System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance

Metabolome profiling of cacao (Theobroma cacao L.) callus under drought stress conditions induced by polyethylene glycol (PEG) as osmoticant

INTRODUCTION

The cacao tree (Theobroma cacao), a perennial crop that serves as a source of cacao beans, can suffer from drastic climate changes such as irregular rainfall and shorter rainy seasons. The search for hybrids which are capable of producing specific metabolites favoring adaptation in new climatic conditions is a challenge in cacao farming.

OBJECTIVES

We aimed to (1) analyze the metabolic changes in calli of three cacao genotypes during water deficit induced by incubation with polyethylene glycol and (2) assess their response to water deficit stress with regard to somatic embryo differentiation.

METHODS

Metabolic profiling was carried out using 1H-NMR spectroscopy and multivariate data analysis was applied to crude extracts of calli grown in non-stress or water deficit stress conditions.

RESULTS

Water deficit stress influences the capacity of calli to produce embryos. The SCA12 genotype exhibited the best conversion capacity under severe conditions and was considered as tolerant to drought, followed by the SCA6 genotype (mid-tolerant) and the MA12 genotype (sensitive). Fifty-four metabolites were identified in the three cacao genotypes and discriminant metabolites were identified. Metabolites involved in water stress tolerance such as fructose, trans-aconitic acid, leucine, and hydroxybenzene derivatives were observed in SCA12, the tolerant genotype.

CONCLUSION

These results demonstrate the utility of 1H-NMR metabolomics as an essential tool for the analysis of the drought tolerance characteristics of T. cacao.

Metabolomic responses to the mechanical wounding of Catharanthus roseus' upper leaves

Purpose

Plant secondary metabolites are used to treat various human diseases. However, it is difficult to produce a large number of specific metabolites, which largely limits their medicinal applications. Many methods, such as drought and nutrient application, have been used to induce the biosynthetic production of secondary metabolites. Among these secondary metabolite-inducing methods, mechanical wounding maintains the composition of secondary metabolites with little potential risk. However, the effects of mechanical stress have not been fully investigated, and thus this method remains widely unused.

Methods

In this study, we used metabolomics to investigate the metabolites produced in the upper and lower leaves of Catharanthus roseus in response to mechanical wounding.

Results

In the upper leaves, 13 different secondary metabolites (three terpenoid indole alkaloids and 10 phenolic compounds) were screened using an orthogonal partial least squares discriminant analysis (OPLS-DA) score plot. The mechanical wounding of different plant parts affected the production of secondary metabolites. Specifically, when lower leaves were mechanically wounded, the upper leaves became a strong source of resources. Conversely, when upper leaves were injured, the upper leaves themselves became a resource sink. Changes in the source-sink relationship reflected a new balance between resource tradeoff and the upregulation or downregulation of certain metabolic pathways.

Conclusion

Our findings suggest that mechanical wounding to specific plant parts is a novel approach to increase the biosynthetic production of specific secondary metabolites. These results indicate the need for a reevaluation of production practices for secondary metabolites from select commercial plants.

Analysis of fruit ripening in Theobroma cacao pod husk based on untargeted metabolomics

The pod husk of Theobroma cacao (CPH) plays an important agronomical role, as its appearance is used as indicator of ripening, guiding the farmers in the harvest process. Cacao harvesting is not a standardized practice because farmers harvest between six up to eight months from flowering, guided by pod's color and shape. The mixture of cacao beans from different ripening stages (RS), negatively affecting the quality and price of grain. A way to help the farmers in the harvest standardization could be through the use of chemical markers and visual indicators of CPH ripening. This study analyses CPH's metabolic distribution of two cacao clones, ICS95 and CCN51 at six, seven, and eight months of ripening. Untargeted metabolomics was done using HPLC-MS/MS for biomarker discovery and association to cacao ripening. The results indicated a strong metabolic differentiation of the sixth month with the rest of the months independent of the variety. Also, metabolic differences were found between cacao clones for the seventh and eighth month. We annotated five potential biochemical markers including 3-caffeoylpelargodinin 5-glucoside, indoleacetaldehyde, procyanidin A dimer, procyanidin C1, and kaempferol. We further looked for correlation between patterns of progression of our markers against quantitative indicators of CPH appearance and texture, at the same ripening stages. We also performed a functional analysis and three possible metabolic pathways: flavone and flavonol biosynthesis, flavonoid biosynthesis, and tryptophan metabolism were identified associated with stress sensing, plant development and defense respectively. We found significant and positive correlations between green color density and all metabolites. For texture, the correlations were significantly negative with all metabolites. Our results suggest that about the sixth month is appropriate for harvesting cacao in the region of Caldas, Colombia in order to avoid all the metabolic variations occurring at later stages of ripening which impact the cacao bean quality. Therefore, studying the cacao ripening process can help in the estimation of the best harvest time and contribute to the standardization of harvest practices.

