulated proteins from the derivatives (UC 1110 × PI 610750) in the F₁₀ recombinant inbred line population which differed in cold-tolerance, altogether 223 proteins with significantly altered abundance were identified. The comparison of 10 cold-sensitive descendant lines with 10 cold-tolerant descendant lines identified 140 proteins that showed decreased protein abundance, such as the components of the photosynthesis apparatus and cell-wall metabolism. The identified proteins were classified into the following main groups: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, sulfur metabolism, nitrogen metabolism, RNA metabolism, energy production, cell-wall metabolism, membrane and transportation, and signal transduction. Results of quantitative real-time PCR of 20 differentially accumulated proteins indicated that the transcriptional expression patterns of 10 genes were consistent with their protein expression models. Virus-induced gene silencing of Hsp90, BBI, and REP14 genes indicated that virus-silenced plants subjected to cold stress had more severe drooping and wilting, an increased rate of relative electrolyte leakage, and reduced relative water content compared to viral control plants. Furthermore, ultrastructural changes of virus-silenced plants were destroyed more severely than those of viral control plants. These results indicate that Hsp90, BBI, and REP14 potentially play vital roles in conferring cold tolerance in bread wheat.

Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)

BACKGROUND

Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Lentil is a cool season grain legume that is challenged by winter frost in some areas of its cultivation.

RESULTS

To better understand the genetic base of frost tolerance differential gene expression in response to cold acclimation was investigated. Recombinant inbred lines (RILs) from the cross Precoz x WA8649041 were first classified as cold tolerant or cold susceptible according to their response to temperatures between -3 to -15 °C. Then, RILs from both extremes of the response curve were cold acclimated and the leaf transcriptomes of two bulks each of eight frost tolerant and seven cold susceptible RILs were investigated by Deep Super-SAGE transcriptome profiling. Thus, four RNA bulks were analysed: the acclimated susceptible, the acclimated tolerant and the respective controls (non-acclimated susceptible and non-acclimated tolerant). Approximately 16.5 million 26 nucleotide long Super-SAGE tags were sequenced in the four sets (between ~3 and 5.4 millions). In total, 133,077 different unitags, each representing a particular transcript isoform, were identified in these four sets. Tags which showed a significantly different abundance in any of the bulks (fold change ≥4.0 and a significant p-value <0.001) were selected and used to identify the corresponding lentil gene sequence. Three hundred of such lentil sequences were identified. Most of their known homologs coded for glycine-rich, cold and drought-regulated proteins, dormancy-associated proteins, proline-rich proteins (PRPs) and other membrane proteins. These were generally but not exclusively over-expressed in the acclimated tolerant lines.

CONCLUSIONS

This set of candidate genes implicated in the response to frost in lentil represents an useful base for deeper and more detailed investigations into this important agronomic trait in future.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.

Nitric Oxide and Hydrogen Peroxide Mediate Wounding-Induced Freezing Tolerance through Modifications in Photosystem and Antioxidant System in Wheat

Mechanical wounding is a common stress caused by herbivores or manual and natural manipulations, whereas its roles in acclimation response to a wide spectrum of abiotic stresses remain unclear. The present work showed that local mechanical wounding enhanced freezing tolerance in untreated systemic leaves of wheat plants (Triticum aestivum L.), and meanwhile the signal molecules hydrogen peroxide (H₂O₂) and nitric oxide (NO) were accumulated systemically. Pharmacological study showed that wounding-induced NO synthesis was substantially arrested by pretreatment with scavengers of reactive oxygen species and an inhibitor of NADPH oxidase (respiratory burst oxidase homolog, RBOH). On the contrary, wounding-induced H₂O₂ accumulation was not sensitive to NO synthetic inhibitors or scavenger, indicating that H₂O₂ acts upstream of NO in wounding signal transduction pathways. Cytochemical and vascular tissues localizations approved that RBOH-dependent H₂O₂ acts as long-distance signal in wounding response. Transcriptome analysis revealed that 279 genes were up-regulated in plants treated with wounding and freezing, but not in plants treated with freezing alone. Importantly, freezing- and wounding-induced genes were significantly enriched in the categories of "photosynthesis" and "signaling." These results strongly supported that primary mechanical wounding can induce freezing tolerance in wheat through the systemic accumulation of NO and H₂O₂, and further modifications in photosystem and antioxidant system.

