Comparison of proteomic and metabolomic profiles of two contrasting ecotypes of sweetpotato ( Ipomoea batata L.)

Tandem mass tag-based quantitative proteomics and targeted hormone analysis reveal the response to insect herbivory stress in Ginseng (Panax ginseng, L.)

Ginsenosides are the most important secondary metabolites of ginseng. Ginseng has developed certain insect resistance properties during the course of evolutionary environmental adaptation. However, the mechanism underlying the insect resistance of ginseng is poorly understood. To elucidate the insect resistance mechanism of ginseng, we performed stress experiments on ginseng inoculated with black chafer larvae. The contents of ginsenosides in the ginseng roots, stems and leaves were determined at 0, 72, 120 and 168 h after the inoculation of insects. The tandem-mass-tag technology was used to determine the protein phosphorylation sites. Plant hormones were analyzed by multiple reaction monitoring targeted metabolomics. The results showed that ginsenosides present in the stems and leaves were more responsive to insect herbivory treatment than those present in the roots. Through proteomics, we found that the expression of most of the differentially expressed proteins, including GAPC1, GAPC2, and CSD1, was downregulated by insect herbivory treatment, HSP81-3 expression was up-regulated under insect herbivory stress. Regarding plant hormones, abscisic acid (ABA), gibberellic acid, Typhasterol (TY), iopentene adenine (IP), Cytokinin Riboside (czR) and Thiamethasone (tZ) levels were increased by herbivory treatment. With the increase in herbivory treatment time, the levels of trans-Zeatin-riboside (tzR), Isopentenyl adenosine riboside (iPR), and indole-3-acetic acid (IAA) were increased after 168h. The levels of salicylic acid (SA), jasmonates (JA), cis-PODA, and JA-Ile were increased after 120h but decreased thereafter. Under stress conditions, the expression of many antioxidant-related proteins was down-regulated; however, HSP81-3 expression was up-regulated, indicating that the plants exhibited severe oxidative stress. In conclusion, HSP81-3 plays an important role in ABA-dependent regulations involved in response to insect herbivory stress in ginseng. GAPC1 and GAPC2 also participate in the process of anti-herbivory stress response in ginseng.

Wheat TaNACα18 functions as a positive regulator of high-temperature adaptive responses and improves cell defense machinery

Global wheat production amounted to >780 MMT during 2022-2023 whose market size are valued at >$128 billion. Wheat is highly susceptible to high-temperature stress (HTS) throughout the life cycle and its yield declines 5-7% with the rise in each degree of temperature. Previously, we reported an array of HTS-response markers from a resilient wheat cv. Unnat Halna and described their putative role in heat acclimation. To complement our previous results and identify the key determinants of thermotolerance, here we examined the cytoplasmic proteome of a sensitive cv. PBW343. The HTS-triggered metabolite reprograming highlighted how proteostasis defects influence the formation of an integrated stress-adaptive response. The proteomic analysis identified several promising HTS-responsive proteins, including a NACα18 protein, designated TaNACα18, whose role in thermotolerance remains unknown. Dual localization of TaNACα18 suggests its crucial functions in the cytoplasm and nucleus. The homodimerization of TaNACα18 anticipated its function as a transcriptional coactivator. The complementation of TaNACα18 in yeast and overexpression in wheat demonstrated its role in thermotolerance across the kingdom. Altogether, our results suggest that TaNACα18 imparts tolerance through tight regulation of gene expression, cell wall remodeling and activation of cell defense responses.

The impact of heat stress in plant reproduction

The increment in global temperature reduces crop productivity, which in turn threatens food security. Currently, most of our food supply is produced by plants and the human population is estimated to reach 9 billion by 2050. Gaining insights into how plants navigate heat stress in their reproductive phase is essential for effectively overseeing the future of agricultural productivity. The reproductive success of numerous plant species can be jeopardized by just one exceptionally hot day. While the effects of heat stress on seedlings germination and root development have been extensively investigated, studies on reproduction are limited. The intricate processes of gamete development and fertilization unfold within a brief timeframe, largely concealed within the flower. Nonetheless, heat stress is known to have important effects on reproduction. Considering that heat stress typically affects both male and female reproductive structures concurrently, it remains crucial to identify cultivars with thermotolerance. In such cultivars, ovules and pollen can successfully undergo development despite the challenges posed by heat stress, enabling the completion of the fertilization process and resulting in a robust seed yield. Hereby, we review the current understanding of the molecular mechanisms underlying plant resistance to abiotic heat stress, focusing on the reproductive process in the model systems of Arabidopsis and Oryza sativa.

