Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species

Genome-wide exploration: Evolution, structural characterization, molecular docking, molecular dynamics simulation and expression analysis of sugar transporter (ST) gene family in potato (Solanum tuberosum)

Sugars are the basic structural components of carbohydrates. Sugar transport is crucial for plants to ensure their optimal growth and development. Long-distance sugar transport occurs through either diffusion-based passive or active transport mediated by transporter proteins. In potatoes, STs play a vital role in sugar transport and total sugar accumulation. To better understand the roles of these transporters, in-depth structural, protein characterization, and tissue-specific expression analysis were performed. A total of 61 StSTs were identified and classified into eight sub-families (STP, PLT, ERD6L, INT, TMT, pGlcT, SUC, and VGT). The majority of StSTs were found in the plasma membrane, and all of them were dispersed throughout the 12 chromosomes. Exon and motif counts ranged from 1-18 and 1-10, respectively. In synteny analysis with four plant genomes, the highest (38) orthologous gene pair was found with S. lycopersicum (tomato). In 3D protein modeling, the alpha helix and transmembrane helices range varied from 32 % to 78 % and 53 %-57 %, respectively. During molecular docking analysis, the lowest binding energy was observed for Glu-StINT1 (ΔG: - 6.6 kcal/mol), Fru-StVGT1 (ΔG: - 6.1 kcal/mol), Gal-StSTP10 (ΔG: - 6.5 kcal/mol), and Suc-StINT2 (ΔG: - 7.5 kcal/mol), among 244 docking results. These complexes showed significant hydrogen and hydrophobic interactions, due to having significant amino acid residues. The molecular dynamics (MD) simulation of four complexes (Glu-StINT1, Fru-StVGT1, Gal-StSTP10, and Suc-StINT2) validated the ligand's stable attachment to the intended target proteins and it can be predicted that these complexes are the best sugar transporters of potato. In RNA-seq mediated expression analysis, StSTP12, StERD6L-6, 12, StpGlcT3, StVGT1, and StVGT2, were significantly upregulated in vegetative tissues/organs, revealing their significant role in vegetative organ development. In addition, stu-miRNA395 was the largest family interacting with StERD6L-1 and StTMT2 genes, demonstrating their significant role in sulfate metabolism. The detection and visualization of potential transcription factors (TFs) like ERF, Dof, MYB, BBR-BPC, LBD, and NAC in conjunction with the StSTs gene indicate their significant contribution to stress tolerance and DNA conversion and transcription into RNA. A significant interaction of StSTs in the PPI network might be due to their cumulative role in the same signaling pathways. The integration of these findings will guide the development of programming-based sugar transporter-mediated genetic circuits to improve the sugar accumulation in potatoes using synthetic biology approaches.

Transcription factor MdNAC18.1 regulates malic acid accumulation in apple fruits

Malic acid, the most important organic acid component in the ripe apple fruit, is of great importance for the development of the fruit flavor and regulation of the metabolism. Previous studies have demonstrated that the P3A-ATPase MdMa11 plays a role in determining fruit acidity, and a total of 85 positive clones were identified using yeast one-hybrid screening based on the fragment in MdMa11 promoter. Among these positive clones, the NAM domain protein was designated as MdNAC18.1. The analysis of transgenic apple calli, fruits and tomatoes indicated that MdNAC18.1 induced the organic acids accumulation to regulate fruit acidity. Luciferase (LUC) and glucuronidase (GUS) activation assays showed that MdNAC18.1 binds to the G-box motif (5'-ACGT-3') located 5227 bp upstream of transcription initiation site of the MdMa11, thereby promoting its expression. Meanwhile, the expression of MdWRKY126, MdMDH5, MdtDT, MdMYB1, and MdVHP1 was found to be significantly increased in transgenic apple calli overexpressing MdNAC18.1 and decreased in MdNAC18.1-silenced transgenic apple calli. The G-box was identified in all these five genes. However, the GUS and LUC activation assays exhibited that MdNAC18.1 activated MdWRKY126, MdMDH5, MdtDT, and MdMYB1 expression. Our findings contribute valuable insights into the complex mechanism regulating the accumulation of malate in apple fruits.

Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin

Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, has a significance beyond its role as a commodity, playing a crucial part in the cultural identity of various communities. The intricate natural aging process known as maturation involves a series of reactions that induce changes in the cheese's physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) has emerged as a new trend in studies related to protected designation of origin (PDO) cheese. This mini-summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, and to discuss and recognize that the importance of these studies goes beyond comprehending the cheese biome and extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that, increasingly, multidisciplinary studies spanning various omics sciences will not only contribute to the characterization of these products but will also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. © 2024 Society of Chemical Industry.

