Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening

Cropping with Vicia villosa and native grass improves soil's bacterial structure and ecological network in a jujube orchard

In a jujube orchard, cropping withgrass may influence bacterial diversity and ecological networks due to changes of physicochemical properties in soil, which has a serious effect on the stability of soil ecosystems. The aim of this study was to analyze the effects of different cultivation methods (CK: cleaning tillage; NG: cropping with native grass; VV: cropping with Vicia villosa) on the soil's bacterial structure and its co-occurrence network in a jujube orchard. The results showed that the highest moisture content, total nitrogen, and organic matter in the rhizosphere soil of a jujube orchard was found in the VV group. The soil's moisture content, total nitrogen, and organic matter in the VV group were 2.66%, 0.87 g kg-1, and 5.55 mg kg-1 higher than that found in the CK group. Compared to the CK group, the number of unique species in the rhizosphere soil in the NG and the VV groups increased by 7.33% and 21.44%. The PICRUSt and FAPROTAX analysis showed that sown grass had a greater influence on the ecological function of the soil's bacteria. Cropping with Vicia villosa and native grass significantly increased aerobic chemoheterotrophy, nitrogen respiration, nitrate reduction related to biochemical cycles, and the relative abundance of genes related to carbohydrate metabolism and the biodegradation of xenobiotics. The bacterial network complexity in the NG group was higher than that in the CK and VV groups and was greatest in the hub nodes (OTU42, Bacteroidota; OTU541, Nitrospiraceae). In this study, the ecological benefit seen in the soil's microbial function provides support to the theory that cropping with grass (Vicia villosa) increases the sustainable development of a jujube orchard.

Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism

BACKGROUND

Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved.

RESULTS

We generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening.

CONCLUSION

Our findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.

Multi-omic characterisation as a tool to improve knowledge, valorisation and conservation of wild fruit genetic resources: the case of Arbutus unedo L

The valorisation and conservation of plant genetic resources (PGRs) and wild fruit PGRs are critical to ensure the maintenance of genetic and cultural heritage and to promote new perspectives on resource use. New strategies to characterize PGRs are needed, and the omics approach can provide information that is still largely unknown. The Strawberry tree (Arbutus unedo L.) is an underutilized, drought and fire-resistant species distributed in the Mediterranean area and its berries have large ethnobotanical use. Although their phenolic profile and antioxidant capacity are known, they are not well characterised, particularly from a proteomic perspective. The aim of this work is the characterisation of two ecotypes of A. unedo (Campania and Sicily) from a molecular viewpoint to valorise and encourage the preservation of this wild fruit. Samples were collected from two different geographical areas to assess whether different geographical conditions could influence the characteristics of leaves and fruits at the three stages of ripening (green, veraison, red). Proteomic analysis identified 904 proteins, of which 122 showed significance along the ripening. Some of these differentially abundant proteins, such as chalcone synthase, show a marked increase during ripening. The protein functional classes with the highest representation are involved in protein and amino acid metabolism, glycolysis and in secondary metabolism. From a proteomic perspective, there are no differences between the fruits from the two regions compared by the ripening stage. However, the pedoclimatic metabolic imprinting allowed the observation of good diversity in the metabolomic profiles between the two ecotypes, especially for anthocyanins, 4 times more abundant in the Sicilian veraisoned fruit than in the Campania one, and catechins, with double the abundance in the Campania ecotype compared to the Sicilian ecotype in the green phase, but more abundant (3x) in the Sicilian veraisoned fruit. Phenolic compounds show a 20% greater abundance in the Campania green arbutus fruit than in the Sicilian one, values that then equalise as ripening progresses. Multi-omic characterisation enhanced the knowledge on a wild fruit plant species which shows specific adaptations and responses to the environment to be considered when addressing the issue of local agrobiodiversity.