Proteomic and physiological approach reveals drought-induced changes in rapeseeds: Water-saver and water-spender strategy

The cultivar-dependent differences in Brassica napus L. seed yield are significantly affected by drought stress. Here, the response of leaf proteome to long-term drought (28days) was studied in cultivars (cvs): Californium (C), Cadeli (D), Navajo (N), and Viking (V). Analysis of twenty-four 2-D DIGE gels revealed 134 spots quantitatively changed at least 2-fold; from these, 79 proteins were significantly identified by MALDI-TOF/TOF. According to the differences in water use, the cultivars may be assigned to two categories: water-savers or water-spenders. In the water-savers group (cvs C+D), proteins related to nitrogen assimilation, ATP and redox homeostasis were increased under stress, while in the water-spenders category (cvs N+V), carbohydrate/energy, photosynthesis, stress related and rRNA processing proteins were increased upon stress. Taking all data together, we indicated cv C as a drought-adaptable water-saver, cv D as a medium-adaptable water-saver, cv N as a drought-adaptable water-spender, and cv V as a low-adaptable drought sensitive water-spender rapeseed. Proteomic data help to evaluate the impact of drought and the extent of genotype-based adaptability and contribute to the understanding of their plasticity. These results provide new insights into the provenience-based drought acclimation/adaptation strategy of contrasting winter rapeseeds and link data at gasometric, biochemical, and proteome level.

SIGNIFICANCE

Soil moisture deficit is a real problem for every crop. The data in this study demonstrates for the first time that in stem-prolongation phase cultivars respond to progressive drought in different ways and at different levels. Analysis of physiological and proteomic data showed two different water regime-related strategies: water-savers and spenders. However, not only water uptake rate itself, but also individual protein abundances, gasometric and biochemical parameters together with final biomass accumulation after stress explained genotype-based responses. Interestingly, under a mixed climate profile, both water-use patterns (savers or spenders) can be appropriate for drought adaptation. These data suggest, than complete "acclimation image" of rapeseeds in stem-prolongation phase under drought could be reached only if these characteristics are taken, explained and understood together.

Label-free quantitative proteomic analysis of tolerance to drought in Pisum sativum

Abiotic stresses caused by adverse environmental conditions are responsible for heavy economic losses on pea crop, being drought one of the most important abiotic constraints. Development of pea cultivars well adapted to dry conditions has been one of the major tasks in breeding programs. The increasing food requirements drive the necessity to broaden the molecular basis of tolerance to drought to develop pea cultivars well adapted to dry conditions. We have used a shotgun proteomic approach (nLC-MSMS) to study the tolerance to drought in three pea genotypes that were selected based on differences in the level of water deficit tolerance. Multivariate statistical analysis of data unraveled 367 significant differences of 700 identified when genotypes and/or treatment were compared. More than half of the significantly changed proteins belong to primary metabolism and protein regulation categories. We propose different mechanisms to cope drought in the genotypes studied. Maintenance of the primary metabolism and protein protection seems a strategy for drought tolerance. On the other hand susceptibility might be related to maintenance of the homeostatic equilibrium, a very energy consuming process. Data are available via ProteomeXchange with identifier PXD004587.

