Chilling stress-induced proteomic changes in rice roots

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.

Seedling growth and photosynthetic response of Pterocarpus indicus L. to shading stress

In tropical forests, the shade provided by tree canopies and extreme climate causes inhibition of plant seedling growth due to the lack of light. However, the plants can acclimate to such environmental stress by generating specific responses. The present study aimed to investigate the effects of shading conditions on ecophysiological performance of Narra seedlings (Pterocarpus indicus L.) via a mesocosm experiment. A pot experiment was conducted for 20 weeks in a greenhouse with different shading treatments, 75% (control), 25%, and 4% of full sunlight (FS). As a result, the photosynthetic rate (PN), Rubisco enzyme activity, maximum carboxylation rate (VCmax), and maximum electron transport rate (Jmax) in 25% FS treatment were higher or similar to those in control after three weeks of the beginning of shade treatment, whereas the highest values after ten weeks were observed in control. In contrast, the photosynthetic pigments were highest in control after three weeks, while the values were highest in 25% FS treatment after ten weeks. The growth parameters, such as biomass and leaf area, were highest in 75% FS treatment. The expression of Rubisco, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, and fructose-1,6-bisphosphatase were up-regulated in 4% FS treatment compared to control after ten weeks, contributing to tolerating the shade stress. Our findings indicated the capacity of P. indicus seedlings to tolerate and acclimate low light conditions causing shade stress by generating specific physiological and morphological responses, especially Rubisco enzyme activity as well as gene expression related to photosynthetic activity. The present study will improve our understanding of the tolerance mechanism of Narra plant under light-deficient conditions, thereby providing a better strategy for efficiently growing seedlings of this species in tropical rainforests.

Controlling root zone temperature improves plant growth and pigments in hydroponic lettuce

BACKGROUND AND AIMS

Air and root zone temperatures are important environmental factors affecting plant growth and yield. Numerous studies have demonstrated that air temperature strongly affects plant growth and development. Despite the extensive literature on air temperature, comprehensive studies on the effects of root zone temperature (RZT) on plant growth, elemental composition, and pigments are limited. In this study, we carefully observed the effects of RZT in red leaf lettuce to understand its effect on lettuce growth and pigment content.

METHODS

Lettuce (Lactuca sativa, red leaf cultivar 'Red Fire') was grown hydroponically in a plant factory with artificial light under three RZT treatments (15, 25, or 35 °C) for 13 days. We investigated the comprehensive effects of RZT on the production of red leaf lettuce by metabolome and ionome analyses.

KEY RESULTS

The 25 °C RZT treatment achieved maximum shoot and root dry weight. The 35 °C RZT decreased plant growth but significantly increased pigment contents (e.g. anthocyanins, carotenoids). In addition, a RZT heating treatment during plant cultivation that changed from 25 to 35 °C RZT for 8 days before harvest significantly increased shoot dry weight compared with the 35 °C RZT and significantly increased pigments compared with the 25 °C RZT. The 15 °C RZT resulted in significantly less pigment content relative to the 35 °C RZT. The 15 °C RZT also resulted in shoot and root dry weights greater than the 35 °C RZT but less than the 25 °C RZT.

CONCLUSIONS

This study demonstrated that plant growth and pigments can be enhanced by adjusting RZT during different stages of plant growth to attain enhanced pigment contents while minimizing yield loss. This suggests that controlling RZT could be a viable method to improve lettuce quality via enhancement of pigment content quality while maintaining acceptable yields.

How Antioxidants, Osmoregulation, Genes and Metabolites Regulate the Late Seeding Tolerance of Rapeseeds (Brassica napus L.) during Wintering

Rapeseed seeding dates are largely delayed under the rice-rape rotation system, but how rapeseeds adapt to the delayed environment remains unclear. Here, five seeding dates (20 October, 30 October, 10 November, 20 November and 30 November, T1 to T5) were set and the dynamic differences between two late-seeding-tolerant (LST) and two late-seeding-sensitive (LSS) rapeseed cultivars were investigated in a field experiment. The growth was significantly repressed and the foldchange (LST/LSS) of yield increased from 1.50-T1 to 2.64-T5 with the delay in seeding. Both LST cultivars showed higher plant coverage than the LSS cultivars according to visible/hyperspectral imaging and the vegetation index acquired from an unmanned aerial vehicle. Fluorescence imaging, DAB and NBT staining showed that the LSS cultivars suffered more stress damage than the LST cultivars. Antioxidant enzymes (SOD, POD, CAT, APX) and osmoregulation substances (proline, soluble sugar, soluble protein) were decreased with the delay in seeding, while the LST cultivar levels were higher than those of the LSS cultivars. A comparative analysis of transcriptomes and metabolomes showed that 55 pathways involving 123 differentially expressed genes (DEGs) and 107 differentially accumulated metabolites (DAMs) participated in late seeding tolerance regulation, while 39 pathways involving 60 DEGs and 68 DAMs were related to sensitivity. Levanbiose, α-isopropylmalate, s-ribosyl-L-homocysteine, lauroyl-CoA and argino-succinate were differentially accumulated in both cultivars, while genes including isocitrate dehydrogenase, pyruvate kinase, phosphoenolpyruvate carboxykinase and newgene_7532 were also largely regulated. This study revealed the dynamic regulation mechanisms of rapeseeds on late seeding conditions, which showed considerable potential for the genetic improvement of rapeseed.

Genome-Wide Identification and Functional Characterization of Stress Related Glyoxalase Genes in Brassica napus L

Rapeseed (Brassica napus L.) is not only one of the most important oil crops in the world, but it is also an important vegetable crop with a high value nutrients and metabolites. However, rapeseed is often severely damaged by adverse stresses, such as low temperature, pathogen infection and so on. Glyoxalase I (GLYI) and glyoxalase II (GLYII) are two enzymes responsible for the detoxification of a cytotoxic metabolite methylglyoxal (MG) into the nontoxic S-D-lactoylglutathione, which plays crucial roles in stress tolerance in plants. Considering the important roles of glyoxalases, the GLY gene families have been analyzed in higher plans, such as rice, soybean and Chinese cabbage; however, little is known about the presence, distribution, localizations and expression of glyoxalase genes in rapeseed, a young allotetraploid. In this study, a total of 35 BnaGLYI and 30 BnaGLYII genes were identified in the B. napus genome and were clustered into six and eight subfamilies, respectively. The classification, chromosomal distribution, gene structure and conserved motif were identified or predicted. BnaGLYI and BnaGLYII proteins were mainly localized in chloroplast and cytoplasm. By using publicly available RNA-seq data and a quantitative real-time PCR analysis (qRT-PCR), the expression profiling of these genes of different tissues was demonstrated in different developmental stages as well as under stresses. The results indicated that their expression profiles varied among different tissues. Some members are highly expressed in specific tissues, BnaGLYI11 and BnaGLYI27 expressed in flowers and germinating seed. At the same time, the two genes were significantly up-regulated under heat, cold and freezing stresses. Notably, a number of BnaGLY genes showed responses to Plasmodiophora brassicae infection. Overexpression of BnGLYI11 gene in Arabidopsis thaliana seedlings confirmed that this gene conferred freezing tolerance. This study provides insight of the BnaGLYI and BnaGLYII gene families in allotetraploid B. napus and their roles in stress resistance, and important information and gene resources for developing stress resistant vegetable and rapeseed oil.