Natural variance at the interface of plant primary and specialized metabolism

Plants produce a large number of diverse metabolites when they grow and develop as well as when they respond to the changing external environment. These are an important source of human nutrition and medicine. In this review we emphasized the major issues of the primary-specialized metabolic interface in plant metabolism, described the metabolic flow from primary to specialized metabolism, and the conservation and diversity of primary and specialized metabolites. At the same time, we summarized the regulatory mechanisms underpinning the dynamic balance primary and specialized metabolism based on multi-omics integration analysis, as well as the natural variation of primary and specialized metabolic pathways and genes during the plant evolution. Moreover, the discovery and optimization of the synthesis and regulation elements of various primary to specialized metabolic flows provide the possibility for precise modification and personalized customization of metabolic pathways, which will greatly promote the development of synthetic biology.

Unique metabolite profiles of Indonesian cocoa beans from different origins and their correlation with temperature

Chocolate flavors vary depending on the origin of the cocoa beans used. Differences in soil, microorganisms, and environmental factors contribute to the formation of flavor precursors in cocoa beans. During cocoa bean fermentation, environmental temperature has been shown to alter metabolite concentrations. However, the correlation between the metabolite profile of cocoa beans and the temperature of their region of origin has not been fully defined. In this study, the metabolite profiles of Indonesian cocoa beans of various origins were evaluated using gas chromatography/mass spectrometry-based analysis, and were found to differ depending on the origin of the bean. Subsequently, the correlation between metabolite profile and environmental temperature of the origin was assessed using orthogonal projection to latent structure regression (OPLS-R) analysis. The analysis revealed that seven metabolites were associated with temperature: γ-aminobutyric acid (GABA), ethanolamine, glycerol, isocitric acid + citric acid, succinic acid, malic acid, and saccharic acid. The findings of this study will be valuable to chocolate industries for the production of single-origin chocolates.

Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants

Comprehensive metabolomic investigations provide a large set of stress-related metabolites and metabolic pathways, advancing crops under heat stress conditions. Metabolomics-assisted breeding, including mQTL and mGWAS boosted our understanding of improving numerous quantitative traits under heat stress. During the past decade, metabolomics has emerged as a fascinating scientific field that includes documentation, evaluation of metabolites, and chemical methods for cell monitoring programs in numerous plant species. A comprehensive metabolome profiling allowed the investigator to handle the comprehensive data groups of metabolites and the equivalent metabolic pathways in an extraordinary manner. Metabolomics, together with transcriptomics, plays an influential role in discovering connections between stress and genes/metabolite, phenotyping, and biomarkers documentation. Further, it helps to decode several metabolic systems connected with heat stress (HS) tolerance in plants. Heat stress is a critical environmental factor that is globally affecting the growth and productivity of plants. Thus, there is an urgent need to exploit modern breeding and biotechnological tools like metabolomics to develop cultivars with improved HS tolerance. Several studies have reported that amino acids, carbohydrates, nitrogen metabolisms, etc. and metabolites involved in the biosynthesis and catalyzing actions play a game-changing role in HS response and help plants to cope with the HS. The use of metabolomics-assisted breeding (MAB) allows a well-organized transmission of higher yield and HS tolerance at the metabolome level with specific properties. Progressive metabolomics systematic techniques have accelerated metabolic profiling. Nonetheless, continuous developments in bioinformatics, statistical tools, and databases are allowing us to produce ever-progressing, comprehensive insights into the biochemical configuration of plants and by what means this is inclined by genetic and environmental cues. Currently, assimilating metabolomics with post-genomic platforms has allowed a significant division of genetic-phenotypic connotation in several plant species. This review highlights the potential of a state-of-the-art plant metabolomics approach for the improvement of crops under HS. The development of plants with specific properties using integrated omics (metabolomics and transcriptomics) and MAB can provide new directions for future research to enhance HS tolerance in plants to achieve a goal of "zero hunger".

Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata

Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach

Pulses are one of the most important categories of food plants, and Pea (Pisum sativum L.) as a member of pulses is considered a key crop for food and feed and sustainable agriculture. Integrative multi-omics and microsymbiont impact studies on the plant's immune system are important steps toward more productive and tolerant food plants and thus will help to find solutions against food poverty. Didymella pinodes is a main fungal pathogen of pea plants. Arbuscular mycorrhizal fungi (AMF) promote plant growth and alleviate various stresses. However, it remained unclear as to how the AMF effect on seed metabolism and how this influences resistance against the pathogen. This study assesses the AMF impacts on yield components and seed quality upon D. pinodes infection on two different P. sativum cultivars, susceptible versus tolerant, grown in pots through phenotypic and seed molecular analyses. We found that AMF symbiosis affects the majority of all tested yield components as well as a reduction of disease severity in both cultivars. Seeds of mycorrhizal pea plants showed strong responses of secondary metabolites with nutritional, medicinal, and pharmaceutical attributes, also involved in pathogen response. This is further supported by proteomic data, functionally determining those primary and secondary metabolic pathways, involved in pathogen response and induced upon AMF-colonization. The data also revealed cultivar specific effects of AMF symbiosis that increase understanding of genotype related differences. Additionally, a suite of proteins and secondary metabolites are presented, induced in seeds of P. sativum upon AMF-colonization and pathogen attack, and possibly involved in induced systemic resistance against D. pinodes, useful for modern breeding strategies implementing microsymbionts toward increased pathogen resistance.

Analysis of Antioxidant Activity and Flavonoids Metabolites in Peel and Flesh of Red-Fleshed Apple Varieties

In this research, we compared the phenotypical characters, total anthocyanins content, total phenols content, and antioxidant activity of red-fleshed apple cultivars ‘XJ4’, ‘QN-5’, ‘DH’ and ‘HX1’ at three fruit developmental stages. A further flavonoids metabolites study was conducted in ‘XJ4’ and ‘DH’. We found broader variation of total anthocyanins content in the peel of the four cultivars, which might result in larger differences of free radicals scavenging rate. The most significant difference in fruit phenotype, anthocyanins content, and DPPH scavenging rate was observed between ‘XJ4’ and ‘DH’ at mature stage. Therefore, the flavonoids metabolites of ‘XJ4’ and ‘DH’ at mature stage were compared to unveil the details of anthocyanins compounds. The unique compounds pelargonidin 3-O-β-d-glucoside and cyanidin-3-O-malonylhexoside were detected only in peel and flesh of ‘XJ4’ but not in ‘DH’, which might contribute to the purple peel and dark-red flesh color of ‘XJ4’. Significantly decreased upstream metabolites in the early biosynthetic genes regulated domain were found only in ‘XJ4’ peel but not in the flesh. This might explain why the anthocyanins content in ‘XJ4’ peel was decreased largely at the mature stage. Taken together, our findings will give some insight into the metabolites study in flavonoid biosynthetic pathway of red-fleshed apple.

Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds

In contrast to desiccation-tolerant 'orthodox' seeds, so-called 'intermediate' seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds, but they show a considerable variability in seed desiccation tolerance (DT), which may help to decipher the molecular basis of seed DT in plants. We performed a comparative transcriptome analysis of developing seeds in three coffee species with contrasting desiccation tolerance. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were up-regulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, we detected up-regulation of numerous genes involved in the metabolism, transport, and perception of auxin in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT are better prepared to cease respiration and avoid oxidative stresses.

The pathogen Moniliophthora perniciosa promotes differential proteomic modulation of cacao genotypes with contrasting resistance to witches´ broom disease

BACKGROUND

Witches' broom disease (WBD) of cacao (Theobroma cacao L.), caused by Moniliophthora perniciosa, is the most important limiting factor for the cacao production in Brazil. Hence, the development of cacao genotypes with durable resistance is the key challenge for control the disease. Proteomic methods are often used to study the interactions between hosts and pathogens, therefore helping classical plant breeding projects on the development of resistant genotypes. The present study compared the proteomic alterations between two cacao genotypes standard for WBD resistance and susceptibility, in response to M. perniciosa infection at 72 h and 45 days post-inoculation; respectively the very early stages of the biotrophic and necrotrophic stages of the cacao x M. perniciosa interaction.

RESULTS

A total of 554 proteins were identified, being 246 in the susceptible Catongo and 308 in the resistant TSH1188 genotypes. The identified proteins were involved mainly in metabolism, energy, defense and oxidative stress. The resistant genotype showed more expressed proteins with more variability associated with stress and defense, while the susceptible genotype exhibited more repressed proteins. Among these proteins, stand out pathogenesis related proteins (PRs), oxidative stress regulation related proteins, and trypsin inhibitors. Interaction networks were predicted, and a complex protein-protein interaction was observed. Some proteins showed a high number of interactions, suggesting that those proteins may function as cross-talkers between these biological functions.

CONCLUSIONS

We present the first study reporting the proteomic alterations of resistant and susceptible genotypes in the T. cacao x M. perniciosa pathosystem. The important altered proteins identified in the present study are related to key biologic functions in resistance, such as oxidative stress, especially in the resistant genotype TSH1188, that showed a strong mechanism of detoxification. Also, the positive regulation of defense and stress proteins were more evident in this genotype. Proteins with significant roles against fungal plant pathogens, such as chitinases, trypsin inhibitors and PR 5 were also identified, and they may be good resistance markers. Finally, important biological functions, such as stress and defense, photosynthesis, oxidative stress and carbohydrate metabolism were differentially impacted with M. perniciosa infection in each genotype.

Untargeted Metabolite Profiling for Screening Bioactive Compounds in Digestate of Manure under Anaerobic Digestion

Untargeted metabolite profiling was performed on chicken manure (CHM), swine manure (SM), cattle manure (CM), and their respective digestate by XCMS coupled with MetaboAnalyst programs. Through global chemical profiling, the chemical characteristics of different digestates and types of manure were displayed during the anaerobic digestion (AD) process. As the feed for AD, CM had less easily-degradable organics, SM contained the least O-alkyls and anomerics of carbohydrates, and CHM exhibited relatively lower bio-stability. The derived metabolite pathways of different manure during the AD process were identified by MetaboAnalyst. Twelve, 8, and 5 metabolic pathways were affected by the AD process in CHM, SM, and CM, respectively. Furthermore, bioactive compounds of digestate were detected, such as amino acids (L-arginine, L-ornithine, L-cysteine, and L-aspartate), hormones (L-adrenaline, 19-hydroxy androstenedione, and estrone), alkaloids (tryptamine and N-methyltyramine), and vitamin B5, in different types of manure and their digestates. The combination of XCMS and MetaboAnalyst programs can be an effective strategy for metabolite profiling of manure and its anaerobic digestate under different situations.

Differences in flavonoid pathway metabolites and transcripts affect yellow petal colouration in the aquatic plant Nelumbo nucifera

BACKGROUND

The Asia lotus (Nelumbo nucifera Gaertn.) is an ornamental aquatic plant with high economic value. Flower colour is an important ornamental trait, with much of N. nucifera breeding focusing on its yellow flowers. To explore the yellow flower colouration mechanism in N. nucifera, we analysed its pigment constituents and content, as well as gene expression in the flavonoid pathway, in two N. nucifera cultivars.

RESULTS

We performed metabolomic and gene expression analyses in two N. nucifera cultivars with yellow and white flowers, Molinqiuse (MLQS) and Yeguangbei (YGB), respectively, at five stages of flower colouration. Based on phenotypic observation and metabolite analyses, the later stages of flower colouration (S3-S5) were determined to be key periods for differences between MLQS and YGB, with dihydroflavonols and flavonols differing significantly between cultivars. Dihydroquercetin, dihydrokaempferol, and isorhamnetin were significantly higher in MLQS than in YGB, whereas kaempferol was significantly higher in YGB. Most of the key homologous structural genes in the flavonoid pathway were significantly more active in MLQS than in YGB at stages S1-S4.

CONCLUSION

In this study, we performed the first analyses of primary and secondary N. nucifera metabolites during flower colouration, and found that isorhamnetin and kaempferol shunting resulted in petal colour differences between MLQS and YGB. Based on our data integration analyses of key enzyme expression in the putative flavonoid pathways of the two N. nucifera cultivars, NnFLS gene substrate specificity and differential expression of NnOMTs may be related to petal colour differences between MLQS and YGB. These results will contribute to determining the mechanism of yellow flower colouration in N. nucifera, and will improve yellow petal colour breeding in lotus species.

Metabolomics in Plant Stress Physiology

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Cocoa Bean Proteins-Characterization, Changes and Modifications due to Ripening and Post-Harvest Processing

The protein fractions of cocoa have been implicated influencing both the bioactive potential and sensory properties of cocoa and cocoa products. The objective of the present review is to show the impact of different stages of cultivation and processing with regard to the changes induced in the protein fractions. Special focus has been laid on the major seed storage proteins throughout the different stages of processing. The study starts with classical introduction of the extraction and the characterization methods used, while addressing classification approaches of cocoa proteins evolved during the timeline. The changes in protein composition during ripening and maturation of cocoa seeds, together with the possible modifications during the post-harvest processing (fermentation, drying, and roasting), have been documented. Finally, the bioactive potential arising directly or indirectly from cocoa proteins has been elucidated. The “state of the art” suggests that exploration of other potentially bioactive components in cocoa needs to be undertaken, while considering the complexity of reaction products occurring during the roasting phase of the post-harvest processing. Finally, the utilization of partially processed cocoa beans (e.g., fermented, conciliatory thermal treatment) can be recommended, providing a large reservoir of bioactive potentials arising from the protein components that could be instrumented in functionalizing foods.

Metabolite Storage in Theobroma cacao L. Seed: Cyto-Histological and Phytochemical Analyses

Cocoa (Theobroma cacao L.), an economically important tropical-fruit crop as source of chocolate, has recently gained a considerable attention; its seeds contain a large amount of different bioactive compounds that have attracted interest because may be beneficial to humans by improving cardiovascular health, by cancer chemo-preventive effects and also through neuroprotective activities. The morphological and anatomical characteristics of cocoa seeds are closely related to the aroma and to the nutritional properties. This study aimed to provide more information about the storage of some metabolites in the various components of cocoa seed by microscopical and phytochemical analyses. Polyphenols, sterols, tocopherols and fatty acids were detected in different portions of the seeds (teguments, cotyledons, embryo axis and pulp). Quali and quantitative differences were observed and a characteristic polyphenol pattern was detected in the different portions of the seed; cytological analysis demonstrated the presence of these compounds in big vacuolated polyphenolic cells. Among the analyzed fatty acids, the stearic and oleic acids were the most abundant in all the seed components (teguments, cotyledons and embryo axis). Fatty acids, usually found in the form of esters, thioesters and amides, represent one of the storage substances of cocoa seed probably localized in lipid globules, which in our observations occupied almost the entire volume of small isodiametric cells of cotyledon mesophyll. In the cocoa seeds we observed also a different distribution of sterols: β-sitosterol and Δ5-avenasterol were the most abundant, above all in the embryo axis; stigmasterol and campesterol were less present in embryo axis and more abundant in teguments; campestanol level was again higher in teguments but lower in cotyledons. The specific localization of different kind of sterols was probably related to a peculiar function. Our experiments demonstrated that all seed components contribute to the metabolites storage, but with interesting differences in the localization and amount of each metabolite.