Dynamic Phosphoproteome Analysis of Seedling Leaves in Brachypodium distachyon L. Reveals Central Phosphorylated Proteins Involved in the Drought Stress Response

Drought stress is a major abiotic stress affecting plant growth and development. In this study, we performed the first dynamic phosphoproteome analysis of Brachypodium distachyon L. seedling leaves under drought stress for different times. A total of 4924 phosphopeptides, contained 6362 phosphosites belonging to 2748 phosphoproteins. Rigorous standards were imposed to screen 484 phosphorylation sites, representing 442 unique phosphoproteins. Comparative analyses revealed significant changes in phosphorylation levels at 0, 6, and 24 h under drought stress. The most phosphorylated proteins and the highest phosphorylation level occurred at 6 h. Venn analysis showed that the up-regulated phosphopeptides at 6 h were almost two-fold those at 24 h. Motif-X analysis identified the six motifs: [sP], [Rxxs], [LxRxxs], [sxD], [sF], and [TP], among which [LxRxxs] was also previously identified in B. distachyon. Results from molecular function and protein-protein interaction analyses suggested that phosphoproteins mainly participate in signal transduction, gene expression, drought response and defense, photosynthesis and energy metabolism, and material transmembrane transport. These phosphoproteins, which showed significant changes in phosphorylation levels, play important roles in signal transduction and material transmembrane transport in response to drought conditions. Our results provide new insights into the molecular mechanism of this plant’s abiotic stress response through phosphorylation modification.

Gel-free/label-free proteomic analysis of wheat shoot in stress tolerant varieties under iron nanoparticles exposure

Iron nanoparticles (Fe NPs) have stimulatory effects on the germination ratio and plant growth of wheat. To elucidate the effects of Fe NPs on shoot of drought tolerant Pakistan-13 and salt tolerant NARC-11, a gel-free/label-free proteomic technique was used. The weights/lengths of seedling, shoot, and root of wheat varieties were increased on 5ppm Fe NPs exposure. The number of proteins related to photosynthesis and protein metabolism was decreased and increased in drought tolerant variety and salt tolerant variety, respectively, treated with Fe NPs compared to untreated plants. Differentially changed proteins in drought tolerant variety and salt tolerant variety were mainly related to photosynthesis. Out of photosynthesis related proteins, light reaction was enhanced in salt tolerant variety compared to drought tolerant variety on Fe NPs exposure. The abundance of ribulose bisphosphate carboxylase/oxygenase small chain in drought tolerant variety was higher than that in salt tolerant variety; however, in salt tolerant variety, it was increased 3 fold by Fe NPs exposure compared to untreated plant. These results suggest that Fe NPs improve the growth of wheat seedling, which might be associated with the increase of protein abundance in photosynthesis in salt tolerant variety.

Proteomic Response of Hordeum vulgare cv. Tadmor and Hordeum marinum to Salinity Stress: Similarities and Differences between a Glycophyte and a Halophyte

Response to a high salinity treatment of 300 mM NaCl was studied in a cultivated barley Hordeum vulgare Syrian cultivar Tadmor and in a halophytic wild barley H. marinum. Differential salinity tolerance of H. marinum and H. vulgare is underlied by qualitative and quantitative differences in proteins involved in a variety of biological processes. The major aim was to identify proteins underlying differential salinity tolerance between the two barley species. Analyses of plant water content, osmotic potential and accumulation of proline and dehydrin proteins under high salinity revealed a relatively higher water saturation deficit in H. marinum than in H. vulgare while H. vulgare had lower osmotic potential corresponding with high levels of proline and dehydrins. Analysis of proteins soluble upon boiling isolated from control and salt-treated crown tissues revealed similarities as well as differences between H. marinum and H. vulgare. The similar salinity responses of both barley species lie in enhanced levels of stress-protective proteins such as defense-related proteins from late-embryogenesis abundant family, several chaperones from heat shock protein family, and others such as GrpE. However, there have also been found significant differences between H. marinum and H. vulgare salinity response indicating an active stress acclimation in H. marinum while stress damage in H. vulgare. An active acclimation to high salinity in H. marinum is underlined by enhanced levels of several stress-responsive transcription factors from basic leucine zipper and nascent polypeptide-associated complex families. In salt-treated H. marinum, enhanced levels of proteins involved in energy metabolism such as glycolysis, ATP metabolism, and photosynthesis-related proteins indicate an active acclimation to enhanced energy requirements during an establishment of novel plant homeostasis. In contrast, changes at proteome level in salt-treated H. vulgare indicate plant tissue damage as revealed by enhanced levels of proteins involved in proteasome-dependent protein degradation and proteins related to apoptosis. The results of proteomic analysis clearly indicate differential responses to high salinity and provide more profound insight into biological mechanisms underlying salinity response between two barley species with contrasting salinity tolerance.