Identifying conserved genes involved in crop tolerance to cold stress

Low temperature is a limiting factor for crop productivity in tropical and subtropical climates. Cold stress response in plants involves perceiving and relaying the signal through a transcriptional cascade composed of different transduction components, resulting in altered gene activity. We performed a meta-analysis of four previously published datasets of cold-tolerant and cold-sensitive crops to better understand the gene regulatory networks and identify key genes involved in cold stress tolerance conserved across phylogenetically distant species. Re-analysing the raw data with the same bioinformatics pipeline, we identified common cold tolerance-related genes. We found 236 and 242 commonly regulated genes in sensitive and tolerant genotypes, respectively. Gene enrichment analysis showed that protein modifications, hormone metabolism, cell wall, and secondary metabolism are the most conserved pathways involved in cold tolerance. Upregulation of the abiotic stress (heat and drought/salt) related genes [heat shock N -terminal domain-containing protein, 15.7kDa class I-related small heat shock protein-like, DNAJ heat shock N -terminal domain-containing protein, and HYP1 (HYPOTHETICAL PROTEIN 1)] in sensitive genotypes and downregulation of the abiotic stress (heat and drought/salt) related genes (zinc ion binding and pollen Ole e 1 allergen and extensin family protein) in tolerant genotypes was observed across the species. Almost all development-related genes were upregulated in tolerant and downregulated in sensitive genotypes. Moreover, protein-protein network analysis identified highly interacting proteins linked to cold tolerance. Mapping of abiotic stress-related genes on analysed species genomes provided information that could be essential to developing molecular markers for breeding and building up genetic improvement strategies using CRISPR/Cas9 technologies.

Genome-wide association mapping for root traits associated with frost tolerance in faba beans using KASP-SNP markers

Frost is an abiotic stress factor that threatens plant development and crop productivity not only in cold regions but also in temperate zones. Roots play an important role in plant growth during frost stress. Therefore, variation in root characteristics could be studied to improve frost tolerance in winter faba bean. The present study aimed to identify the genomic regions that control frost tolerance in a winter faba bean population by focusing on root-related traits. A set of 185 genotypes were tested for frost tolerance under artificial frost growth conditions at −16°C, −18°C, and −19°C in a growth chamber. Frost stress reduced the root-related parameters in all genotypes, with a wide variation among genotypes. A genome-wide association study identified nine novel single-nucleotide polymorphisms that are associated with the root-related traits. The most frost-tolerant genotypes were identified; two genotypes, S_028 and S_220, exhibited remarkable performance under frost stress. Moreover, they harbored all four of the alleles favorable for frost tolerance. Remarkably, two markers showed genetic pleiotropic effects with positive allele effects on root fresh matter and root dry matter. Thus, both genotypes can be implemented in a breeding program to provide the alleles for healthier roots under frost conditions to develop more frost-tolerant varieties, and the two markers can be used to screen large collections to select for frost tolerance. These results may provide novel insights for improving frost tolerance in faba beans and in other legume crops.

ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress

Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for a relative and absolute quantification (iTRAQ) labeling-based quantitative proteomics approach was used to detected changes in protein levels. Two-week-old seedlings of the cold tolerant rice variety Kongyu131 were treated at 8°C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to the control group. Functional analysis revealed that most of the regulated proteins are involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulated proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is that it provides new insights into cold stress responses in rice with respect to proteomics and provides candidate genes for cold-tolerance rice breeding.

Chilling tolerance in rice: Past and present

Rice is generally sensitive to chilling stress, which seriously affects growth and yield. Since early in the last century, considerable efforts have been made to understand the physiological and molecular mechanisms underlying the response to chilling stress and improve rice chilling tolerance. Here, we review the research trends and advances in this field. The phenotypic and biochemical changes caused by cold stress and the physiological explanations are briefly summarized. Using published data from the past 20 years, we reviewed the past progress and important techniques in the identification of quantitative trait loci (QTL), novel genes, and cellular pathways involved in rice chilling tolerance. The advent of novel technologies has significantly advanced studies of cold tolerance, and the characterization of QTLs, key genes, and molecular modules have sped up molecular design breeding for cold tolerance in rice varieties. In addition to gene function studies based on overexpression or artificially generated mutants, elucidating natural allelic variation in specific backgrounds is emerging as a novel approach for the study of cold tolerance in rice, and the superior alleles identified using this approach can directly facilitate breeding.

Molecular and Biochemical Insights Into Early Responses of Hemp to Cd and Zn Exposure and the Potential Effect of Si on Stress Response

With the intensification of human activities, plants are more frequently exposed to heavy metals (HM). Zinc (Zn) and cadmium (Cd) are frequently and simultaneously found in contaminated soils, including agronomic soils contaminated by the atmospheric fallout near smelters. The fiber crop Cannabis sativa L. is a suitable alternative to food crops for crop cultivation on these soils. In this study, Cd (20 μM) and Zn (100 μM) were shown to induce comparable growth inhibition in C. sativa. To devise agricultural strategies aimed at improving crop yield, the effect of silicon (Si; 2 mM) on the stress tolerance of plants was considered. Targeted gene expression and proteomic analysis were performed on leaves and roots after 1 week of treatment. Both Cd- and Zn-stimulated genes involved in proline biosynthesis [pyrroline-5-carboxylate reductase (P5CR)] and phenylpropanoid pathway [phenylalanine ammonia-lyase (PAL)] but Cd also specifically increased the expression of PCS1-1 involved in phytochelatin (PC) synthesis. Si exposure influences the expression of numerous genes in a contrasting way in Cd- and Zn-exposed plants. At the leaf level, the accumulation of 122 proteins was affected by Cd, whereas 47 proteins were affected by Zn: only 16 proteins were affected by both Cd and Zn. The number of proteins affected due to Si exposure (27) alone was by far lower, and 12 were not modified by heavy metal treatment while no common protein seemed to be modified by both CdSi and ZnSi treatment. It is concluded that Cd and Zn had a clear different impact on plant metabolism and that Si confers a specific physiological status to stressed plants, with quite distinct impacts on hemp proteome depending on the considered heavy metal.

