Cross-Species Comparison of Fruit-Metabolomics to Elucidate Metabolic Regulation of Fruit Polyphenolics Among Solanaceous Crops

Comparative Analysis of the Wood Metabolites of Three Poplar Clones Using UPLC-Triple-TOF-MS

Poplar, a woody tree species, is widely used for industrial production and as a protective forest belt. Different clones of poplar exhibit clear variation in terms of morphological and physiological features, however, the impact of the genetic variation on the composition and abundance of wood metabolite have not been fully determined. In this study, ultra-high pressure liquid chromatography-triple time of flight-mass spectrometer (UPLC-Triple-TOF-MS) was used to explore the metabolite changes in poplar wood from three clones, including Populus deltoides CL. '55/65', P. deltoides CL. 'Danhong', and P. nigra CL. 'N179'. A total of 699 metabolites were identified. Clustering analysis and principal component analysis display that the metabolic differences of wood have allowed distinguishing different species of poplar. Meanwhile, eight significantly different metabolites were screened between P. deltoides and P. nigra, which may be considered as valuable markers for chemotaxonomy. In addition, the highly discriminant 352 metabolites were obtained among the three clones, and those may be closely related to the distinction in unique properties (e.g., growth, rigidity and tolerance) of the poplar wood cultivars. This study provides a foundation for further studies on wood metabolomics in poplar, and offers chemotaxonomic markers that will stimulate the early screening of potentially superior trees.

Integrating (Nutri-)Metabolomics into the One Health Tendency-The Key for Personalized Medicine Advancement

Metabolomics is an advanced technology, still under development, with multiple research applications, especially in the field of health. Individual metabolic profiles, the functionality of the body, as well as its interaction with the environment, can be established using this technology. The body's response to various external factors, including the food consumed and the nutrients it contains, has increased researchers' interest in nutrimetabolomics. Establishing correlations between diet and the occurrence of various diseases, or even the development of personalized nutrition plans, could contribute to advances in precision medicine. The interdependence between humans, animals, and the environment is of particular importance today, with the dramatic emergence and spread of zoonotic diseases, food, water and soil contamination, and the degradation of resources and habitats. All these events have led to an increase in risk factors for functional diseases, burdening global health. Thus, this study aimed to highlight the importance of metabolomics, and, in particular, nutrimetabolomics, as a technical solution for a holistic, collaborative, and precise approach for the advancement of the One Health strategy.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

Analysis of flavonoid-related metabolites in different tissues and fruit developmental stages of blackberry based on metabolome analysis

Blackberry is an economically important shrub species of Rubus in the Rosaceae family. It is rich in phenolic compounds, which have many health effects and pharmaceutical value. The utilization of metabolites from various blackberry tissues is still in the primary stage of development, so investigating the metabolites in various tissues is of practical significance. In this study, nontargeted LC - MS metabolomics was used to identify and measure metabolites in the roots, stems, leaves and fruits (green, red, and black fruits) of blackberry "Chester". We found that 1,427 and 874 metabolites were annotated in the positive and negative ion modes (POS; NEG), respectively. Differentially abundant metabolites (DAMs) between the leaf and root groups were the most abundant (POS: 249; NEG: 141), and the DAMs between the green and red fruit groups were the least abundant (POS: 21; NEG: 14). Moreover, the DAMs in different fruit development stages were far less than those in different tissues. There were significant differences in flavonoid biosynthesis-related pathways among the comparison groups. Trend analysis showed that the profile 10 had the largest number of metabolites. This study provides a scientific basis for the classification and efficient utilization of resources in various tissues of blackberry plants and the directional development of blackberry products.

Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology

In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.