Complementary iTRAQ Proteomic and Transcriptomic Analyses of Leaves in Tea Plant ( Camellia sinensis L.) with Different Maturity and Regulatory Network of Flavonoid Biosynthesis

The quality of tea is highly related with the maturity of the fresh tea leaves at harvest. The present study investigated the proteomic and transcriptomic profiles of tea leaves with different maturity, using iTRAQ and RNA-seq technologies. A total of 4455 proteins and 27 930 unigenes were identified, with functional enrichment analyses of GO categorization and KEGG annotation. The compositions of flavonoids (catechins and flavonols) in tea leaves were determined. The total content of flavonoids decreased with leaf maturity, in accordance with the protein regulation patterns of shikimate, phenylpropanoid, and flavonoid pathways. The abundance of ANR had a positive correlation with epi-catechin content, while LAR abundance was positively related with catechin content ( P < 0.05). The biosynthetic network of flavonoid biosynthesis was discussed in combination with photosynthesis, primary metabolism, and transcription factors. Bud had the lowest activities of photosynthesis and carbon fixation but the highest flavonoid biosynthesis ability in opposite to mature leaf. SUS-INV switch might be an important joint for carbon flow shifting into the follow-up biochemical syntheses. This work provided a comprehensive overview on the functional protein profile changes of tea leaves at different growing stages and also proposed a research direction regarding the correlations between primary metabolism and flavonoid biosynthesis.

Analysis of minor low molecular weight carbohydrates in cocoa beans by chromatographic techniques coupled to mass spectrometry

The low molecular weight carbohydrate (LMWC) profile of cocoa beans has recently been studied using hydrophilic interaction liquid chromatography coupled to electrospray ionization-time of flight mass spectrometry (HILIC-ESI-TOF MS) and HILIC-ESI-tandem mass spectrometry (HILIC-ESI-MSⁿ). However, different LMWC could not be unambiguously identified. Thus, as a first approach in this paper, gas chromatography coupled to mass spectrometry (GC-MS) was used as a complementary analytical technique to characterize LMWC of cocoa beans. Different mono-, di-, tri- and tetrasaccharides, as well as myo-inositol, galactinol and a diglycosil glycerol were detected. scyllo-Inositol, 1-kestose and 6-kestose were identified in unfermented cocoa beans for the first time. Moreover, other minor LMWC were tentatively assigned as fructosyl-fructose, fructosyl-glucose and glucosyl-sucrose. As a second step, in order to evaluate new possible indicators of cocoa bean origin or fermentation status, scyllo-inositol, 1-kestose and galactinol were selected as target compounds and a HILIC-ESI-TOF MS method was optimized for their analysis. The optimized conditions, using an acetonitrile:water gradient with 0.05% ammonium hydroxide at 40 °C showed narrow peaks (w_h: 0.3-0.5 min) with good resolution values (R_s: 0.83-2.83). The validated HILIC-ESI-TOF MS method was applied to the analysis of 35 cocoa bean samples from different origins and fermentation status. The content of scyllo-inositol, 1-kestose and galactinol in unfermented beans (n = 21) was in the range of traces-504.9, 36.1-133.5 and traces-1970.4 μg g^-1 cocoa DM respectively. In fermented beans (n = 14), the content of scyllo-inositol and 1-kestose was in the range of 15.5-491.9 and traces-115.5 μg g^-1 cocoa DM respectively. Galactinol was absent in fermented beans, indicating that it could be a potential indicator of fermentation status. The methodology proposed could be used for quality control of natural products and other food ingredients containing inositols and oligosaccharides.

Expression analysis of Cell wall invertase under abiotic stress conditions influencing specialized metabolism in Catharanthus roseus

Catharanthus roseus is a commercial source for anti-cancer terpenoid indole alkaloids (TIAs: vincristine and vinblastine). Inherent levels of these TIAs are very low, hence research studies need to focus on enhancing their levels in planta. Since primary metabolism provides precursors for specialized-metabolism, elevating the former can achieve higher amounts of the latter. Cell Wall Invertase (CWIN), a key enzyme in sucrose-metabolism catalyses the breakdown of sucrose into glucose and fructose, which serve as carbon-skeleton for specialized-metabolites. Understanding CWIN regulation could unravel metabolic-engineering approaches towards enhancing the levels of TIAs in planta. Our study is the first to characterize CWIN at gene-expression level in the medicinal plant, C. roseus. The CWINs and their inter-relationship with sucrose and TIA metabolism was studied at gene and metabolite levels. It was found that sucrose-supplementation to C. roseus leaves significantly elevated the monomeric TIAs (vindoline, catharanthine) and their corresponding genes. This was further confirmed in cross-species, wherein Nicotiana benthamiana leaves transiently-overexpressing CrCWIN2 showed significant upregulation of specialized-metabolism genes: NbPAL2, Nb4CL, NbCHS, NbF3H, NbANS, NbHCT and NbG10H. The specialized metabolites- cinnamic acid, coumarin, and fisetin were significantly upregulated. Thus, the present study provides a valuable insight into metabolic-engineering approaches towards augmenting the levels of therapeutic TIAs.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