Cold response and tolerance in cereal roots

Cold stress adversely affects plant growth and is a limiting factor in crop productivity. Temperature volatility as a consequence of climate change will increase the effects of cold stress on crop cultivation. Low temperatures frequently occur early after planting in temperate climates and severely affect root development in cereals. In this review we address the question how cereal root systems respond to cold on different scales. First, we summarize the morphological, physiological and cellular responses of cereal roots to cold stress and how these processes are regulated by phytohormones. Subsequently, we highlight the status of the genetic and molecular dissection of cold tolerance with emphasis on the role of cold-responsive genes in improving cold tolerance in cereal roots. Finally, we discuss the role of beneficial microorganisms and mineral nutrients in ameliorating the effects of cold stress in cereal roots. A comprehensive knowledge of the molecular mechanisms underlying cold tolerance will ensure yield stability by enabling the generation of cold-tolerant crop genotypes.

Root responses of contrasting rice genotypes to low temperature stress

Rice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as the number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H₂O₂ accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

Proteomic Approaches to Identify Proteins Responsive to Cold Stress

Changing environmental conditions greatly affect the accumulation of many proteins; therefore, the analysis of alterations in the proteome is essential to understand the plant response to abiotic stress. Proteomics provides a platform for the identification and quantification of plant proteins responsive to cold stress and taking part in cold acclimation. Here, we describe the preparation of proteins for LC-MS measurement to monitor the changes of protein patterns during cold treatment in Arabidopsis thaliana. In our protocol, proteins are precipitated using TCA/acetone, quantified with 2D Quant Kit and digested with trypsin using a filter-based method and analyzed using an LC-MS approach. The acquired results can be further applied for label-free protein quantification.

HSP Transcript and Protein Accumulation in Brassinosteroid Barley Mutants Acclimated to Low and High Temperatures

In temperature stress, the main role of heat-shock proteins (HSP) is to act as molecular chaperones for other cellular proteins. However, knowledge about the hormonal regulation of the production of the HSP is quite limited. Specifically, little is known about the role of the plant steroid hormones—brassinosteroids (BR)—in regulating the HSP expression. The aim of our study was to answer the question of how a BR deficit or disturbances in its signaling affect the accumulation of the HSP90, HSP70, HSP18, and HSP17 transcripts and protein in barley growing at 20 °C (control) and during the acclimation of plants at 5 °C and 27 °C. In barley, the temperature of plant growth modified the expression of HSPs. Furthermore, the BR-deficient mutants (mutations in the HvDWARF or HvCPD genes) and BR-signaling mutants (mutation in the HvBRI1 gene) were characterized by altered levels of the transcripts and proteins of the HSP group compared to the wild type. The BR-signaling mutant was characterized by a decreased level of the HSP transcripts and heat-shock proteins. In the BR-deficient mutants, there were temperature-dependent cases when the decreased accumulation of the HSP70 and HSP90 transcripts was connected to an increased accumulation of these HSP. The significance of changes in the accumulation of HSPs during acclimation at 27 °C and 5 °C is discussed in the context of the altered tolerance to more extreme temperatures of the studied mutants (i.e., heat stress and frost, respectively).

The Roots of Plant Frost Hardiness and Tolerance

Frost stress severely affects agriculture and agroforestry worldwide. Although many studies about frost hardening and resistance have been published, most of them focused on the aboveground organs and only a minority specifically targets the roots. However, roots and aboveground tissues have different physiologies and stress response mechanisms. Climate models predict an increase in the magnitude and frequency of late-frost events, which, together with an observed loss of soil insulation, will greatly decrease plant primary production due to damage at the root level. Molecular and metabolic responses inducing root cold hardiness are complex. They involve a variety of processes related to modifications in cell wall composition, maintenance of the cellular homeostasis and the synthesis of primary and secondary metabolites. After a summary of the current climatic models, this review details the specificity of freezing stress at the root level and explores the strategies roots developed to cope with freezing stress. We then describe the level to which roots can be frost hardy, depending on their age, size category and species. After that, we compare the environmental signals inducing cold acclimation and frost hardening in the roots and aboveground organs. Subsequently, we discuss how roots sense cold at a cellular level and briefly describe the following signal transduction pathway, which leads to molecular and metabolic responses associated with frost hardening. Finally, the current options available to increase root frost tolerance are explored and promising lines of future research are discussed.

Proteomics of Sago Palm Towards Identifying Contributory Proteins in Stress-Tolerant Cultivar

Metroxylon sagu Rottb. or locally known as sago palm is a tropical starch crop grown for starch production in commercial plantations in Malaysia, especially in Sarawak, East Malaysia. This plant species accumulate the highest amount of edible starch compared to other starch-producing crops. However, the non-trunking phenomenon has been observed to be one of the major issues restricting the yield of sago palm starch. In this study, proteomics approach was utilised to discover differences between trunking and non-trunking proteomes in sago palm leaf tissues. Total protein from 16 years old trunking and non-trunking sago palm leaves from deep peat area were extracted with PEG fractionation extraction method and subjected to two-dimensional gel electrophoresis (2D PAGE). Differential protein spots were subjected to MALDI-ToF/ToF MS/MS. Proteomic analysis has identified 34 differentially expressed proteins between trunking and non-trunking sago samples. From these protein spots, all 19 proteins representing different enzymes and proteins have significantly increased in abundance in non-trunking sago plant when subjected to mass spectrometry. The identified proteins mostly function in metabolic pathways including photosynthesis, tricarboxylic acid cycle, glycolysis, carbon utilization and oxidative stress. The current study indicated that the several proteins identified through differentially expressed proteome contributed to physical differences in trunking and non-trunking sago palm.

Proteomic analysis of mashua (Tropaeolum tuberosum) tubers subjected to postharvest treatments

Mashua (Tropaeolum tuberosum) is an important food in certain areas of the Andean region, where it is popularly believed to possess medicinal properties. Several studies have previously shown the potential of this tuber as a source of bioactive compounds. Traditionally, the tuber is exposed to the sun before consumption, in order to reduce its bitterness. The present work aims to study, at the proteome level, the differential abundance of proteins in tubers subjected to different postharvest treatments: sun-exposure (SUN), shade (SHA), refrigeration (COLD) and shade combined with sun-exposure (SHA-SUN) compared to recently harvested tubers (INIT). Results showed that sun exposure for prolonged times (9 days) resulted in increased abundance of proteins classified as heat shock proteins, intracellular traffic, disease/defense and protein degradation. Our results reflect that the sun treatment activates defense systems and osmoprotection adjustment against water loss and reactive oxygen species.

Transcriptome analysis reveals that barnyard grass exudates increase the allelopathic potential of allelopathic and non-allelopathic rice (Oryza sativa) accessions

BACKGROUND

Allelopathy in rice (Oryza sativa) is a chemically induced response that is elevated by the exogenous application of chemical compounds and barnyard grass root exudates. An in-depth understanding of the response mechanisms of rice to chemical induction is necessary for the identification of target genes for increasing the allelopathic potential of rice. However, no previous studies have evaluated the transcriptomic changes associated with allelopathy in rice in response to barnyard grass exudates treatment. Thus, the aim of the present study was to reveal differentially expressed genes (DEGs) in allelopathic and non-allelopathic rice seedlings treated with barnyard grass exudates to identify target allelopathy genes.

RESULTS

The inhibitory effect of the culture solutions on the allelopathic rice accession PI312777 (PI) and the non-allelopathic rice accession Lemont (LE) significantly increased (P < 0.05) after treatment with barnyard grass root exudates. The RNA sequencing results revealed that 14,891 genes in PI(+B) vs. LE(+B), 12,505 genes in PI(+B) vs. PI(-B), and 5857 genes in LE(+B) vs. LE(-B) were differentially expressed following root exudates treatment. These DEGs were classified into three categories and 32 functional groups, i.e., 12 groups in the biological process category, 12 groups in the cellular component category, and eight groups in the molecular function category. There were 5857 and 2846 upregulated genes and 135 and 50 upregulated Gene Ontology terms (P < 0.05) in the biological process category in PI(+B) vs. PI(-B) and LE(+B) vs. LE(-B), respectively. These results indicated that the allelopathic accession PI is more sensitive than the non-allelopathic accession LE to exogenous root exudates treatment. Genes related to rice allelochemical-related biosynthesis pathways, particularly the shikimic acid and acetic acid pathways, were significantly differentially expressed in both rice accessions. These findings suggested that phenolic acids, fatty acids, and flavonoids, which constitute the downstream metabolites of the shikimic acid and acetic acid pathways, are significantly expressed in response to root exudates of barnyard grass.

CONCLUSIONS

The allelopathic potential of both rice accessions could be significantly enhanced by barnyard grass root exudates application. Furthermore, genes related to the biosynthesis pathways of reported rice allelochemicals were significantly differentially expressed in both accessions. Phenylalanine ammonia lyase was determined to be a potential target for the regulation of chemical induction.

Preliminary Validation of a Short Form of the Perceived Stress Questionnaire for Use in Clinical Rehabilitation Counseling Research and Practice

Background

The purpose of this study was to develop and validate a short form of the Perceived Stress Questionnaire (PSQ) in people with spinal cord injury (SCI).

Methods

The sample consisted of 274 individuals with SCI. Measures administered were the PSQ-20, Center for Epidemiological Studies-Depression Scale, and Rand Short-Form 36 General Health Scale.

Results

Results showed that after selecting two items from each subscale of the PSQ-20, factor analysis results supported a unidimensional measure for the PSQ-8. The PSQ-8 total score demonstrated a high correlation with the PSQ-20 total score. The reliability of the PSQ-8 was adequate and similar to the PSQ-20. The PSQ-8 measurement correlated well with the external correlates of depression and health status. The mediation analysis indicated depression as a partial mediator for the relationship between perceived stress and health status, indicating people with higher levels of perceived stress had poorer health outcome in this study.

Conclusions

This study provides evidence to support the psychometric properties of PSQ-8 in people with SCI. The PSQ-8 is a brief, reliable, unidimensional, and psychometrically sound measure of perceived stress that can be used in clinical rehabilitation and mental health counseling research and practice.

Enhanced arsenic tolerance and secondary metabolism by modulation of gene expression and proteome profile in Artemisia annua L. after application of exogenous salicylic acid

This study was designed to investigate the effect of exogenous application of salicylic acid (SA) on proteins pattern and secondary metabolites in arsenic (As) stressed Artemisia annua. A. annua was treated by As 100 μM, SA 100 μM and combined treatment of SA 100 μM + As 100 μM upto 3 days. Significant accumulation of As was observed in roots than shoots at As 100 μM treatment. Under As treatment, oxidative stress was induced as indicated by increased TBARS content. Biomass, carotenoid, flavonoids were enhanced whereas total chlorophyll pigment was reduced under As treatment. Combined treatment of SA 100 μM + As 100 μM was more effective for increment of biomass, total chlorophyll content, and flavonoids as compared to As 100 μM treatment. Protein profiling revealed 20 differentially abundant proteins by 2-DE PAGE and MALDI-TOF-MS analysis. Identified proteins were related to photosynthesis, energy metabolism, transcriptional regulators, secondary metabolism, lipid metabolism, transport proteins and unknown/hypothetical proteins. All identified proteins were significantly increased in abundance under combined treatments of SA 100 μM + As 100 μM. The expression analysis of key genes involved in biosynthesis of lipid metabolism, signal molecule, transcriptional regulators, artemisinin biosynthetic genes, isoprenoids pathway, terpenes and flavonoids pathway were significantly upregulated under combined treatments of SA 100 μM + As 100 μM, suggesting a fine linkage in regulation of primary and secondary metabolism to modulate tolerance capacity and to improve phytoremediation property of A. annua against arsenic toxicity.