Heterologous Overexpression of Apple MdKING1 Promotes Fruit Ripening in Tomato

Fruit ripening is governed by a complex regulatory network, and ethylene plays an important role in this process. MdKING1 is a γ subunit of SNF1-related protein kinases (SnRKs), but the function was unclear. Here, we characterized the role of MdKING1 during fruit ripening, which can promote fruit ripening through the ethylene pathway. Our findings reveal that MdKING1 has higher expression in early-ripening cultivars than late-ripening during the early stage of apple fruit development, and its transcription level significantly increased during apple fruit ripening. Overexpression of MdKING1 (MdKING1 OE) in tomatoes could promote early ripening of fruits, with the increase in ethylene content and the loss of fruit firmness. Ethylene inhibitor treatment could delay the fruit ripening of both MdKING1 OE and WT fruits. However, MdKING1 OE fruits turned fruit ripe faster, with an increase in carotenoid content compared with WT. In addition, the expression of genes involved in ethylene biosynthesis (SlACO1, SlACS2, and SlACS4), carotenoid biosynthesis (SlPSY1 and SlGgpps2a), and fruit firmness regulation (SlPG2a, SlPL, and SlCEL2) was also increased in the fruits of MdKING1 OE plants. In conclusion, our results suggest that MdKING1 plays a key role in promoting tomato fruit ripening, thus providing a theoretical basis for apple fruit quality improvement by genetic engineering in the future.

The Effect of Ripening Stages on the Accumulation of Polyphenols and Antioxidant Activity of the Fruit Extracts of Solanum Species

The aim of the research was to evaluate the influence of the ripening stage on the accumulation of polyphenols and antioxidant activity in fruits of Solanum species. The experiment included two factors: I-four different Solanum species (S. melanocerasum, S. nigrum, S. villosum, and S. retroflexum) and II-three ripening stages. High-performance liquid chromatography (HPLC) was used to analyze the individual phenolic compounds (flavonoids and phenolic acids), and the spectrophotometric method was applied to determine antioxidant activity. The results revealed that the accumulation of polyphenols and antioxidant activity in fruits of Solanum species depends on the stage of ripening and species. All studied Solanum species fruits had the highest content of total phenolic acid at ripening stage III and the greatest antioxidant activity at ripening stage I. Fully ripe fruits of S. melanocerasum contained significantly more total flavonoids, whereas S. nigrum contained significantly more total phenolic acids than other investigated Solanum species fruits. The significantly highest antioxidant activity was found in S. melanocerasum fruits at ripening stage I.

Partial compression increases acidity, but decreases phenolics in jujube fruit: Evidence from targeted metabolomics

Jujube fruit (Ziziphus jujuba Mill.) is extremely susceptible to mechanical injury by extrusion and collision during storage, transportation and processing. In this study, we examined the morphology and endogenous metabolism of jujubes at three developmental stages after applying partial compression (PC) to mimic mechanical injury. Generally, PC did not affect the total soluble solids content, but increased the acidity and decreased the amount of phenolics in the jujube fruit. Targeted metabolomics analysis further confirmed that acid and phenolics content were differentially altered in response to PC. To our knowledge, this is the first study to characterize metabolic variations in ready-to-eat fruit that occur in response to physical damage. The results will provide insight into the understanding the consequences of mechanical injury on fruit nutrition and health benefits.

Advances in Physiological, Transcriptomic, Proteomic, Metabolomic, and Molecular Genetic Approaches for Enhancing Mango Fruit Quality

Mango (Mangifera indica L.) is a nutritionally important fruit of high nutritive value, delicious in taste with an attractive aroma. Due to their antioxidant and therapeutic potential, mango fruits are receiving special attention in biochemical and pharmacognosy-based studies. Fruit quality determines consumer's acceptance, and hence, understanding the physiological, biochemical, and molecular basis of fruit development, maturity, ripening, and storage is essential. Transcriptomic, metabolomic, proteomic, and molecular genetic approaches have led to the identification of key genes, metabolites, protein candidates, and quantitative trait loci that are associated with enhanced mango fruit quality. The major pathways that determine the fruit quality include amino acid metabolism, plant hormone signaling, carbohydrate metabolism and transport, cell wall biosynthesis and degradation, flavonoid and anthocyanin biosynthesis, and carotenoid metabolism. Expression of the polygalacturonase, cutin synthase, pectin methyl esterase, pectate lyase, β-galactosidase, and ethylene biosynthesis enzymes are related to mango fruit ripening, flavor, firmness, softening, and other quality processes, while genes involved in the MAPK signaling pathway, heat shock proteins, hormone signaling, and phenylpropanoid biosynthesis are associated with diseases. Metabolomics identified volatiles, organic acids, amino acids, and various other compounds that determine the characteristic flavor and aroma of the mango fruit. Molecular markers differentiate the mango cultivars based on their geographical origins. Genetic linkage maps and quantitative trait loci studies identified regions in the genome that are associated with economically important traits. The review summarizes the applications of omics techniques and their potential applications toward understanding mango fruit physiology and their usefulness in future mango breeding.