Mathematical Modeling Approaches in Plant Metabolomics

The experimental analysis of a plant metabolome typically results in a comprehensive and multidimensional data set. To interpret metabolomics data in the context of biochemical regulation and environmental fluctuation, various approaches of mathematical modeling have been developed and have proven useful. In this chapter, a general introduction to mathematical modeling is presented and discussed in context of plant metabolism. A particular focus is laid on the suitability of mathematical approaches to functionally integrate plant metabolomics data in a metabolic network and combine it with other biochemical or physiological parameters.

Environmental Growing Conditions in Five Production Systems Induce Stress Response and Affect Chemical Composition of Cocoa (Theobroma cacao L.) Beans

Cocoa beans are produced all across the humid tropics under different environmental conditions provided by the region but also by the season and the type of production system. Agroforestry systems compared to monocultures buffer climate extremes and therefore provide a less stressful environment for the understory cocoa, especially under seasonally varying conditions. We measured the element concentration as well as abiotic stress indicators (polyamines and total phenolic content) in beans derived from five different production systems comparing monocultures and agroforestry systems and from two harvesting seasons. Concentrations of N, Mg, S, Fe, Mn, Na, and Zn were higher in beans produced in agroforestry systems with high stem density and leaf area index. In the dry season, the N, Fe, and Cu concentration of the beans increased. The total phenolic content increased with proceeding of the dry season while other abiotic stress indicators like spermine decreased, implying an effect of the water availability on the chemical composition of the beans. Agroforestry systems did not buffer the variability of stress indicators over the seasons compared to monocultures. The effect of environmental growing conditions on bean chemical composition was not strong but can contribute to variations in cocoa bean quality.

Rhizobium Impacts on Seed Productivity, Quality, and Protection of Pisum sativum upon Disease Stress Caused by Didymella pinodes: Phenotypic, Proteomic, and Metabolomic Traits

In field peas, ascochyta blight is one of the most common fungal diseases caused by Didymella pinodes. Despite the high diversity of pea cultivars, only little resistance has been developed until to date, still leading to significant losses in grain yield. Rhizobia as plant growth promoting endosymbionts are the main partners for establishment of symbiosis with pea plants. The key role of Rhizobium as an effective nitrogen source for legumes seed quality and quantity improvement is in line with sustainable agriculture and food security programs. Besides these growth promoting effects, Rhizobium symbiosis has been shown to have a priming impact on the plants immune system that enhances resistance against environmental perturbations. This is the first integrative study that investigates the effect of Rhizobium leguminosarum bv. viceae (Rlv) on phenotypic seed quality, quantity and fungal disease in pot grown pea (Pisum sativum) cultivars with two different resistance levels against D. pinodes through metabolomics and proteomics analyses. In addition, the pathogen effects on seed quantity components and quality are assessed at morphological and molecular level. Rhizobium inoculation decreased disease severity by significant reduction of seed infection level. Rhizobium symbiont enhanced yield through increased seed fresh and dry weights based on better seed filling. Rhizobium inoculation also induced changes in seed proteome and metabolome involved in enhanced P. sativum resistance level against D. pinodes. Besides increased redox and cell wall adjustments light is shed on the role of late embryogenesis abundant proteins and metabolites such as the seed triterpenoid Soyasapogenol. The results of this study open new insights into the significance of symbiotic Rhizobium interactions for crop yield, health and seed quality enhancement and reveal new metabolite candidates involved in pathogen resistance.