Comparative proteomics analysis of whitetop (Lepidium draba L.) seedlings in response to exogenous glucose

In this research, a comparative proteomics approach was conducted to understand the physiological processes behind the sulforaphane formation in whitetop seedlings in response to exogenous glucose. Initially, 5-day-old whitetop seedlings were elicited by different concentrations (0, 166, 250, 277, 360 mM) of glucose for 72 h. According to the results, sulforaphane formation was influenced in a dose-dependent manner by glucose, and was maximized with the concentrations of 166 and 250 mM. Consequently, 2-dimensional gel electrophoresis was performed on the 166 mM glucose-elicited seedlings and it was shown that 25 protein spots were differentially expressed between glucose-elicited seedlings and control. Two hypothetical (were down-regulated) and 9 unique proteins (44% and 56% up- and down-regulated, respectively) were identified based on the Mass spectrometry analysis. According to the functional classification of the unique proteins, photosynthetic, chaperone, energy metabolism, signaling and sorting related proteins are marked in response to the glucose elicitation. This is the first report to successfully identify the Abscisic acid receptor PYR1-like and sorting nexin 1 isoform X1 by proteomics technique. In addition, the role of the sorting nexin 1 isoform X1 in the glucose-elicited whitetop seedling is reported for the first time.

Diurnal changes in CN metabolism and response of rice seedlings to UV-B radiation

Plants regulate a number of primary metabolites, including carbohydrates, organic acids, and amino acids, in response to UV-B radiation. Therefore, it is essential to understand the time-dependent response of rice plants to UV-B stress. This study focused on the response of plants to UV-B at different leaf developmental phases (emerging, growing, and maturing) in an attempt to fully comprehend the metabolic shift. We analyzed the expression levels of genes related to starch/sucrose metabolism in the leaf blades of rice seedlings (Oryza sativa L. "Saechuchenog") exposed to UV-B irradiation for short (1 day) and long terms (5 days) using quantitative real-time polymerase chain reaction. We also examined the diurnal variations in the contents of primary metabolites using an established GCTOF-MS (gas chromatography time of flight-mass spectrometry) method. The results showed that the levels of primary metabolites were largely dependent upon the diurnal rhythm and leaf developmental phase. The young leaves (sink) produced and accumulated starch rather than sucrose. The short-term (4 h, 1 day) UV-B exposure inhibited sucrose synthesis, which could be the first target of UV-B radiation. Following short- and long-term (5 days) exposure to UV-B radiation, the dynamic response of primary metabolites was evaluated. It was found that the content of carbohydrates decreased throughout the period of exposure to UV-B stress, especially in terms of sucrose concentration. However, the content of the majority of amino acids increased after an early decrease. Our data revealed that the metabolic response, as well as the gene expression, differed with the period (intensity) of exposure to UV-B radiation and with the phase of leaf development. These findings provide new insights for a better understanding of the metabolic response of a variety of plant species exposed to a wide range of UV-B radiation.

Comparative proteomic analysis of Pogostemon cablin leaves after continuous cropping

A proteomic approach was used to understand the molecular mechanisms underlying obstacles to the continuous cropping of Pogostemon cablin. We examined differences in protein abundance between control (CK) and continuously cropped (TR) P. cablin leaves at different time points (90, 150, and 210 days after culture). Comparative analysis by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) revealed 183 differentially expressed protein spots, of which 87 proteins or isoforms were identified using mass spectrometry. Among these differentially expressed proteins (DEPs), 50 proteins or isoforms showed increased abundance and 37 proteins or isoforms showed decreased abundance in the TR sample compared with the abundance in the CK sample. Bioinformatic tools were used to analyze the DEPs. These proteins were classified into 12 categories according to clusters of orthologous groups (COG) analysis, with the majority being involved in post-translational modification, protein turnover, and chaperones, followed by carbohydrate transport and metabolism, and finally, energy production and conversion. Protein-protein interactions revealed that 18 DEPs were involved in energy metabolism, 6 DEPs were involved in stress response, and 4 DEPs were involved in amino acid biosynthesis. Continuous cropping altered the expression of proteins related to energy metabolism, carbohydrate metabolism, and amino acid metabolism in P. cablin leaves. Among these processes, the most affected was energy metabolism, which may be pivotal for resistance to continuous cropping.

Differential gene expression profiling through transcriptome approach of Saccharum spontaneum L. under low temperature stress reveals genes potentially involved in cold acclimation

Sugarcane (Saccharum sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8-9 months mainly due to winter's low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant S. spontaneum IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and transcriptome was validated using qRT-PCR. The differential gene expression (DGE) analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated upon low temperature stress. A total of 170 cold responsive transcriptional factors belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a DNA binding transcriptional activation protein associated with cold acclimation and freezing tolerance was differentially upregulated. Many low temperature responsive genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity, calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially upregulated. Potential cold responsive genes and transcriptional factors involved in cold tolerance mechanism in cold tolerant S. spontaneum IND 00-1037 were identified. Together, this study provides insights into the cold tolerance to low temperature stress in S. spontaneum, thus opening applications in the genetic improvement of cold stress tolerance in sugarcane.

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.

Proteomic Analysis of Rice Seedlings Under Cold Stress

Low temperature can greatly restrict the growth and development of rice. The rice seedlings show growth retardation, lamina wrap, and part of blade even died under the condition of low temperature. In order to get more information about cold stress responses in rice, two dimensional electrophoresis and bioinformatics analysis of mass spectrometry were used to preliminary survey the cold tolerance of cold sensitive line 9311 and cold resistance variety Fujisaka 5 under cold stress. Two dimensional electrophoresis maps of 9311 and Fujisaka 5 were established under cold treatment. With analysis of bioinformation, the proteins were found involve in many aspects of rice development. The largest category of proteins is functioning on metabolism. By comparing the proteins from the two varieties, it can be found that most proteins from 9311 were down-regulated and were up-regulated in Fujisaka 5. The results showed that the membrane composition and structure were damaged, metabolism changed dramatically and rice defense system was activated under the cold stimulation. Fifty-nine proteins related to the resistance of cold stress were identified in our study, and we have investigated and classified all of their biological functions. The importance of our study are providing some conduct for the research of rice resistant to cold stress, supporting auxiliary technique for rice varieties and widening the search field of cold tolerance in plants.

Comparative proteomic analysis of alfalfa revealed new salt and drought stress-related factors involved in seed germination

Salinity and drought are two major environmental factors that limit the growth and yield of many forage crops in semi-arid and arid regions. Alfalfa (Medicago sativa L.) is one of the most important forage crops in many countries. We aim to investigate the molecular mechanisms of alfalfa in response to salt and drought stresses in this study. Physiological and proteomic analyses were applied to examine the Zhongmu NO.3 alfalfa seed germination stage with 200 mM NaCl and 180 g·L^-1 polyethylene glycol (PEG) treatments. The germination ability of the seed and the accumulation of osmotic solutes were quite different between the NaCl and PEG treatments. More than 800 protein spots were detected by proteomics technology on two-dimensional electrophoresis (2-DE) gels. The abundance of twenty-eight proteins were decreased or increased after salt and drought stress. Seventeen of these proteins were identified and classified into six functional categories through mass spectrometry (MS). The six groups involved in salt- and PEG-mediated stress included defense response, energy metabolism, protein synthesis and degradation, oxidative stress, carbohydrate metabolism-associated proteins, and unknown proteins. We discovered that some proteins related to carbohydrate metabolism and energy production increased in abundance under salt- and PEG-mediated drought stress. This demonstrates a common mechanism of energy consumption during abiotic stresses. Further study of these proteins with unknown function will provide insights into the molecular mechanisms of abiotic stress and the discovery of new candidate markers.

Proteomic analysis by iTRAQ-MRM of soybean resistance to Lamprosema Indicate

BACKGROUND

Lamprosema indicate is a major leaf feeding insect pest to soybean, which has caused serious yield losses in central and southern China. To explore the defense mechanisms of soybean resistance to Lamprosema indicate, a highly resistant line (Gantai-2-2) and a highly susceptible line (Wan 82-178) were exposed to Lamprosema indicate larval feedings for 0 h and 48 h, and the differential proteomic analyses of these two lines were carried out.

RESULTS

The results showed that 31 differentially expressed proteins (DEPs) were identified in the Gantai-2-2 when comparing 48 h feeding with 0 h feeding, and 53 DEPs were identified in the Wan 82-178. 28 DEPs were identified when comparing Gantai-2-2 with Wan 82-178 at 0 h feeding. The bioinformatic analysis results showed that most of the DEPs were associated with ribosome, linoleic acid metabolism, flavonoid biosynthesis, phenylpropanoid biosynthesis, peroxisome, stilbenoid, diarylheptanoid and gingerol biosynthesis, glutathione metabolism, pant hormone signal transduction, and flavone and flavonol biosynthesis, as well as other resistance related metabolic pathways. The MRM analysis showed that the iTRAQ results were reliable.

CONCLUSIONS

According to the analysis of the DEPs results, the soybean defended or resisted the Lamprosema indicate damage by the induction of a synthesis of anti-digestive proteins which inhibit the growth and development of insects, reactive oxygen species scavenging, signaling pathways, secondary metabolites synthesis, and so on.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

Changes in the proteome of grapevine leaves (Vitis vinifera L.) during long-term drought stress

The essence of exploring and understanding mechanisms of plant adaptation to environmental stresses lies in the determination of patterns of the expression of proteins, identification of stress proteins and their association with the specific functions in metabolic pathways. To date, little information has been provided about the proteomic response of grapevine to the persistent influence of adverse environmental conditions. This article describes changes in the profile of protein accumulation in leaves of common grapevine (Vitis vinifera L.) seedlings in response to prolonged drought. Isolated proteins were separated by two-dimensional electrophoresis (2 DE), and the proteins whose level of accumulation changed significantly due to the applied stress factors were identified with tandem mass spectrometry MALDI TOF/TOF type. Analysis of the proteome of grapevine leaves led to the detection of many proteins whose synthesis changed in response to the applied stressor. Drought caused the most numerous changes in the accumulation of proteins associated with carbohydrate and energy metabolism, mostly connected with the pathways of glycolysis and photosystem II protein components. The biological function of the identified proteins is discussed with reference to the stress of drought. Some of the identified proteins, especially the ones whose accumulation increased during drought stress, may be responsible for the adaptation of grapevine to drought.

Proteomic analysis of common bean stem under drought stress using in-gel stable isotope labeling

Drought is an abiotic stress that strongly influences plant growth, development and productivity. Proteome changes in the stem of the drought-tolerant common bean (Phaseolus vulgaris L.) cultivar Tiber have were when the plants were exposed to drought. Five-week-old plants were subjected to water deficit by withholding irrigation for 7, 12 and 17days, whereas control plants were regularly irrigated. Relative water content (RWC) of leaves, as an indicator of the degree of cell and tissue hydration, showed the highest statistically significant differences between control and drought-stressed plants after 17days of treatment, where RWC remained at 90% for control and declined to 45% for stressed plants. Plants exposed to drought for 17days and control plants at the same developmental stage were included in quantitative proteomic analysis using in-gel stable isotope labeling of proteins in combination with mass spectrometry. The quantified proteins were grouped into several functional groups, mainly into energy metabolism, photosynthesis, proteolysis, protein synthesis and proteins related to defense and stress. 70kDa heat shock protein showed the greatest increase in abundance under drought of all the proteins, suggesting its role in protecting plants against stress by re-establishing normal protein conformations and thus cellular homeostasis. The abundance of proteins involved in protein synthesis also increased under drought stress, important for recovery of damaged proteins involved in the plant cell's metabolic activities. Other important proteins in this study were related to proteolysis and folding, which are necessary for maintaining proper cellular protein homeostasis. Taken together, these results reveal the complexity of pathways involved in the drought stress response in common bean stems and enable comparison with the results of proteomic analysis of leaves, thus providing important information to further understand the biochemical and molecular mechanisms of drought response in this important legume.

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.

Effect of postharvest ultraviolet-C treatment on the proteome changes in fresh cut mango (Mangifera indica L. cv. Chokanan)

BACKGROUND

Postharvest treatments of fruits using techniques such as ultraviolet-C have been linked with maintenance of the fruit quality as well as shelf-life extension. However, the effects of this treatment on the quality of fruits on a proteomic level remain unclear. This study was conducted in order to understand the response of mango fruit to postharvest UV-C irradiation.

RESULTS

Approximately 380 reproducible spots were detected following two-dimensional gel electrophoresis. Through gel analysis, 24 spots were observed to be differentially expressed in UV-C treated fruits and 20 were successfully identified via LCMS/MS. Postharvest UV-C treatment resulted in degradative effects on these identified proteins of which 40% were related to stress response, 45% to energy and metabolism and 15% to ripening and senescence. In addition, quality and shelf-life analysis of control and irradiated mangoes was evaluated. UV-C was found to be successful in retention of quality and extension of shelf-life up to 15 days. Furthermore, UV-C was also successful in increasing antioxidants (total flavonoid, reducing power and ABTS scavenging activity) in mangoes.

CONCLUSION

This study provides an overview of the effects of UV-C treatment on the quality of mango on a proteomic level as well as the potential of this treatment in shelf-life extension of fresh-cut fruits. © 2015 Society of Chemical Industry.

Comparative Study of Early Cold-Regulated Proteins by Two-Dimensional Difference Gel Electrophoresis Reveals a Key Role for Phospholipase Dα1 in Mediating Cold Acclimation Signaling Pathway in Rice

To understand the early signaling steps that regulate cold responses in rice, two-dimensional difference gel electrophoresis (2-D DIGE)(1)was used to study early cold-regulated proteins in rice seedlings. Using mass spectrometry, 32 spots, which represent 26 unique proteins that showed an altered expression level within 5 min of cold treatment were identified. Among these proteins, Western blot analyses confirmed that the cellular phospholipase D α1 (OsPLDα1) protein level was increased as early as 1 min after cold treatment. Genetic studies showed that reducing the expression ofOsPLDα1makes rice plants more sensitive to chilling stress as well as cold acclimation increased freezing tolerance. Correspondingly, cold-regulated proteomic changes and the expression of the cold-responsive C repeat/dehydration-responsive element binding 1 (OsDREB1) family of transcription factors were inhibited in thepldα1mutant. We also found that the expression ofOsPLDα1is directly regulated by OsDREB1A. This transcriptional regulation ofOsPLDα1could provide positive feedback regulation of the cold signal transduction pathway in rice. OsPLDα1 hydrolyzes phosphatidylcholine to produce the signal molecule phosphatidic acid (PA). By lipid-overlay assay, we demonstrated that the rice cold signaling proteins, MAP kinase 6 (OsMPK6) and OsSIZ1, bind directly to PA. Taken together, our results suggest that OsPLDα1 plays a key role in transducing cold signaling in rice by producing PA and regulatingOsDREB1s' expression by OsMPK6, OsSIZ1, and possibly other PA-binding proteins.

The effects of cold stress on the phenolic compounds and antioxidant capacity of grapevine (Vitis vinifera L.) leaves

According to some estimates, a 70% increase in crop yield could be achieved if the environmental conditions were close to the optimum ones for a given plant, which is why the identification and control of adverse environmental effects is a top priority in many countries worldwide. This paper contains a discussion of the changes in selected elements of the secondary metabolism in the leaves of two grapevine varieties (Vitis vinifera L.) with a different degree of tolerance to cold stress during prolonged and constant low temperature stress. The analyses have shown that the more-tolerant variety was characterized by a higher content of phenolic compounds, better radical-scavenging capacity and stronger reducing power. However, the cold stress caused a decrease in the concentration of the phenolics and decreased the scavenging capacity in the leaves of both varieties. Four phenolic acids have been identified in the extracts from the leaves of both grapevines: caffeic acid, p-coumaric acid, ferulic acid and a caffeic acid derivative. Caffeic acid appeared in the highest concentrations in all the leaf extracts. Additionally, it has been noted that in the leaves of the varieties susceptible and tolerant to cold stress, the prolonged exposure to low temperature caused a considerable reduction of the content of all identified phenolic acids. The results of the analyses have demonstrated large differences in the functioning of the secondary metabolism in response to the same stressor.

Understanding salinity responses and adopting 'omics-based' approaches to generate salinity tolerant cultivars of rice

Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using 'omics-based' tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary 'omics-based' approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice.

Proteomic and metabolomic profiling of Valencia orange fruit after natural frost exposure

The aim of this study was to evaluate the response of orange fruit (Citrus sinensis var. Valencia Late) to freezing stress in planta, both immediately after the natural event and after a week, in order to understand the biochemical and molecular basis of the changes that later derive in internal and external damage symptoms. Using two-dimensional differential gel electrophoresis to analyze exposed and non-exposed fruit, 27 differential protein spots were detected in juice sacs and flavedo, among all comparisons made. Also, primary and secondary metabolites relative contents were analyzed in both tissues by gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry, respectively. Proteins and compounds involved in regulatory functions, iron metabolism, oxidative damage and carbohydrate metabolism were the most affected. Interestingly, three glycolytic enzymes were induced by cold, and there was an increase in fermentation products (volatiles); all of that suggests that more energy generation might be required from glycolysis to counter the cold stress. Moreover, a notable increase in sugar levels was observed after frost, but it was not at the expense of organic acids utilization. Consequently, these results suggest a probable redistribution of photoassimilates in the frost-exposed plants, tending to restore the homeostasis altered by that severe type of stress. Isosinensetin was the most cold-sensitive secondary metabolite because it could not be detected at all after the frost, constituting a possible tool to early diagnose freezing damage.

Proteomic analyses reveal differences in cold acclimation mechanisms in freezing-tolerant and freezing-sensitive cultivars of alfalfa

Cold acclimation in alfalfa (Medicago sativa L.) plays a crucial role in cold tolerance to harsh winters. To examine the cold acclimation mechanisms in freezing-tolerant alfalfa (ZD) and freezing-sensitive alfalfa (W5), holoproteins, and low-abundance proteins (after the removal of RuBisCO) from leaves were extracted to analyze differences at the protein level. A total of 84 spots were selected, and 67 spots were identified. Of these, the abundance of 49 spots and 24 spots in ZD and W5, respectively, were altered during adaptation to chilling stress. Proteomic results revealed that proteins involved in photosynthesis, protein metabolism, energy metabolism, stress and redox and other proteins were mobilized in adaptation to chilling stress. In ZD, a greater number of changes were observed in proteins, and autologous metabolism and biosynthesis were slowed in response to chilling stress, thereby reducing consumption, allowing for homeostasis. The capability for protein folding and protein biosynthesis in W5 was enhanced, which allows protection against chilling stress. The ability to perceive low temperatures was more sensitive in freezing-tolerant alfalfa compared to freezing-sensitive alfalfa. This proteomics study provides new insights into the cold acclimation mechanism in alfalfa.

Plant mitochondrial proteomics

Mitochondrial proteomics has significantly developed since the first plant mitochondrial proteomes were published in 2001. Many studies have added to our knowledge of the protein components that make up plant mitochondria in a wide range of species. Here we present two common and one emerging quantitative proteomic techniques that can be used to study the abundance of mitochondrial proteins. For this publication, we have described the methods as an approach to determine the amount of contamination in a mitochondrial isolation to contrast historical approaches that involved the use of use of antibodies to specific marker proteins or the measurement of activity of marker enzymes. However, these approaches could easily be adapted to carry out control versus treatment studies.