Recent finding on sucrose synthase research: not the only key for starch and cellulose synthesis

Sucrose synthase (SUS), an enzyme that breaks down sucrose, is known to play an important role in the production of UDP-glucose and ADP-glucose. An established and highly debated theory holds that SUS is necessary for providing UDP-glucose and ADP-glucose for the biosynthesis of cellulose and starch, respectively. This article is focused on two recent reports which refuted the long-held theory that SUS is the sole regulator in cellulose and starch synthesis.

Introgression of a novel cold and drought regulatory-protein encoding CORA-like gene, SbCDR, induced osmotic tolerance in transgenic tobacco

A potent cold and drought regulatory-protein encoding gene, SbCDR was cloned from an extreme halophyte Salicornia brachiata. In vitro localisation study, performed with SbCDR::RFP gene-construct revealed that SbCDR is a membrane protein. Overexpression of the SbCDR gene in tobacco plants confirmed tolerance against major environmental constraints such as salinity, drought and cold, as evidenced by improved chlorophyll contents, plant morphology, plant biomass, root length, shoot length and seed germination efficiency. Transgenic lines also exhibited high accumulation of proline, total sugar, reducing sugar, free amino acid and polyphenol, besides the low level of malondialdehyde (MDA) contents. SbCDR transgenic lines showed better relative water contents, membrane stability index and osmotic water potential. Furthermore, higher expression of ROS scavenging genes was observed in transgenic lines under stress. Moreover, microarray analysis revealed that several host genes were upregulated and downregulated under drought and salt stress conditions in SbCDR transgenic line compared with control (WT) plants. The results demonstrated that the overexpression of the halophytic SbCDR gene has intense effects on the abiotic stress tolerance of transgenic tobacco plants. However, the exact mode of action of SbCDR in multiple abiotic stress tolerance of plants is yet to be unveiled. It is believed that the precise role of SbCDR gene will provide additional information to comprehend the abiotic stress tolerance mechanism. Furthermore, it will appear as a promising candidate gene for improving stress tolerance in different crop plants for sustainable agriculture and crop productivity.

CaHSP18.1a, a Small Heat Shock Protein from Pepper (Capsicum annuum L.), Positively Responds to Heat, Drought, and Salt Tolerance

Pepper is a thermophilic crop, shallow-rooted plant that is often severely affected by abiotic stresses such as heat, salt, and drought. The growth and development of pepper is seriously affected by adverse stresses, resulting in decreases in the yield and quality of pepper crops. Small heat shock proteins (s HSPs) play a crucial role in protecting plant cells against various stresses. A previous study in our laboratory showed that the expression level of CaHSP18.1a was highly induced by heat stress, but the function and mechanism of CaHSP18.1a responding to abiotic stresses is not clear. In this study, we first analyzed the expression of CaHSP18.1a in the thermo-sensitive B6 line and thermo-tolerant R9 line and demonstrated that the transcription of CaHSP18.1a was strongly induced by heat stress, salt, and drought stress in both R9 and B6, and that the response is more intense and earlier in the R9 line. In the R9 line, the silencing of CaHSP18.1a decreased resistance to heat, drought, and salt stresses. The silencing of CaHSP18.1a resulted in significant increases in relative electrolyte leakage (REL) and malonaldehyde (MDA) contents, while total chlorophyll content decreased under heat, salt, and drought stresses. Overexpression analyses of CaHSP18.1a in transgenic Arabidopsis further confirmed that CaHSP18.1a functions positively in resistance to heat, drought, and salt stresses. The transgenic Arabidopsis had higherchlorophyll content and activities of superoxide dismutase, catalase, and ascorbate peroxidase than the wild type (WT). However, the relative conductivity and MDA content were decreased in transgenic Arabidopsis compared to the wild type (WT). We further showed that the CaHSP18.1a protein is localized to the cell membrane. These results indicate CaHSP18.1a may act as a positive regulator of responses to abiotic stresses.