DIA-Based Quantitative Proteomics in the Flower Buds of Two Malus sieversii (Ledeb.) M. Roem Subtypes at Different Overwintering Stages

Malus sieversii is considered the ancestor of the modern cultivated apple, with a high value for apple tolerance breeding. Despite studies on the temperature adaptability of M. sieversii carried out at a physiological response and the genome level, information on the proteome changes of M. sieversii during dormancy is limited, especially about the M. sieversii subtypes. In this study, a DIA-based approach was employed to screen and identify differential proteins involved in three overwintering periods of flower buds in two M. sieversii subtypes (Malus sieversii f. luteolus, GL; Malus sieversii f. aromaticus, HC) with different overwintering adaptabilities. The proteomic analysis revealed that the number of the down-regulated differential expression proteins (DEPs) was obviously higher than that of the up-regulated DEPs in the HC vs. GL groups, especially at the dormancy stage and dormancy-release stage. Through functional classification of those DEPs, the majority of the DEPs in the HC vs. GL groups were associated with protein processing in the endoplasmic reticulum, oxidative phosphorylation, starch and sucrose metabolism and ribosomes. Through WGCNA analysis, tricarboxylic acid cycle and pyruvate metabolism were highly correlated with the overwintering stages; oxidative phosphorylation and starch and sucrose metabolism were highly correlated with the Malus sieversii subtypes. This result suggests that the down-regulation of DEPs, which are predominantly enriched in these pathways, could potentially contribute to the lower cold tolerance observed in HC during overwintering stage.

Application of quantitative proteomics to investigate fruit ripening and eating quality

The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.

Combined nature and human selections reshaped peach fruit metabolome

Background

Plant metabolites reshaped by nature and human beings are crucial for both their lives and human health. However, which metabolites respond most strongly to selection pressure at different evolutionary stages and what roles they undertake on perennial fruit crops such as peach remain unclear.

Results

Here, we report 18,052 significant locus-trait associations, 12,691 expression-metabolite correlations, and 294,676 expression quantitative trait loci (eQTLs) for peach. Our results indicate that amino acids accumulated in landraces may be involved in the environmental adaptation of peaches by responding to low temperature and drought. Moreover, the contents of flavonoids, the major nutrients in fruits, have kept decreasing accompanied by the reduced bitter flavor during both domestication and improvement stages. However, citric acid, under the selection of breeders’ and consumers’ preference for flavor, shows significantly different levels between eastern and western varieties. This correlates with differences in activity against cancer cells in vitro in fruit from these two regions. Based on the identified key genes regulating flavonoid and acid contents, we propose that more precise and targeted breeding technologies should be designed to improve peach varieties with rich functional contents because of the linkage of genes related to bitterness and acid taste, antioxidant and potential anti-cancer activity that are all located at the top of chromosome 5.

Conclusions

This study provides powerful data for future improvement of peach flavor, nutrition, and resistance in future and expands our understanding of the effects of natural and artificial selection on metabolites.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-022-02719-6.

Comparative Metabolomics Analysis Reveals the Taste Variations among Three Selected Wampee Cultivars

Sugars and acids of wampee predominantly influence consumer taste preference and its commercial value. The molecular basis of taste variations is currently unknown due to the lack of a large-scale investigation of metabolites in wampee. Here, three tastes cultivars, including YF1 (sweet), YF2 (sweet-sour) and YF3 (sour) wampees with sugar-acid ratios ranging from 1.74 to 26.32, were selected. Then, UPLC-MS/MS based widely targeted metabolome analysis was performed to uncover the molecular mechanism underlying these taste variations, followed by the analysis of KEGG pathways. Results showed that 449, 470, 147 metabolites differed between YF1 vs YF2, YF1 vs YF3, and YF2 vs YF3. Fifty of them were screened as common differential metabolites (DMs) by Venn diagram, including 9 phenolic acids. Among them, the abundance level of methyl 3-O-methyl gallate (M3MG) showed a positive correlation with the titratable acids (R² = 0.9009) and negative correlation with sugar-acid ratio (R² = 0.9802) in three cultivars. Therefore, M3MG could be a taste biomarker for wampees. KEGG pathway enrichment analysis also verified that M3MG played a crucial role in the "biosynthesis of amino acids" pathway. These results above provide important insights into the taste-forming mechanism of wampee and will be beneficial for superior eating quality wampee breeding.

