Proteomic analysis of two divergently responding potato genotypes ( Solanum tuberosum L.) following osmotic stress treatment in vitro

Root transcriptomic provides insights on molecular mechanisms involved in the tolerance to water deficit in Pisum sativum inoculated with Pseudomonas sp

MAIN CONCLUSION

Root transcriptomics and biochemical analyses in water-stressed Pisum sativum plants inoculated with Pseudomonas spp. suggested preservation of ABA-related pathway and ROS detoxification, resulting in an improved tolerance to stress. Drought already affects agriculture in large areas of the globe and, due to climate change, these areas are predicted to become increasingly unsuitable for agriculture. For several years, plant growth-promoting bacteria (PGPB) have been used to improve legume yields, but many aspects of this interaction are still unclear. To elucidate the mechanisms through which root-associated PGPB can promote plant growth in dry environments, we investigated the response of pea plants inoculated with a potentially beneficial Pseudomonas strain (PK6) and subjected to two different water regimes. Combined biometric, biochemical, and root RNA-seq analyses revealed that PK6 improved pea growth specifically under water deficit, as inoculated plants showed an increased biomass, larger leaves, and longer roots. Abscisic acid (ABA) and proline quantification, together with the transcriptome analysis, suggested that PK6-inoculated plant response to water deficit was more diversified compared to non-inoculated plants, involving alternative metabolic pathways for the detoxification of reactive oxygen species (ROS) and the preservation of the ABA stress signaling pathway. We suggest that the metabolic response of PK6-inoculated plants was more effective in their adaptation to water deprivation, leading to their improved biometric traits. Besides confirming the positive role that PGPB can have in the growth of a legume crop under adverse conditions, this study offers novel information on the mechanisms regulating plant-bacteria interaction under varying water availability. These mechanisms and the involved genes could be exploited in the future for the development of legume varieties, which can profitably grow in dry climates.

A comprehensive and conceptual overview of omics-based approaches for enhancing the resilience of vegetable crops against abiotic stresses

Abiotic stresses adversely affect the productivity and production of vegetable crops. The increasing number of crop genomes that have been sequenced or re-sequenced provides a set of computationally anticipated abiotic stress-related responsive genes on which further research may be focused. Knowledge of omics approaches and other advanced molecular tools have all been employed to understand the complex biology of these abiotic stresses. A vegetable can be defined as any component of a plant that is eaten for food. These plant parts may be celery stems, spinach leaves, radish roots, potato tubers, garlic bulbs, immature cauliflower flowers, cucumber fruits, and pea seeds. Abiotic stresses, such as deficient or excessive water, high temperature, cold, salinity, oxidative, heavy metals, and osmotic stress, are responsible for the adverse activity in plants and, ultimately major concern for decreasing yield in many vegetable crops. At the morphological level, altered leaf, shoot and root growth, altered life cycle duration and fewer or smaller organs can be observed. Likewise different physiological and biochemical/molecular processes are also affected in response to these abiotic stresses. In order to adapt and survive in a variety of stressful situations, plants have evolved physiological, biochemical, and molecular response mechanisms. A comprehensive understanding of the vegetable's response to different abiotic stresses and the identification of tolerant genotypes are essential to strengthening each vegetable's breeding program. The advances in genomics and next-generation sequencing have enabled the sequencing of many plant genomes over the last twenty years. A combination of modern genomics (MAS, GWAS, genomic selection, transgenic breeding, and gene editing), transcriptomics, and proteomics along with next-generation sequencing provides an array of new powerful approaches to the study of vegetable crops. This review examines the overall impact of major abiotic stresses on vegetables, adaptive mechanisms and functional genomic, transcriptomic, and proteomic processes used by researchers to minimize these challenges. The current status of genomics technologies for developing adaptable vegetable cultivars that will perform better in future climates is also examined.

Proteomics approach to investigating osmotic stress effects on pistachio

Osmotic stress can occur due to some stresses such as salinity and drought, threatening plant survival. To investigate the mechanism governing the pistachio response to this stress, the biochemical alterations and protein profile of PEG-treated plants was monitored. Also, we selected two differentially abundant proteins to validate via Real-Time PCR. Biochemical results displayed that in treated plants, proline and phenolic content was elevated, photosynthetic pigments except carotenoid decreased and MDA concentration were not altered. Our findings identified a number of proteins using 2DE-MS, involved in mitigating osmotic stress in pistachio. A total of 180 protein spots were identified, of which 25 spots were altered in response to osmotic stress. Four spots that had photosynthetic activities were down-regulated, and the remaining spots were up-regulated. The biological functional analysis of protein spots exhibited that most of them are associated with the photosynthesis and metabolism (36%) followed by stress response (24%). Results of Real-Time PCR indicated that two of the representative genes illustrated a positive correlation among transcript level and protein expression and had a similar trend in regulation of gene and protein. Osmotic stress set changes in the proteins associated with photosynthesis and stress tolerance, proteins associated with the cell wall, changes in the expression of proteins involved in DNA and RNA processing occur. Findings of this research will introduce possible proteins and pathways that contribute to osmotic stress and can be considered for improving osmotic tolerance in pistachio.

Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars

Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly identified and constituted 54% of the current soybean phosphosite repository. These phosphosites were converted into the highly conserved kinase docking sites by bioinformatics analysis, which predicted six kinase families that matched with those newly found nine kinase families. The overly post-translationally modified proteins (OPP) occupies 2.1% of these leading phosphoproteins. Most of these OPPs are photoreceptors, mRNA-, histone-, and phospholipid-binding proteins, as well as protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of phosphosites of phosphoproteins follows the exponential decay law, Y = 4.13e-0.098X - 0.04. Out of 218 significantly regulated unique phosphopeptide groups, 188 phosphoproteins were regulated by the drought-tolerant cultivar under the water loss condition. These significantly regulated phosphoproteins (SRP) are mainly enriched in the biological functions of water transport and deprivation, methionine metabolic processes, photosynthesis/light reaction, and response to cadmium ion, osmotic stress, and ABA response. Seventeen and 15 SRPs are protein kinases/phosphatases and transcription factors, respectively. Bioinformatics analysis again revealed that three members of the calcium dependent protein kinase family (CAMK family), GmSRK2I, GmCIPK25, and GmAKINβ1 kinases, constitute a phosphor-relay-mediated signal transduction network, regulating ion channel activities and many nuclear events in this drought-tolerant cultivar, which presumably contributes to the development of the soybean drought tolerance under water deprivation process.

Salinity Stress in Potato: Understanding Physiological, Biochemical and Molecular Responses

Among abiotic stresses, salinity is a major global threat to agriculture, causing severe damage to crop production and productivity. Potato (Solanum tuberosum) is regarded as a future food crop by FAO to ensure food security, which is severely affected by salinity. The growth of the potato plant is inhibited under salt stress due to osmotic stress-induced ion toxicity. Salinity-mediated osmotic stress leads to physiological changes in the plant, including nutrient imbalance, impairment in detoxifying reactive oxygen species (ROS), membrane damage, and reduced photosynthetic activities. Several physiological and biochemical phenomena, such as the maintenance of plant water status, transpiration, respiration, water use efficiency, hormonal balance, leaf area, germination, and antioxidants production are adversely affected. The ROS under salinity stress leads to the increased plasma membrane permeability and extravasations of substances, which causes water imbalance and plasmolysis. However, potato plants cope with salinity mediated oxidative stress conditions by enhancing both enzymatic and non-enzymatic antioxidant activities. The osmoprotectants, such as proline, polyols (sorbitol, mannitol, xylitol, lactitol, and maltitol), and quaternary ammonium compound (glycine betaine) are synthesized to overcome the adverse effect of salinity. The salinity response and tolerance include complex and multifaceted mechanisms that are controlled by multiple proteins and their interactions. This review aims to redraw the attention of researchers to explore the current physiological, biochemical and molecular responses and subsequently develop potential mitigation strategies against salt stress in potatoes.

Genetical genomics of quality related traits in potato tubers using proteomics

BACKGROUND

Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D-gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins.

RESULTS

We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed.

CONCLUSIONS

From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.

Comparison between the impacts of two different modes of salicylic acid application on tomato (Solanum lycopersicum) responses to salinity

Exogenous application of salicylic acid may improve tolerance to salinity. To investigate whether exogenous salicylic acid application had similar protective effects when applied as a priming agent or concomitantly with NaCl, tomato seedlings primed or not with 10 µM salicylic acid were further treated with 125 mM NaCl, 10 µM salicylic acid or combined treatments. Both priming and concomitant application of salicylic acid increased plant growth of salt-stressed plants but their positive impact was not additive. The endogenous salicylic acid concentration increased in the leaves after concomitant application but not in response to priming, suggesting that salicylic acid accumulated during priming was metabolized subsequently. Priming increased Na⁺ and K⁺ accumulation in leaves of salt-treated plants while concomitant application had no impact on shoot Na⁺ and K⁺ accumulation. Both priming and concomitant salicylic acid decreased osmotic potential values in salt-treated plants. Carbon isotope discrimination showed that combination of both salicylic acid application methods were required to maintain a good water use efficiency in salt-treated plants. Our work demonstrated that both procedures of salicylic acid application have positive impact on salt resistance but that the underlying properties sustaining these adaptations differ according to application methods.

Proteomics survey of Solanaceae family: Current status and challenges ahead

Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.

Calcium and Calmodulin Are Involved in Nitric Oxide-Induced Adventitious Rooting of Cucumber under Simulated Osmotic Stress

Osmotic stress is a major form of abiotic stress that adversely affects growth and development of plants and subsequently reduces yield and quality of crops. In this study, the effect of nitric oxide (NO) and calcium (Ca2+) on the process of adventitious rooting in cucumber (Cucumis sativus L.) under simulated osmotic stress was investigated. The results revealed that the effect of exogenous NO and Ca2+ in promoting the development of adventitious roots in cucumber seedlings under simulated osmotic stress was dose-dependent, with a maximal biological response at 10 μM NO donor nitroprusside (SNP) or 200 μM Ca2+. The application of Ca2+ chelators or channel inhibitors and calmodulin (CaM) antagonists significantly reversed NO-induced adventitious rooting, implying that endogenous Ca2+/CaM might be involved in NO-induced adventitious rooting under osmotic stress. Moreover, intracellular Ca amount was also increased by NO in cucumber hypocotyls during the development of adventitious roots under osmotic stress. This increase of endogenous Ca2+ was inhibited by NO specific scavenger 2-(4-carboxyphenyl) -4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide potassium salt (cPTIO), nitrate reductase inhibitors tungstate (Na2WO4) and sodium azide (NaN3). This gives an indication that Ca2+ might be a downstream signaling molecule in the adventitious root development by NO under osmotic condition. The results also show that NO or Ca2+ play a positive role in improving plant water status and photosynthetic system by increasing chlorophyll content and photochemical activity in leaves. Furthermore, NO and Ca2+ treatment might alleviate the negative effects of osmotic stress by decreasing membrane damage and reactive oxygen species (ROS) production by enhancing the activities of superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX). Therefore, Ca2+/CaM may act as a downstream signaling molecule in NO-induced development of adventitious root under simulated osmotic stress through improving the photosynthetic performance of leaves and activating antioxidative system in plants.

Comparative shoot proteome analysis of two potato (Solanum tuberosum L.) genotypes contrasting in nitrogen deficiency responses in vitro

Aiming at a better understanding of the physiological and biochemical background of nitrogen use efficiency, alterations in the shoot proteome under N-deficiency were investigated in two contrasting potato genotypes grown in vitro with 60 and 7.5mM N, respectively. A gel based proteomic approach was applied to identify candidate proteins associated with genotype specific responses to N-deficiency. 21% of the detected proteins differed in abundance between the two genotypes. Between control and N-deficiency conditions 19.5% were differentially accumulated in the sensitive and 15% in the tolerant genotype. 93% of the highly N-deficiency responsive proteins were identified by MALDI TOF/TOF mass spectrometry. The major part was associated with photosynthesis, carbohydrate metabolism, stress response and regulation. Differential accumulation of enzymes involved in the Calvin cycle and glycolysis suggest activation of alternative carbohydrate pathways. In the tolerant genotype, increased abundance under N-deficiency was also found for enzymes involved in chlorophyll synthesis and stability of enzymes, which increase photosynthetic carbon fixation efficiency. Out of a total of 106 differentially abundant proteins, only eight were detected in both genotypes. Our findings suggest that mutually responsive proteins reflect universal stress responses while adaptation to N-deficiency in metabolic pathways is more genotype specific.

SIGNIFICANCE

Nitrogen losses from arable farm land considerably contribute to environmental pollution. In potato, this is a special problem due cultivation on light soils, irrigation and the shallow root system. Therefore, breeding of cultivars with improved nitrogen use efficiency and stable yields under reduced N fertilization is an important issue. Knowledge of genotype dependent adaptation to N-deficiency at the proteome level can help to understand regulation of N efficiency and development of N-efficient cultivars.