Analysis of the Fruit Quality of Pear (Pyrus spp.) Using Widely Targeted Metabolomics

Pear is a kind of common temperate fruit, whose metabolite composition that contributes to the difference in fruit quality is unclear. This study identified and quantified the metabolites using a widely targeted LC-MS/MS approach in three pear species, including Pyrus bretschneideri (PB), Pyrus usssuriensis (PU) and Pyrus pyrifolia (PP). A total of 493 metabolites were identified, consisting of 68 carbohydrates, 47 organic acids, 50 polyphenols, 21 amino acids, 20 vitamins, etc. The results of PCA and OPLS-DA demonstrated that the metabolite compositions differed distinctly with cultivar variability. Our results also involved some metabolic pathways that may link to the fruit quality based on KEGG pathway analysis, the pathway of phenylalanine metabolism revealed significant differences between PB and PP (p < 0.05). Furthermore, the study selected D-xylose, formononetin, procyanidin A1 and β-nicotinamide mononucleotide as the major differentially expressed metabolites in the three species. The present study can open new avenues for explaining the differences in fruit quality of the major commercial pear cultivars in China.

The Phenolics and Antioxidant Properties of Black and Purple versus White Eggplant Cultivars

The total phenolic content, anthocyanins, phenolic acids, antioxidant capacity and α-amylase inhibitory activity of black (Aydin Siyahi), purple (Kadife Kemer) and white (Trabzon Kadife) eggplants grown in Turkey were subjected to a comparative investigation. The black cultivar exhibited the highest total phenolic (17,193 and 6552 mg gallic acid equivalent/kg fw), flavonoid (3019 and 1160 quercetin equivalent/kg fw) and anthocyanin (1686 and 6167 g delphinidin-3-O-glucoside equivalent/kg fw) contents in crude extracts of the peel and pulp. The majority of the caffeic acid was identified in the ester (2830 mg/kg fw) and ester-bound (2594 mg/kg fw) forms in the peel of ‘Kadife Kemer’ and in the glycoside form (611.9 mg/kg fw) in ‘Aydin Siyahi’, as well as in the pulp of these two eggplants. ‘Kadife Kemer’ (purple eggplant) contained the majority of the chlorogenic acid in free form (27.55 mg/kg fw), compared to ‘Aydin Siyahi’ in the ester (7.82 mg/kg fw), glycoside (294.1 mg/kg dw) and ester-bound (2.41 mg/kg fw) forms. The eggplant cultivars (peel and pulp, mg/kg fw) exhibited a relatively high delphinidin-3-O-rutinoside concentration in the peel of ‘Aydin Siyahi’ (avg. 1162), followed by ‘Kadife Kemer’ (avg. 336.6), and ‘Trabzon Kadife’ (avg. 215.1). The crude phenolic extracts of the eggplants exhibited the highest antioxidant capacity values (peel and pulp, µmoL Trolox equivalent/kg fw) of 2,2-diphenyl-1-picrylhydrazyl (DPPH, 8156 and 2335) and oxygen radical absorbance capacity (ORAC, 37,887 and 17,648). The overall results indicate that black and purple eggplants are the cultivars with greater potential benefits in terms of their phenolics and antioxidant values than the white eggplant.

Comparison of blood tonic efficacy and chemical constituents of Kadsura interior A.C. Smith and its closely related species

BACKGROUND

The stems of Kadsura interior A. C. Smith are used as traditional Chinese medicine (TCM) Kadsurae Caulis, with the traditional efficacy of tonifying and invigorating the blood, therefore being favored to treat blood deficiency (BD) widely. However, the stems of K. interior and its closely related species are morphologically similar and they may readily be misused as Kadsurae Caulis, thus likely to exert negative effects on clinical efficacy and clinical medication safety.

METHODS

Firstly, blood tonic efficacies of the stems of K. interior (KIS) and its closely related species were compared using BD mouse model induced by 1-acetyl-2-phenylhydrazine (APH) and cyclophosphamide (CTX). Secondly, the chemical constituents from the stems of K. interior and its closely related species were evaluated and compared using a plant metabolomics approach. Plant metabolomics in this study aims at discovering differential metabolites and comprehensively assessing the chemical constituents by combining state-of-the-art high-resolution UPLC-Q/TOF-MS/MS technique and multivariate data analysis. Finally, based on the pharmacological data and the chemical constituents in UPLC-Q/TOF-MS fingerprints, the potential blood tonic active markers were screened by the spectrum-effect relationship analysis and quantified by UPLC-UV-DAD.