Identification and verification of key taste components in wampee using widely targeted metabolomics

Due to the lack of comprehensive evaluation of all metabolites in wampee, the metabolic reasons for taste differences are unclear. Here, two local varieties YF1 (sweet taste) and YF2 (sweet-sour taste), were selected for quality analysis, followed by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) based widely targeted metabolomic analysis. YF1 and YF2 were clearly separated by principal component analysis (PCA) and cluster analysis, and 449 metabolites were different between the cultivars, including 29 carbohydrates and 29 organic acids. Among them, d-galactose, d-mannose, and d-fructose 6-phosphate contributed mainly to the sweet taste of the YF1 wampee. l-citramalic acid, 2-hydroxyglutaric acid, and 3-methylmalic acid were the dominant organic acids in YF2 wampee, and therefore, contributed primarily to the sweet-sour taste. The differential metabolites were significantly enriched in the "ascorbate and aldarate metabolism" and "C5-branched dibasic acid metabolism" pathways. Ascorbate played a crucial role in the regulation of sugars and organic acids through those pathways. In addition, high-performance liquid chromatography (HPLC) based quantitative verification exhibited the same specific cultivar variations.

Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

Sensory attributes, physicochemical and antioxidant characteristics, and protein profile of wild prickly pear fruits (O. macrocentra Engelm., O. phaeacantha Engelm., and O. engelmannii Salm-Dyck ex Engelmann.) and commercial prickly pear fruits (O. ficus-indica (L.) Mill.)

Mexico presents the highest richness of Opuntia Mill. species. These species are an important economic factor for the country, and source of nutrients, bioactive compounds, pigments, and nutraceuticals which can be of interest for the food and pharmaceutical industry. However, there are some wild Opuntia species in the Chihuahua desert, that have not been analyzed to establish their properties and potential use. The aim of study was to evaluate the sensory, physicochemical and protein profile in wild prickly pear fruits (O. macrocentra Engelm. (OM), O. phaeacantha Engelm. (OP), and O. engelmannii Salm-Dyck ex Engelmann. (OE)) from Samalayuca, Chihuahua and compare them with two commercial prickly pear fruits (O. ficus-indica (L.) Mill. (green-OFG, red-OFR). The sensory profile of wild species was characterized by highest color, odor, and sour taste compared to the commercial fruits. Pulp, peel, and seeds from wild prickly pear fruits showed lower pH, and higher titratable total acidity, total phenolic compounds, total flavonoids, antioxidant capacity, protein, lipids, ash, carbohydrates (only peel), and crude fiber content than commercial Opuntia species. Furthermore, O. engelmannii showed a tendency to present the highest betacyanins, betaxanthins, and betalains contents. A total of 181, 122, 113, 183 and 140 different proteins were identified in OM, OP, OE, OFG, OFR species, respectively. All species showed the highest enrichment in three main pathways such as amino acids biosynthesis, glycolysis (dark)/gluconeogenesis (light), and the citric acid cycle. The wild prickly pear fruits of this study showed important nutritional, protein, and antioxidant properties with biological interest, and can be a potential source of functional ingredients and nutraceuticals.

Genome-Wide Identification and Expression Analysis of Sugar Transporter (ST) Gene Family in Longan (Dimocarpus longan L.)

Carbohydrates are nutrients and important signal molecules in higher plants. Sugar transporters (ST) play important role not only in long-distance transport of sugar, but also in sugar accumulations in sink cells. Longan (Dimocarpus longan L.) is one of the most important commercial tropical/subtropical evergreen fruit species in Southeast Asia. In this study, a total of 52 longan sugar transporter (DlST) genes were identified and they were divided into eight clades according to phylogenetic analysis. Out of these 52 DlST genes, many plant hormones (e.g., MeJA and gibberellin), abiotic (e.g., cold and drought), and biotic stress responsive element exist in their promoter region. Gene structure analysis exhibited that each of the clades have closely associated gene architectural features based on similar number or length of exons. The numbers of DlSTs, which exhibited alternative splicing (AS) events, in flower bud is more than that in other tissues. Expression profile analysis revealed that ten DlST members may regulate longan flowerbud differentiation. In silico expression profiles in nine longan organs indicated that some DlST genes were tissue specificity and further qRT-PCR analysis suggested that the transcript level of seven DlSTs (DlINT3, DlpGlcT1, DlpGlcT2, DlPLT4, DlSTP1, DlVGT1 and DlVGT2) was consistent with sugar accumulation in fruit, indicating that they might be involved in sugar accumulations during longan fruit development. Our findings will contribute to a better understanding of sugar transporters in woody plant.