Identification of Winter-Responsive Proteins in Bread Wheat Using Proteomics Analysis and Virus-Induced Gene Silencing (VIGS)

Proteomic approaches were applied to identify protein spots involved in cold responses in wheat. By comparing the differentially accumulated proteins from two cultivars (UC1110 and PI 610750) and their derivatives, as well as the F10 recombinant inbred line population differing in cold-tolerance, a total of 20 common protein spots representing 16 unique proteins were successfully identified using 2-DE method. Of these, 14 spots had significantly enhanced abundance in the cold-sensitive parental cultivar UC1110 and its 20 descendant lines when compared with the cold-tolerant parental cultivar PI 610750 and its 20 descendant lines. Six protein spots with reduced abundance were also detected. The identified protein spots are involved in stress/defense, carbohydrate metabolism, protein metabolism, nitrogen metabolism, energy metabolism, and photosynthesis. The 20 differentially expressed protein spots were chosen for quantitative real-time polymerase chain reaction (qRT-PCR) to investigate expression changes at the RNA level. The results indicated that the transcriptional expression patterns of 11 genes were consistent with their protein expression models. Among the three unknown proteins, Spot 20 (PAP6-like) showed high sequence similarities with PAP6. qRT-PCR results implied that cold and salt stresses increased the expression of PAP6-like in wheat leaves. Furthermore, VIGS (virus-induced gene silencing)-treated plants generated for PAP6-like were subjected to freezing stress, these plants had more serious droop and wilt, an increased rate of relative electrolyte leakage, reduced relative water content (RWC) and decreased tocopherol levels when compared with viral control plants. However, the plants that were silenced for the other two unknown proteins had no significant differences in comparison to the BSMV0-inoculated plants under freezing conditions. These results indicate that PAP6-like possibly plays an important role in conferring cold tolerance in wheat.

Proteomic analysis of Mortierella isabellina M6-22 during cold stress

We aimed to gain a better understanding of cold adaption in Mortierella isabellina M6-22 by using proteomics approaches. The temperature range and optimal temperature for M6-22 growth were investigated, and composition changes in fatty acids were analyzed. Accompanied with the 2-D gel electrophoresis, MALDI-TOF/TOF-MS analysis was conducted to characterize alterations in protein profiling in M6-22 cultured at 30 °C for 24 h and 15 °C for another 24 h when compared with those cultured at 30 °C for 48 h. Gene Ontology (GO) cluster analysis was finally conducted for successfully identified proteins. M6-22 cells could grow well at temperatures ranging from 15 to 30 °C. As temperature decreased from 30 to 15 °C, LA and GLA significantly increased from 11.63 to 17.85 % and from 9.12 to 13.19 %, respectively, while oleic acid significantly decreased from 47.25 to 36.53 %. Proteomics analyses revealed 111 differentially expressed protein spots, among which 5 unique proteins (A38, A40, A47, A49 and A58), 29 up-regulated proteins and 10 down-regulated proteins were identified by MALDI-TOF/TOF-MS. GO enrichment analysis demonstrated that these proteins mainly involved in glycolytic pathway (A34 and A50), electron transport (A28), ATP production (A35 and B39) and protein modification (A38). A total of 44 differentially expressed proteins have been successfully identified in M. isabellina M6-22 cultured at 15 °C. These proteins may play important roles in cold adaption via regulation of ATP synthesis, activation of cold-adaptive proteins, degradation of needless protein, accumulation of PUFAs, etc.