RESULTS

The ethanol extract of the stems of K. interior significantly increased the levels of hematocrit (HCT), hemoglobin (HGB), and red blood cells (RBC) in BD mice. In addition, it significantly increased the serum levels of interleukin 3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), and macrophage-stimulating factor (M-CSF) in BD mice (P < 0.01). The blood tonic efficacy of the stems of K. interior was superior to those of its closely related species, especially at the dose of 200 mg/kg. Six differential compounds in the stems of K. interior were screened out to distinguish it from its closely related species. In combination with the results of the spectrum-effect relationship analysis, heteroclitin D, interiorin C, and heteroclitin G were identified as potential bioactive markers. The contents of heteroclitin D and heteroclitin G in the freeze-dried powder of KIS were 15.90 and 3.74 μg/mg.

CONCLUSIONS

This study illustrated the differences in the blood tonic efficacies and the chemical constituents of the stems of K. interior and its closely related species, and pinpointed the potential bioactive markers of K. interior.

Metabolomics for Crop Breeding: General Considerations

The development of new, more productive varieties of agricultural crops is becoming an increasingly difficult task. Modern approaches for the identification of beneficial alleles and their use in elite cultivars, such as quantitative trait loci (QTL) mapping and marker-assisted selection (MAS), are effective but insufficient for keeping pace with the improvement of wheat or other crops. Metabolomics is a powerful but underutilized approach that can assist crop breeding. In this review, basic methodological information is summarized, and the current strategies of applications of metabolomics related to crop breeding are explored using recent examples. We briefly describe classes of plant metabolites, cellular localization of metabolic pathways, and the strengths and weaknesses of the main metabolomics technique. Among the commercialized genetically modified crops, about 50 with altered metabolic enzyme activities have been identified in the International Service for the Acquisition of Agri-biotech Applications (ISAAA) database. These plants are reviewed as encouraging examples of the application of knowledge of biochemical pathways. Based on the recent examples of metabolomic studies, we discuss the performance of metabolic markers, the integration of metabolic and genomic data in metabolic QTLs (mQTLs) and metabolic genome-wide association studies (mGWAS). The elucidation of metabolic pathways and involved genes will help in crop breeding and the introgression of alleles of wild relatives in a more targeted manner.

Scrapped but not neglected: Insights into the composition, molecular modulation and antioxidant capacity of phenols in peel of eggplant (Solanum melongena L.) fruits at different developmental stages

Eggplant fruits are normally harvested and marketed when they reach the commercial maturity, that precedes the physiological ripening when dramatic changes in taste, composition and peel color take place. The biochemical changes in fruit peel across the developmental stages, characterized also by a sizeable decrement of anthocyanins, were studied in four eggplant genotypes differing for fruit pigmentation. HPLC-DAD, HPLC-ESI-MS and NMR analyses identified naringenin chalcone and naringenin 7-O-glucoside as the main phenolic compounds in extracts from the physiological ripe stage, along with compounds tentatively identified as glycosylated naringenin chalcone, naringenin and kaempferol. On average, the levels of anthocyanins, responsible for the peel pigmentation, dropped by 75% during development, while, surprisingly, the level of total phenols showed a slight decrease of 16%, with a final concentration of more than 1000 mg/100g dw. RT-qPCR expression profiling of nine genes coding for enzymes putatively acting at different steps of the involved pathways showed modulation mostly consistent with the observed changes in phenolic composition, with a remarkable decrease in the activity of flavonol reductase and an increase in flavonol synthase during berry development. Antioxidant activity monitored by peroxyl scavenging was similar at all developmental stages while Fremy's analysis evidenced a slight decrement at full physiological ripening. These results are valuable to address the improvement of eggplant commercial fruit quality and the valorization of unmarketable physiological ripe fruits, especially for the newly accumulation of the health-promoting compounds chalcones and flavanones.