Wheat 2-Cys peroxiredoxin plays a dual role in chlorophyll biosynthesis and adaptation to high temperature

The molecular mechanism of high-temperature stress (HTS) response, in plants, has so far been investigated using transcriptomics, while the dynamics of HTS-responsive proteome remain unexplored. We examined the adaptive responses of the resilient wheat cultivar 'Unnat Halna' and dissected the HTS-responsive proteome landscape. This led to the identification of 55 HTS-responsive proteins (HRPs), which are predominantly involved in metabolism and defense pathways. Interestingly, HRPs included a 2-cysteine peroxiredoxin (2CP), designated Ta2CP, presumably involved in stress perception and adaptation. Complementation of Ta2CP in yeast and heterologous expression in Arabidopsis demonstrated its role in thermotolerance. Both Ta2CP silencing and overexpression inferred the involvement of Ta2CP in plant growth and chlorophyll biosynthesis. We demonstrated that Ta2CP interacts with protochlorophyllide reductase b, TaPORB. Reduced TaPORB expression was found in Ta2cp-silenced plants, while upregulation was observed in Ta2CP-overexpressed plants. Furthermore, the downregulation of Ta2CP in Taporb-silenced plants and reduction of protochlorophyllide in Ta2cp-silenced plants suggested the key role of Ta2CP in chlorophyll metabolism. Additionally, the transcript levels of AGPase1 and starch were increased in Ta2cp-silenced plants. More significantly, HTS-treated Ta2cp-silenced plants showed adaptive responses despite increased reactive oxygen species and peroxide concentrations, which might help in rapid induction of high-temperature acclimation.

Non-target metabolomics revealed the differences between Rh. tanguticum plants growing under canopy and open habitats

BACKGROUND

Rheum tanguticum (Rh. tanguticum) is an important traditional Chinese medicine plant, "Dahuang", which contains productive metabolites and occupies wide habitats on the Qinghai-Tibet plateau. Plants occupying wide habitats usually vary in phenotypes such as in morphology and metabolism, thereby developing into different ecotypes. Under canopy and open habitats are a pair of dissimilar habitats which possess Rh. tanguticum plants. However, few studies have focused on the effect of habitats on Rh. tanguticum growth, particularly combining morphological and metabolic changes. This study focused on Rh. tanguticum plants growing in under canopy and open habitats where morphology and metabolism changes were quantified using non-target metabolism methods.

RESULTS

The obtained results indicated that the two dissimilar habitats led to Rh. tanguticum developing into two distinct ecotypes where the morphology and metabolism were simultaneously changed. Under canopy habitats bred morphologically smaller Rh. tanguticum plants which had a higher level of metabolites (22 out of 31) which included five flavonoids, four isoflavonoids, and three anthracenes. On the other hand, the open habitats produced morphologically larger Rh. tanguticum plants having a higher level of metabolites (9 out of 31) including four flavonoids. 6 of the 31 metabolites were predicted to have effect targets, include 4 represent for under canopy habitats and 2 for open habitats. Totally, 208 targets were connected, among which 42 were communal targets for both under canopy and open habitats represent compounds, and 100 and 66 were unique targets for under canopy superior compounds and open habitats superior compounds, respectively. In addition, aloe-emodin, emodin, chrysophanol, physcion, sennoside A and sennoside B were all more accumulated in under canopy habitats, and among which aloe-emodin, emodin, chrysophanol and physcion were significantly higher in under canopy habitats.

CONCLUSIONS

This study determined that Rh. tanguticum growing in under canopy and in open habitats developed into two distinct ecotypes with morphological and metabolic differences. Results of network pharmacology study has indicated that "Dahuang" coming from different habitats, such as under canopy and open habitats, are different in effect targets and thus may have different medicinal use. According to target metabolomics, under canopy habitats may grow better "Dahuang".

Comparative proteomic analysis of the sweetpotato provides insights into response mechanisms to Fusarium oxysporum f. sp. batatas

The Fusarium wilt disease caused by Fusarium oxysporum f. sp. batatas (Fob) is one of the devastating diseases of sweetpotato. However, the molecular mechanisms of sweetpotato response to Fob is poorly understood. In the present study, comparative quantitative proteomic analysis was conducted to investigate the defense mechanisms involved. Two sweetpotato cultivars with differential Fob infection responses were inoculated with Fob spore suspensions and quantitatively analyzed by Tandem Mass Tags (TMT). 2267 proteins were identified and 1897 of them were quantified. There were 817 proteins with quantitative ratios of 1.2-fold change between Fob-inoculated and mock-treated samples. Further, nine differentially expressed proteins were validated by Parallel Reaction Monitoring (PRM). According to Gene Ontology (GO) annotation information, the proteins functioned in molecular metabolism, cellular component formation, and biological processes. Interestingly, the results showed that sweetpotato resistant response to Fob infection included many proteins associated with signaling transduction, plant resistance, chitinase and subtilisin-like protease. The functions and possible roles of those proteins were discussed. The results provides first insight into molecular mechanisms involved in sweetpotato defense responses to Fob.

Proteomic and metabolic profile analysis of low-temperature storage responses in Ipomoea batata Lam. tuberous roots

BACKGROUND

Sweetpotato (Ipomoea batatas L.) is one of the seven major food crops grown worldwide. Cold stress often can cause protein expression pattern and substance contents variations for tuberous roots of sweetpotato during low-temperature storage. Recently, we developed proteometabolic profiles of the fresh sweetpotatoes (cv. Xinxiang) in an attempt to discern the cold stress-responsive mechanism of tuberous root crops during post-harvest storage.

RESULTS

For roots stored under 4 °C condition, the CI index, REC and MDA content in roots were significantly higher than them at control temperature (13 °C). The activities of SOD, CAT, APX, O₂^.- producing rate, proline and especially soluble sugar contents were also significantly increased. Most of the differentially expressed proteins (DEPs) were implicated in pathways related to metabolic pathway, especially phenylpropanoids and followed by starch and sucrose metabolism. L-ascorbate peroxidase 3 and catalase were down-regulated during low temperature storage. α-amylase, sucrose synthase and fructokinase were significantly up-regulated in starch and sucrose metabolism, while β-glucosidase, glucose-1-phosphate adenylyl-transferase and starch synthase were opposite. Furthermore, metabolome profiling revealed that glucosinolate biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis as well as protein digestion and absorption played a leading role in metabolic pathways of roots. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.

CONCLUSIONS

Our proteomic and metabolic profile analysis of sweetpotatoes stored at low temperature reveal that the antioxidant enzymes activities, proline and especially soluble sugar content were significantly increased. Most of the DEPs were implicated in phenylpropanoids and followed by starch and sucrose metabolism. The discrepancy between proteomic (L-ascorbate peroxidase 3 and catalase) and biochemical (CAT/APX activity) data may be explained by higher H₂O₂ levels and increased ascorbate redox states, which enhanced the CAT/APX activity indirectly. Glucosinolate biosynthesis played a leading role in metabolic pathways. Leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.

A Highly Efficient Agrobacterium-Mediated Method for Transient Gene Expression and Functional Studies in Multiple Plant Species

Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.

Crop Enhancement of Cucumber Plants under Heat Stress by Shungite Carbon

Heat stress negatively impacts plant growth and yield. The effects of carbon materials on plants in response to abiotic stress and antioxidant activity are poorly understood. In this study, we propose a new method for improving heat tolerance in cucumber (Cucumis sativus L.) using a natural carbon material, shungite, which can be easily mixed into any soil. We analyzed the phenotype and physiological changes in cucumber plants maintained at 35 °C or 40 °C for 1 week. Our results show that shungite-treated cucumber plants had a healthier phenotype, exhibiting dark green leaves, compared to the plants in the control soil group. Furthermore, in the shungite-treated plants, the monodehydroascorbate content (a marker of oxidative damage) of the leaf was 34% lower than that in the control group. In addition, scavengers against reactive oxygen species, such as superoxide dismutase, catalase, and peroxidase were significantly upregulated. These results indicate that the successive pre-treatment of soil with a low-cost natural carbon material can improve the tolerance of cucumber plants to heat stress, as well as improve the corresponding antioxidant activity.

Dehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses

Chloroplast, the energy organelle unique to photosynthetic eukaryotes, executes several crucial functions including photosynthesis. While chloroplast development and function are controlled by the nucleus, environmental stress modulated alterations perceived by the chloroplasts are communicated to the nucleus via retrograde signaling. Notably, coordination of chloroplast and nuclear gene expression is synchronized by anterograde and retrograde signaling. The chloroplast proteome holds significance for stress responses and adaptation. We unraveled dehydration-induced alterations in the chloroplast proteome of a grain legume, chickpea and identified an array of dehydration-responsive proteins (DRPs) primarily involved in photosynthesis, carbohydrate metabolism and stress response. Notably, 12 DRPs were encoded by chloroplast genome, while the rest were nuclear-encoded. We observed a coordinated expression of different multi-subunit protein complexes viz., RuBisCo, photosystem II and cytochrome b6f, encoded by both chloroplast and nuclear genome. Comparison with previously reported stress-responsive chloroplast proteomes showed unique and overlapping components. Transcript abundance of several previously reported markers of retrograde signaling revealed relay of dehydration-elicited signaling events between chloroplasts and nucleus. Additionally, dehydration-triggered metabolic adjustments demonstrated alterations in carbohydrate and amino acid metabolism. This study offers a panoramic catalogue of dehydration-responsive signatures of chloroplast proteome and associated retrograde signaling events, and cellular metabolic reprograming.

Physiological plasticity to high temperature stress in chickpea: Adaptive responses and variable tolerance

High temperature stress (HTS) is one of the most crucial factors that limits plant growth and development, and reduces crop yields worldwide. Cool-season crops, particularly the legumes, are severely affected by increasing ambient temperature associated with global climate change. We characterized the HTS-induced modulations of morpho-physicochemical traits and gene expression of several chickpea genotypes and the metabolic profile of the tolerant cultivar. Higher water use efficiency and photosynthetic capacity, minimal membrane lipid peroxidation in conjunction with increased abundance of osmolytes and secondary metabolites depicted thermotolerance of ICC 1205. The adaptive responses were accompanied by high transcript abundance of heat shock proteins and antioxidant enzymes. To integrate stress-responsive signalling and metabolic networks, the HTS-induced physicochemical analysis was further extended to metabolite profiling of the thermotolerant cultivar. The screening of the metabolome landscape led to the identification of 49 HTS-responsive metabolites that include polycarboxylic acid, sugar acids, sugar alcohols and amino acids which might confer thermotolerance in chickpea. The present study, to our knowledge, is the most comprehensive of its kind in dissecting cultivar-specific differential adaptive responses to HTS in chickpea, which might potentiate the identification of genetic traits extendible to improvement of thermotolerance of crops.

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

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

Identification and Analysis of OVATE Family Members from Genome of the Early Land Plants Provide Insights into Evolutionary History of OFP Family and Function

Mosses, liverworts, hornworts and lycophytes represent transition stages between the aquatic to terrestrial/land plants. Several morphological and adaptive novelties driven by genomic components including emergence and expansion of new or existing gene families have played a critical role during and after the transition, and contributed towards successful colonization of terrestrial ecosystems. It is crucial to decipher the evolutionary transitions and natural selection on the gene structure and function to understand the emergence of phenotypic and adaptive diversity. Plants at the "transition zone", between aquatic and terrestrial ecosystem, are also the most vulnerable because of climate change and may contain clues for successful mitigation of the challenges of climate change. Identification and comparative analyses of such genetic elements and gene families are few in mosses, liverworts, hornworts and lycophytes. Ovate family proteins (OFPs) are plant-specific transcriptional repressors and are acknowledged for their roles in important growth and developmental processes in land plants, and information about the functional aspects of OFPs in early land plants is fragmentary. As a first step towards addressing this gap, a comprehensive in silico analysis was carried out utilizing publicly available genome sequences of Marchantia polymorpha (Mp), Physcomitrella patens (Pp), Selaginella moellendorffii (Sm) and Sphagnum fallax (Sf). Our analysis led to the identification of 4 MpOFPs, 19 PpOFPs, 6 SmOFPs and 3 SfOFPs. Cross-genera analysis revealed a drastic change in the structure and physiochemical properties in OFPs suggesting functional diversification and genomic plasticity during the evolutionary course. Knowledge gained from this comparative analysis will form the framework towards deciphering and dissection of their developmental and adaptive role/s in early land plants and could provide insights into evolutionary strategies adapted by land plants.

Ectopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato

Storage proteins in plants, because of high nutrient value, have been a subject of intensive investigation. These proteins are synthesized de novo in the cytoplasm and transported to the storage organelles where they serve as reservoir of energy and supplement of nitrogen during rapid growth and development. Sweetpotato is the seventh most important food crop worldwide, and has a significant contribution to the source of nutrition, albeit with low protein content. To determine the behaviour of seed storage proteins in non-native system, a seed albumin, AmA1, was overexpressed in sweetpotato with an additional aim of improving nutritional quality of tuber proteins. Introduction of AmA1 imparted an increase in protein and amino acid contents as well as the phytophenols. The proteometabolomics analysis revealed a rebalancing of the proteome, with no significant effects on the global metabolome profile of the transgenic tubers. Additionally, the slower degradation of starch and cellulose in transgenic tubers, led to increased post-harvest durability. Present study provides a new insight into the role of a seed storage protein in the modulation of photoassimilate movement and nutrient acquisition.