Differential protein expression in Phalaenopsis under low temperature

A comparative proteomic analysis was carried out to explore the molecular mechanisms of responses to cold stress in Phalaenopsis after treated by low temperature (13/8 °C day/night) for 15 days. Differentially expressed proteins were examined using two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-TOF/MS). Among 85 differentially expressed proteins, 73 distinct proteins were identified. Comparative analysis revealed that the identified proteins mainly participate in photosynthesis, protein synthesis, folding and degradation, respiration, defense response, amino acid metabolism, energy pathway, cytoskeleton, transcription regulation, signal transduction, and seed storage protein, while the functional classification of the remaining four proteins was not determined. These data suggested that the proteins might work cooperatively to establish a new homeostasis under cold stress; 37 % of the identified cold-responsive proteins were associated with various aspects of chloroplast physiology, and 56 % of them were predicted to be located in the chloroplasts, implying that the cold stress tolerance of Phalaenopsis was achieved, at least partly, by regulation of chloroplast function. Moreover, the protein destination control, which was mediated by chaperones and proteases, plays an important role in tolerance to cold stress.

Physiological and proteomic alterations in rice (Oryza sativa L.) seedlings under hexavalent chromium stress

Rice plants employ two strategies to cope with Cr toxicity: immobilizing Cr ions into cell walls to reduce its translocation and activating antioxidant defense to mitigate Cr-induced oxidative stress. The investigation aimed at understanding the physiological and proteomic responses of rice seedlings to hexavalent chromium (Cr(6+)) stress was conducted using two rice genotypes, which differ in Cr tolerance and accumulation. Cr toxicity (200 µM) heavily increased the accumulation of H2O2 and [Formula: see text], enhanced lipid peroxidation, decreased cell viability and consequently inhibited rice plant growth. Proteomic analyses suggest that the response of rice proteome to Cr stress is genotype- and Cr dosage-dependent and tissue specific. Sixty-four proteins, which show more than fourfold difference under either two Cr levels, have been successfully identified. They are involved in a range of cellular processes, including cell wall synthesis, energy production, primary metabolism, electron transport and detoxification. Two proteins related to cell wall structure, NAD-dependent epimerase/dehydratase and reversibly glycosylated polypeptide were greatly up-regulated by Cr stress. Their enhancements coupled with callose accumulation by Cr suggest that cell wall is an important barrier for rice plants to resist Cr stress. Some enzymes involved in antioxidant defense, such as ferredoxin-NADP reductase, NADP-isocitrate dehydrogenase, glyoxalase I (Gly I) and glutamine synthetase 1 (GS1) have also been identified in response to Cr stress. However, they were only detected in Cr-tolerant genotype, indicating the genotypic difference in the capacity of activating the defense system to fight against Cr-induced oxidative stress. Overall, two strategies in coping with Cr stress in rice plants can be hypothesized: (i) immobilizing Cr ions into cell walls to reduce its translocation and (ii) activating antioxidant defense to mitigate Cr-induced oxidative stress.

Cytokinin modulates proteomic, transcriptomic and growth responses to temperature shocks in Arabidopsis

As sessile organisms, plants must sense environmental conditions and adjust their growth and development processes accordingly, through adaptive responses regulated by various internal factors, including hormones. A key environmental factor is temperature, but temperature-sensing mechanisms are not fully understood despite intense research. We investigated proteomic responses to temperature shocks (15 min cold or heat treatments) with and without exogenous applications of cytokinin in Arabidopsis. Image and mass spectrometric analysis of the two-dimensionally separated proteins detected 139 differentially regulated spots, in which 148 proteins were identified, most of which have not been previously linked to temperature perception. More than 70% of the temperature-shock response proteins were modulated by cytokinin, mostly in a similar manner as heat shock. Data mining of previous transcriptomic datasets supported extensive interactions between temperature and cytokinin signalling. The biological significance of this finding was tested by assaying an independent growth response of Arabidopsis seedlings to heat stress: hypocotyl elongation. This response was strongly inhibited in mutants with deficiencies in cytokinin signalling or endogenous cytokinin levels. Thus, cytokinins may directly participate in heat signalling in plants. Finally, large proportions of both temperature-shock and cytokinin responsive proteomes co-localize to the chloroplast, which might therefore host a substantial proportion of the temperature response machinery.

Abiotic stress responses in plant roots: a proteomics perspective

Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abundance that can be best explored through proteomics. This review summarizes comparative proteomic studies conducted with roots of various plant species subjected to different abiotic stresses especially drought, salinity, flood, and cold. The main purpose of this article is to highlight and classify the protein level changes in abiotic stress response pathways specifically in plant roots. Shared as well as stressor-specific proteome signatures and adaptive mechanism(s) are simultaneously described. Such a comprehensive account will facilitate the design of genetic engineering strategies that enable the development of broad-spectrum abiotic stress-tolerant crops.

Research advances in major cereal crops for adaptation to abiotic stresses

With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers' fields.

Comparative proteomic analysis of the stolon cold stress response between the C4 perennial grass species Zoysia japonica and Zoysia metrella

Zoysiagrass, the most cold-tolerant grass among the warm-season turfgrasses, is often used as a model species for isolating cellular components related to cold stress. To understand the proteomic responses to cold stress in zoysiagrass stolons, we extracted stolon proteins from Zoysiajaponica, cv. Meyer (cold-tolerant) and Z. metrella, cv. Diamond (cold-sensitive), which were grown with or without cold treatment. Approximately 700 proteins were resolved on 2-DE gels, and 70 protein spots were differentially accumulated. We further observed that 45 of the identified proteins participate in 10 metabolic pathways and cellular processes. A significantly greater number of proteins accumulated in the Meyer than in the Diamond and 15 increased proteins were detected only in the Meyer cultivar under cold stress. Furthermore, we propose a cold stress-responsive protein network composed of several different functional components that exhibits a balance between reactive oxygen species (ROS) production and scavenging, accelerated protein biosynthesis and proteolysis, reduced protein folding, enhanced photosynthesis, abundant energy supply and enhanced biosynthesis of carbohydrates and nucleotides. Generally, the cold-tolerant Meyer cultivar showed a greater ROS scavenging ability, more abundant energy supply and increased photosynthesis and protein synthesis than did the cold-sensitive Diamond cultivar, which may partly explain why Meyer is more cold tolerant.