Consumption of Phenolic-Rich Food and Dietary Supplements as a Key Tool in SARS-CoV-19 Infection

The first cases of COVID-19, which is caused by the SARS-CoV-2, were reported in December 2019. The vertiginous worldwide expansion of SARS-CoV-2 caused the collapse of health systems in several countries due to the high severity of the COVID-19. In addition to the vaccines, the search for active compounds capable of preventing and/or fighting the infection has been the main direction of research. Since the beginning of this pandemic, some evidence has highlighted the importance of a phenolic-rich diet as a strategy to reduce the progression of this disease, including the severity of the symptoms. Some of these compounds (e.g., curcumin, gallic acid or quercetin) already showed capacity to limit the infection of viruses by inhibiting entry into the cell through its binding to protein Spike, regulating the expression of angiotensin-converting enzyme 2, disrupting the replication in cells by inhibition of viral proteases, and/or suppressing and modulating the host's immune response. Therefore, this review intends to discuss the most recent findings on the potential of phenolics to prevent SARS-CoV-2.

Cross-Species Metabolic Profiling of Floral Specialized Metabolism Facilitates Understanding of Evolutional Aspects of Metabolism Among Brassicaceae Species

Plants produce a variety of floral specialized (secondary) metabolites with roles in several physiological functions, including light-protection, attraction of pollinators, and protection against herbivores. Pigments and volatiles synthesized in the petal have been focused on and characterized as major chemical factors influencing pollination. Recent advances in plant metabolomics have revealed that the major floral specialized metabolites found in land plant species are hydroxycinnamates, phenolamides, and flavonoids albeit these are present in various quantities and encompass diverse chemical structures in different species. Here, we analyzed numerous floral specialized metabolites in 20 different Brassicaceae genotypes encompassing both different species and in the case of crop species different cultivars including self-compatible (SC) and self-incompatible (SI) species by liquid chromatography-mass spectrometry (LC-MS). Of the 228 metabolites detected in flowers among 20 Brassicaceae species, 15 metabolite peaks including one phenylacyl-flavonoids and five phenolamides were detected and annotated as key metabolites to distinguish SC and SI plant species, respectively. Our results provide a family-wide metabolic framework and delineate signatures for compatible and incompatible genotypes thereby providing insight into evolutionary aspects of floral metabolism in Brassicaceae species.

Comparative Metabolomic Profiling of Citrullus spp. Fruits Provides Evidence for Metabolomic Divergence during Domestication

Watermelon (Citrullus lanatus) is one of the most nutritional fruits that is widely distributed in the whole world. The nutritional compositions are mainly influenced by the genotype and environment. However, the metabolomics of different domestication status and different flesh colors watermelon types is not fully understood. In this study, we reported an extensive assessment of metabolomic divergence in the fruit flesh among Citrullus sp. and within Citrullus sp. We demonstrate that metabolic profiling was significantly different between the wild and cultivated watermelons, the apigenin 6-C-glucoside, luteolin 6-C-glucoside, chrysoeriol C-hexoside, naringenin C-hexoside, C-pentosyl-chrysoeriol O-hexoside, and sucrose are the main divergent metabolites. Correlation analysis results revealed that flavonoids were present in one tight metabolite cluster. The main divergent metabolites in different flesh-colored cultivated watermelon fruits are p-coumaric acid, 2,3-dihydroflavone, catechin, N-(3-indolylacetyl)-l-alanine, 3,4-dihydroxycinnamic acid, and pelargonidin o-hexoside. A total of 431 differentially accumulated metabolites were identified from pairwise comparative analyses. C. lanatus edible-seed watermelon (cultivars) and C. mucosospermus (wild) have similar fruit metabolic profiles and phenotypic traits, indicating that edible-seed watermelon may be a relative of wild species and a relatively primitive differentiation type of cultivated watermelon. Our data provide extensive knowledge for metabolomics-based watermelon improvement of Citrullus fruits meet their enhanced nutritive properties or upgraded germplasm utility values.

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

Simple Summary

This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health.

Abstract

Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.

Special Issue on "Fruit Metabolism and Metabolomics"

Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies.