Comparative proteomics and gene expression analysis in Arachis duranensis reveal stress response proteins associated to drought tolerance

The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance

Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.

Sustaining yield and nutritional quality of peanuts in harsh environments: Physiological and molecular basis of drought and heat stress tolerance

Climate change is significantly impacting agricultural production worldwide. Peanuts provide food and nutritional security to millions of people across the globe because of its high nutritive values. Drought and heat stress alone or in combination cause substantial yield losses to peanut production. The stress, in addition, adversely impact nutritional quality. Peanuts exposed to drought stress at reproductive stage are prone to aflatoxin contamination, which imposes a restriction on use of peanuts as health food and also adversely impact peanut trade. A comprehensive understanding of the impact of drought and heat stress at physiological and molecular levels may accelerate the development of stress tolerant productive peanut cultivars adapted to a given production system. Significant progress has been achieved towards the characterization of germplasm for drought and heat stress tolerance, unlocking the physiological and molecular basis of stress tolerance, identifying significant marker-trait associations as well major QTLs and candidate genes associated with drought tolerance, which after validation may be deployed to initiate marker-assisted breeding for abiotic stress adaptation in peanut. The proof of concept about the use of transgenic technology to add value to peanuts has been demonstrated. Advances in phenomics and artificial intelligence to accelerate the timely and cost-effective collection of phenotyping data in large germplasm/breeding populations have also been discussed. Greater focus is needed to accelerate research on heat stress tolerance in peanut. A suits of technological innovations are now available in the breeders toolbox to enhance productivity and nutritional quality of peanuts in harsh environments. A holistic breeding approach that considers drought and heat-tolerant traits to simultaneously address both stresses could be a successful strategy to produce climate-resilient peanut genotypes with improved nutritional quality.

Comparative transcriptomics of drought stress response of taproot meristem region of contrasting purple carrot breeding lines supported by physio-biochemical parameters

Carrot is one of the nutritious vegetable crops sensitive to drought stress resulting in loss of quality and yield. There are a lot of studies on detailed molecular mechanisms of drought stress response of main crops; however, very little information available on vegetables, including carrots. Hence, in this study, we investigated root transcriptome profiles from the meristematic region of two contrasting purple carrot (B7262A, drought tolerant; P1129, drought sensitive) lines under varying stress levels (85% and 70%) by using RNA-Seq technique. The morpho-physiological and biochemical response of B7262A line exhibited tolerance behavior to both DS (85% and 70%). RNA-Seq analysis revealed that 15,839 genes were expressed commonly in both carrot lines. The carrot line B7262A showed regulation of 514 genes in response to 85% DS, whereas P1129 showed differential regulation of 622 genes under 70% DS. The B7262A carrot line showed higher upregulation of transcripts that suggested its resilient behavior contrary to P1129 line. Furthermore, validation of transcript gene by qRT-PCR also confirmed the RNA-Seq analysis resulting in elevated expression levels of MYB48 transcription factor, MAPK mitogen-activated protein kinase ANP1, GER geraniol 8-hydroxylase, ABA ABA-induced in somatic embryo 3, FBOX putative F-box protein, FRO ferric reduction oxidase, and PDR probable disease resistance protein. Current study provided unprecedented insights of purple carrot lines that can be potentially exploited for the screening and development of resilient carrot.

Drought Stress Induces Morpho-Physiological and Proteome Changes of Pandanus amaryllifolius

Drought is one of the significant threats to the agricultural sector. However, there is limited knowledge on plant response to drought stress and post-drought recovery. Pandanus amaryllifolius, a moderate drought-tolerant plant, is well-known for its ability to survive in low-level soil moisture conditions. Understanding the molecular regulation of drought stress signaling in this plant could help guide the rational design of crop plants to counter this environmental challenge. This study aimed to determine the morpho-physiological, biochemical, and protein changes of P. amaryllifolius in response to drought stress and during recovery. Drought significantly reduced the leaf relative water content and chlorophyll content of P. amaryllifolius. In contrast, relative electrolyte leakage, proline and malondialdehyde contents, and the activities of antioxidant enzymes in the drought-treated and recovered samples were relatively higher than the well-watered sample. The protein changes between drought-stressed, well-watered, and recovered plants were evaluated using tandem mass tags (TMT)-based quantitative proteomics. Of the 1415 differentially abundant proteins, 74 were significantly altered. The majority of proteins differing between them were related to carbon metabolism, photosynthesis, stress response, and antioxidant activity. This is the first study that reports the protein changes in response to drought stress in Pandanus. The data generated provide an insight into the drought-responsive mechanisms in P. amaryllifolius.

Differential protein abundance of vetiver grass in response to acid mine drainage

Acid mine drainage (AMD) is an acidic and metalliferous discharge that imposes oxidative stress on living things through bioaccumulation and physical exposure. The abandoned Tab-Simco mining site of Southern Illinois generates highly acidic AMD with elevated sulfate (SO₄ ^2- ) and various metals. Vetiver grass (Chrysopogon zizanioides) is effective for the remediation of Tab-Simco AMD at both mesocosm and microcosm levels over extended periods. In this study, we conducted a proteomic investigation of vetiver shoots under short and long-term exposure to AMD. Our objective was to decipher the physiological responses of vetiver to the combined abiotic stresses of AMD (metal and low pH). Differential regulation was observed for longer-term (56 days) exposure to AMD, which resulted in 17 upregulated and nine downregulated proteins, whereas shorter-term (7 days) exposure led to 14 upregulated and 14 downregulated proteins. There were significant changes to photosynthesis, including upregulation of electron transport chain proteins for light-dependent reactions after 56 days, whereas differential regulation of enzymes relating to C₄ carbon fixation was observed after 7 days. Significant changes in amino acid and nitrogen metabolism, including upregulation of ethylene and flavonoid biosynthesis, along with plant response to nitrogen starvation, were observed. Short-term changes also included upregulation of glutathione reductase and methionine sulfoxide reductase, whereas longer-term changes included changes in protein misfolding and ER-associated protein degradation for stress management and acclimation.

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

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

Ectopic expression of an expansin-like B gene from wild Arachis enhances tolerance to both abiotic and biotic stresses

Plant expansins are structural cell wall-loosening proteins implicated in several developmental processes and responses to environmental constraints and pathogen infection. To date, there is limited information about the biological function of expansins-like B (EXLBs), one of the smallest and less-studied subfamilies of plant expansins. In the present study, we conducted a functional analysis of the wild Arachis AdEXLB8 gene in transgenic tobacco (Nicotiana tabacum) plants to clarify its putative role in mediating defense responses to abiotic and biotic stresses. First, its cell wall localization was confirmed in plants expressing an AdEXLB8:eGFP fusion protein, while nanomechanical assays indicated cell wall reorganization and reassembly due to AdEXLB8 overexpression without compromising the phenotype. We further demonstrated that AdEXLB8 increased tolerance not only to isolated abiotic (drought) and biotic (Sclerotinia sclerotiorum and Meloidogyne incognita) stresses but also to their combination. The jasmonate and abscisic acid signaling pathways were clearly favored in transgenic plants, showing an activated antioxidative defense system. In addition to modifications in the biomechanical properties of the cell wall, we propose that AdEXLB8 overexpression interferes with phytohormone dynamics leading to a defense primed state, which culminates in plant defense responses against isolated and combined abiotic and biotic stresses.

Defining the combined stress response in wild Arachis

Nematodes and drought are major constraints in tropical agriculture and often occur simultaneously. Plant responses to these stresses are complex and require crosstalk between biotic and abiotic signaling pathways. In this study, we explored the transcriptome data of wild Arachis species subjected to drought (A-metaDEG) and the root-knot nematode Meloidogyne arenaria (B-metaDEG) via meta-analysis, to identify core-stress responsive genes to each individual and concurrent stresses in these species. Transcriptome analysis of a nematode/drought bioassay (cross-stress) showed that the set of stress responsive DEGs to concurrent stress is distinct from those resulting from overlapping A- and B-metaDEGs, indicating a specialized and unique response to combined stresses in wild Arachis. Whilst individual biotic and abiotic stresses elicit hormone-responsive genes, most notably in the jasmonic and abscisic acid pathways, combined stresses seem to trigger mainly the ethylene hormone pathway. The overexpression of a cross-stress tolerance candidate gene identified here, an endochitinase-encoding gene (AsECHI) from Arachis stenosperma, reduced up to 30% of M. incognita infection and increased post-drought recovery in Arabidopsis plants submitted to both stresses. The elucidation of the network of cross-stress responsive genes in Arachis contributes to better understanding the complex regulation of biotic and abiotic responses in plants facilitating more adequate crop breeding for combined stress tolerance.

Comparative proteomic and transcriptomic analysis reveals high pH-induced expression signatures of Chinese shrimp Fenneropenaeus chinensis

pH has a great impact on the distribution, growth, behavior, and physiology in many aquatic animals. The comparison of proteomics between normal and high pH stress samples was successfully achieved using iTRAQ proteomic analysis to screen key response proteins and pathways. After high pH stress, 124 upregulated and 41 downregulated proteins were identified. The higher expression levels of proteins like citrate synthase, glutathione S-transferase, glutathione peroxidase, and cytochrome c oxidase are associated with oxidative stress and mitochondrial dysfunction. The upregulation of glucose-regulated protein 78 indicated that the endoplasmic reticulum stress is induced by high pH stress. There were significant upregulation expressions of V-type H⁺-ATPase, Na⁺, K⁺-ATPase, 14-3-3 protein, as well as ATP-binding cassette transmembrane transporters after high pH exposure, which indicating their important roles in response to high pH stress. The abundance of proteins involved in protein glycosylation, oxidative pentose phosphate pathway, protein export, and glutathione metabolism were found enriched in high pH group than in control group. Quantitative proteomic profiling and integrated analysis with transcriptomic data provide new insights into the mechanisms underlying the molecular response to high pH stress in Fenneropenaeus chinensis.

The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms

Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.

Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses

Raffinose family oligosaccharides (RFOs) are implicated in plant regulatory mechanisms of abiotic stresses tolerance and, despite their antinutritional proprieties in grain legumes, little information is available about the enzymes involved in RFO metabolism in Fabaceae species. In the present study, the systematic survey of legume proteins belonging to five key enzymes involved in the metabolism of RFOs (galactinol synthase, raffinose synthase, stachyose synthase, alpha-galactosidase, and beta-fructofuranosidase) identified 28 coding-genes in Arachis duranensis and 31 in A. ipaënsis. Their phylogenetic relationships, gene structures, protein domains, and chromosome distribution patterns were also determined. Based on the expression profiling of these genes under water deficit treatments, a galactinol synthase candidate gene (AdGolS3) was identified in A. duranensis. Transgenic Arabidopsis plants overexpressing AdGolS3 exhibited increased levels of raffinose and reduced stress symptoms under drought, osmotic, and salt stresses. Metabolite and expression profiling suggested that AdGolS3 overexpression was associated with fewer metabolic perturbations under drought stress, together with better protection against oxidative damage. Overall, this study enabled the identification of a promising GolS candidate gene for metabolic engineering of sugars to improve abiotic stress tolerance in crops, whilst also contributing to the understanding of RFO metabolism in legume species.

Quantitative proteomics analysis of high and low polyphenol expressing recombinant inbred lines (RILs) of peanut (Arachis hypogaea L.)

To facilitate selective breeding of polyphenol-rich peanuts, we looked for mass spectrometry-based proteomic evidence, investigating a subset of recombinant inbred lines (RILs) developed by the Australian peanut breeding program. To do this, we used label-free shotgun proteomics for protein and peptide quantitation, statistically analyzed normalized spectral abundance factors using R-package, as well as assayed important antioxidants. Results revealed statistically significant protein expression changes in 82 proteins classified between high or low polyphenols expressing RILs. Metabolic changes in polyphenol-rich RIL p27-362 point towards increased enzymatic breakdown of sugars and phenylalanine biosynthesis. The study revealed phenylpropanoid pathway overexpression resulting in increased polyphenols biosynthesis. Overexpression of antioxidant enzymes such as catalase, by 73.4 fold was also observed. A strong metabolic correlation exists with the observed phenotypic traits. Peanut RIL p27-362 presents a superior nutritional composition with antioxidant-rich peanut phenotype and could yield commercial profits. Data are available via ProteomeXchange with identifierPXD015493.

Current Perspectives on Introgression Breeding in Food Legumes

Food legumes are important for defeating malnutrition and sustaining agri-food systems globally. Breeding efforts in legume crops have been largely confined to the exploitation of genetic variation available within the primary genepool, resulting in narrow genetic base. Introgression as a breeding scheme has been remarkably successful for an array of inheritance and molecular studies in food legumes. Crop wild relatives (CWRs), landraces, and exotic germplasm offer great potential for introgression of novel variation not only to widen the genetic base of the elite genepool for continuous incremental gains over breeding cycles but also to discover the cryptic genetic variation hitherto unexpressed. CWRs also harbor positive quantitative trait loci (QTLs) for improving agronomic traits. However, for transferring polygenic traits, "specialized population concept" has been advocated for transferring QTLs from CWR into elite backgrounds. Recently, introgression breeding has been successful in developing improved cultivars in chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), peanut (Arachis hypogaea), lentil (Lens culinaris), mungbean (Vigna radiata), urdbean (Vigna mungo), and common bean (Phaseolus vulgaris). Successful examples indicated that the usable genetic variation could be exploited by unleashing new gene recombination and hidden variability even in late filial generations. In mungbean alone, distant hybridization has been deployed to develop seven improved commercial cultivars, whereas in urdbean, three such cultivars have been reported. Similarly, in chickpea, three superior cultivars have been developed from crosses between C. arietinum and Cicer reticulatum. Pigeonpea has benefited the most where different cytoplasmic male sterility genes have been transferred from CWRs, whereas a number of disease-resistant germplasm have also been developed in Phaseolus. As vertical gene transfer has resulted in most of the useful gene introgressions of practical importance in food legumes, the horizontal gene transfer through transgenic technology, somatic hybridization, and, more recently, intragenesis also offer promise. The gains through introgression breeding are significant and underline the need of bringing it in the purview of mainstream breeding while deploying tools and techniques to increase the recombination rate in wide crosses and reduce the linkage drag. The resurgence of interest in introgression breeding needs to be capitalized for development of commercial food legume cultivars.

H2S Regulation of Metabolism in Cucumber in Response to Salt-Stress Through Transcriptome and Proteome Analysis

In a previous study, we found that H₂S alleviates salinity stress in cucumber by maintaining the Na⁺/K⁺ balance and by regulating H₂S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H₂S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H₂S-regulated salt-stress tolerance. In total, 11,761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H₂S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense, and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase, and Peroxidase 2. We present the first global analysis of the mechanism underlying H₂S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.

Proteome Analysis of the Gametophytes of a Western Himalayan Fern Diplazium maximum Reveals Their Adaptive Responses to Changes in Their Micro-Environment

Ferns have survived changing habitats and environmental extremes of different eras, wherein, the exploratory haploid gametophytes are believed to have played a major role. Therefore, the proteome of in vitro grown gametophytes of a temperate Himalayan fern, Diplazium maximum in response to 0 (G0), 1 (G1), and 3% (G3) sucrose was studied. A total of 110 differentially abundant protein spots (DAPs) were obtained. Among these, only 67 could be functionally categorized as unique proteins involved in various metabolic processes. Calcium dependent proteins, receptor like kinases, G proteins, proteins related to hormonal signaling and their interaction with other pathways, and regulatory proteins were recorded indicating the involvement of five different signaling pathways. DAPs involved in the activation of genes and transcription factors of signaling and transduction pathways, transport and ion channels, cell-wall and structural proteins, defense, chaperons, energy metabolism, protein synthesis, modification, and turnover were identified. The gametophytes responded to changes in their micro-environment. There was also significant increase in prothallus biomass and conversion of two-dimensional prothalli into three-dimensional prothallus clumps at 3% sucrose. The three-D clumps had higher photosynthetic surface area and also closer proximity for sexual reproduction and sporophyte formation. Highest accumulation of proline, enhanced scavenging of reactive oxygen species (ROS) and DAPs of mostly, abiotic stress tolerance, secondary metabolite synthesis, and detoxification at 3% sucrose indicated an adaptive response of gametophytes. Protein Protein Interaction network and Principal Component analyses, and qRT-PCR validation of genes encoding 12 proteins of various metabolic processes indicated differential adjustment of gametophytes to different levels of sucrose in the culture medium. Therefore, a hypothetical mechanism was proposed to show that even slight changes in the micro-environment of D. maximum gametophytes triggered multiple mechanisms of adaptation. Many DAPs identified in the study have potential use in crop improvement and metabolic engineering programs, phytoremediation and environmental protection.

iTRAQ-based proteomics reveals key role of γ-aminobutyric acid (GABA) in regulating drought tolerance in perennial creeping bentgrass (Agrostis stolonifera)

γ-Aminobutyric acid (GABA), a non-proteinaceous amino acid, modulates plant growth and stress tolerance. However, the potential role of GABA in regulating key metabolic pathways and stress-defensive proteins against drought in plants has never been explored. Creeping bentgrass (Agrostis stolonifera) plants were pretreated with or without GABA and then subjected to water stress for 8 days in controlled growth chambers (23/19 °C, day/night). Physiological analysis showed that elevated endogenous GABA level via exogenous GABA application significantly mitigated water stress damage to creeping bentgrass, as manifested by increased leaf relative water content, water use efficiency, osmotic adjustment (OA), photochemical efficiency (Fv/Fm), net photosynthetic rate, and reduced oxidative damage. iTRAQ-based proteomics found that enhanced chaperones accumulation, carbohydrates, amino acids, and energy metabolism played important roles in protein protection, OA, energy maintenance, and metabolic balance, which is important adaptive response to drought stress in creeping bentgrass. The GABA further promoted energy production and conversion, antioxidant defense, and DHN3 accumulation that were essential for energy requirement, ROS-scavenging, and the prevention of cell dehydration in leaf during drought stress. In addition, GABA-treated plants maintained significantly higher abundance of dicarboxylate transporter 2.1, ATP-dependent zinc metalloprotease, receptor-like protein kinase HERK1, o-acyltransferase WSD1, omega-6 fatty acid desaturase, and two-component response regulator ORR21 than untreated plants under drought stress. The result provides new evidences that GABA-induced drought tolerance is possibly involved in the improvement of nitrogen recycling, protection of photosystem II, mitigation of drought-depressed cell elongation, wax biosynthesis, fatty acid desaturase, and delaying leaf senescence in creeping bentgrass.