The Application of Ultra-High-Performance Liquid Chromatography Coupled with a LTQ-Orbitrap Mass Technique to Reveal the Dynamic Accumulation of Secondary Metabolites in Licorice under ABA Stress

The traditional medicine licorice is the most widely consumed herbal product in the world. Although much research work on studying the changes in the active compounds of licorice has been reported, there are still many areas, such as the dynamic accumulation of secondary metabolites in licorice, that need to be further studied. In this study, the secondary metabolites from licorice under two different methods of stress were investigated by ultra-high-performance liquid chromatography coupled with hybrid linear ion trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap-MS). A complex continuous coordination of flavonoids and triterpenoids in a network was modulated by different methods of stress during growth. The results showed that a total of 51 secondary metabolites were identified in licorice under ABA stress. The partial least squares-discriminate analysis (PLS-DA) revealed the distinction of obvious compounds among stress-specific districts relative to ABA stress. The targeted results showed that there were significant differences in the accumulation patterns of the deeply targeted 41 flavonoids and 10 triterpenoids compounds by PCA and PLS-DA analyses. To survey the effects of flavonoid and triterpenoid metabolism under ABA stress, we inspected the stress-specific metabolic changes. Our study testified that the majority of flavonoids and triterpenoids were elevated in licorice under ABA stress, while the signature metabolite affecting the dynamic accumulation of secondary metabolites was detected. Taken together, our results suggest that ABA-specific metabolite profiling dynamically changed in terms of the biosynthesis of flavonoids and triterpenoids, which may offer new trains of thought on the regular pattern of dynamic accumulation of secondary metabolites in licorice at the metabolite level. Our results also provide a reference for clinical applications and directional planting and licorice breeding.

Metabolic profiling of Garcinia mangostana (mangosteen) based on ripening stages

Metabolomics is an emerging research field based on exhaustive metabolite profiling that have been proven useful to facilitate the study of postharvest fruit development and ripening. Specifically, tracking changes to the metabolome as fruit ripens should provide important clues for understanding ripening mechanisms and identify bio-markers to improve post-harvest technology of fruits. This study conducted a time-course metabolome analysis in mangosteen, an economically important tropical fruit valued for its flavor. Mangosteen is a climacteric fruit that requires an important plant hormone ethylene to regulate ripening processes and rate. We first categorized mangosteen samples in different ripening stages based on color changes, an established indicator of ripening. Using gas chromatography/mass spectrometry, small hydrophilic metabolites were profiled from non-ripened to fully ripened (ripening stages 0-6). These metabolites were then correlated with color changes to verify their involvement mangosteen ripening. Our results suggest that the increase of 2-aminoisobutyric acid, psicose, and several amino acids (phenylalanine, valine, isoleucine, serine, and tyrosine) showed a correlation with the progression of mangosteen ripening. This is the first report of the application of non-targeted metabolomics in mangosteen.

Metabolomics Characterization of Two Apocynaceae Plants, Catharanthus roseus and Vinca minor, Using GC-MS and LC-MS Methods in Combination

Catharanthus roseus (C. roseus) and Vinca minor (V. minor) are two common important medical plants belonging to the family Apocynaceae. In this study, we used non-targeted GC-MS and targeted LC-MS metabolomics to dissect the metabolic profile of two plants with comparable phenotypic and metabolic differences. A total of 58 significantly different metabolites were present in different quantities according to PCA and PLS-DA score plots of the GC-MS analysis. The 58 identified compounds comprised 16 sugars, eight amino acids, nine alcohols and 18 organic acids. We subjected these metabolites into KEGG pathway enrichment analysis and highlighted 27 metabolic pathways, concentrated on the TCA cycle, glycometabolism, oligosaccharides, and polyol and lipid transporter (RFOS). Among the primary metabolites, trehalose, raffinose, digalacturonic acid and gallic acid were revealed to be the most significant marker compounds between the two plants, presumably contributing to species-specific phenotypic and metabolic discrepancy. The profiling of nine typical alkaloids in both plants using LC-MS method highlighted higher levels of crucial terpenoid indole alkaloid (TIA) intermediates of loganin, serpentine, and tabersonine in V. minor than in C. roseus. The possible underlying process of the metabolic flux from primary metabolism pathways to TIA synthesis was discussed and proposed. Generally speaking, this work provides a full-scale comparison of primary and secondary metabolites between two medical plants and a metabolic explanation of their TIA accumulation and phenotype differences.

Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding

Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism

Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed similarities to Concord grape and indicates the strong effect of genetic background on metabolic partitioning in primary and secondary metabolism.