Interactions of melatonin, reactive oxygen species, and nitric oxide during fruit ripening: an update and prospective view

Fruit ripening is a physiological process that involves a complex network of signaling molecules that act as switches to activate or deactivate certain metabolic pathways at different levels, not only by regulating gene and protein expression but also through post-translational modifications of the involved proteins. Ethylene is the distinctive molecule that regulates the ripening of fruits, which can be classified as climacteric or non-climacteric according to whether or not, respectively, they are dependent on this phytohormone. However, in recent years it has been found that other molecules with signaling potential also exert regulatory roles, not only individually but also as a result of interactions among them. These observations imply the existence of mutual and hierarchical regulations that sometimes make it difficult to identify the initial triggering event. Among these 'new' molecules, hydrogen peroxide, nitric oxide, and melatonin have been highlighted as prominent. This review provides a comprehensive outline of the relevance of these molecules in the fruit ripening process and the complex network of the known interactions among them.

Controlled atmosphere storage alleviates internal browning in flat peach fruit by regulating energy and sugar metabolisms

Flat peach fruit are cold-sensitive and vulnerable to chilling injury (CI), particularly internal browning (IB) during cold storage, which limits the consumer acceptance and market value of the fruit. Controlled atmosphere (CA) has been used to alleviate IB in fruit. However, the mechanisms of CA on IB in peach remains unknown. This study investigated the effects of CA (3-3.5% Oxygen, 3-3.5% Carbon dioxide, and 93-94% nitrogen) treatment on IB development, sugar metabolism, and energy metabolism in cold-stored (1 ± 0.5 °C) peach. The CA treatment effectively inhibited the development of IB and markedly inhibited the reduction of sugar contents and energy charge. The protein expression of the V-type proton ATPase subunit was significantly inhibited by the CA treatment, accompanied by higher adenosine triphosphate (ATP) content, and energy charge than the control fruit. Notably, the expressions of the pyruvate kinase family of proteins, pyruvate decarboxylases, and sucrose synthase were induced by CA treatment that had complex protein interactions with the ATPase and the energy metabolism pathway. These results indicated that CA treatment enhanced the chilling tolerance attributed to maintaining higher levels of energy status and sugar contents by regulating the expression of key proteins involved in energy metabolism during cold storage and shelf life. Taken together, our study can provide theoretical support for the research and development of fresh-keeping and cold-chain logistics technology.

Comparative Proteomics Study on the Postharvest Senescence of Volvariella volvacea

Volvariella volvacea is difficult to store after harvest, which restricts the production and circulation of V. volvacea fruiting bodies. Low-temperature storage is the traditional storage method used for most edible fungi. However, V. volvacea undergoes autolysis at low temperatures. When fruiting bodies are stored at 15 °C (suitable temperature), V. volvacea achieves the best fresh-keeping effect. However, the molecular mechanism underlying the postharvest senescence of V. volvacea remains unclear. Based on this information, we stored V. volvacea fruiting bodies at 15 °C after harvest and then analyzed the texture and phenotype combined with the results of previous physiological research. Four time points (0, 24, 60, and 96 h) were selected for the comparative proteomics study of V. volvacea during storage at 15 °C. A variety of proteins showed differential expressions in postharvest V. volvacea at 15 °C. Further comparison of the gene ontology (GO) enrichment analysis and KEGG pathways performed at different sampling points revealed proteins that were significantly enriched at several time points. At the same time, we also analyzed differentially expressed proteins (DEPs) related to the RNA transport, fatty acid biosynthesis and metabolism, and amino acid biosynthesis and metabolism pathways, and discussed the molecular functions of the PAB1, RPG1, ACC1, ADH3, ADH2, ALD5, and SDH2 proteins in postharvest V. volvacea senescence. Our results showed that many biological processes of the postharvest senescence of V. volvacea changed. Most importantly, we found that most RNA transport-related proteins were down-regulated, which may lead to a decrease in related gene regulation. Our results also showed that the expression of other important proteins, such as the fatty acid metabolism related proteins increased; and changes in fatty acid composition affected the cell membrane, which may accelerate the ripening and perception of V. volvacea fruiting bodies. Therefore, our research provides a reference for further studies on the aging mechanism of V. volvacea.

Mitochondrial protein expression during sweet pepper (Capsicum annuum L.) fruit ripening: iTRAQ-based proteomic analysis and role of cytochrome c oxidase

The physiological process of fruit ripening is associated with the late developmental stages of plants in which mitochondrial organelles play an important role in the final success of this whole process. Thus, an isobaric tag for relative and absolute quantification (iTRAQ)-based analysis was used to quantify the mitochondrial proteome in pepper fruits in this study. Analysis of both green and red pepper fruits identified a total of 2284 proteins, of which 692 were found to be significantly more abundant in unripe green fruits as compared to red fruits, while 497 showed lower levels as the ripening process proceeded. Of the total number of proteins identified, 2253 (98,6%) were found to share orthologs with Arabidopsis thaliana. Proteomic analysis identified 163 proteins which were categorized as cell components, the major part assigned to cellular, intracellular space and other subcellular locations such as cytosol, plastids and, to a lesser extent, to mitochondria. Of the 224 mitochondrial proteins detected in pepper fruits, 78 and 48 were more abundant in green and red fruits, respectively. The majority of these proteins which displayed differential abundance in both fruit types were involved in the mitochondrial electron transport chain (mETC) and the tricarboxylic acid (TCA) cycle. The abundance levels of the proteins from both pathways were higher in green fruits, except for cytochrome c (CYC2), whose abundance was significantly higher in red fruits. We also investigated cytochrome c oxidase (COX) activity during pepper fruit ripening, as well as in the presence of molecules such as nitric oxide (NO) and hydrogen peroxide (H₂O₂), which promote thiol-based oxidative post-translational modifications (oxiPTMs). Thus, with the aid of in vitro assays, cytochrome c oxidase (COX) activity was found to be potentially inhibited by the PTMs nitration, S-nitrosation and carbonylation. According to protein abundance data, the final segment of the mETC appears to be a crucial locus with regard to fruit ripening, but also because in this location the biosynthesis of ascorbate, an antioxidant which plays a major role in the metabolism of pepper fruits, occurs.

Quantitative Transcriptomic and Proteomic Analysis of Fruit Development and Ripening in Watermelon (Citrullus lanatus)

Fruit ripening is a highly complicated process, which is modulated by phytohormones, signal regulators and environmental factors playing in an intricate network that regulates ripening-related genes expression. Although transcriptomics is an effective tool to predict protein levels, protein abundances are also extensively affected by post-transcriptional and post-translational regulations. Here, we used RNA sequencing (RNA-seq) and tandem mass tag (TMT)-based quantitative proteomics to study the comprehensive mRNA and protein expression changes during fruit development and ripening in watermelon, a non-climacteric fruit. A total of 6,226 proteins were quantified, and the large number of quantitative proteins is comparable to proteomic studies in model organisms such as Oryza sativa L. and Arabidopsis. Base on our proteome methodology, integrative analysis of the transcriptome and proteome showed that the mRNA and protein levels were poorly correlated, and the correlation coefficients decreased during fruit ripening. Proteomic results showed that proteins involved in alternative splicing and the ubiquitin proteasome pathway were dynamically expressed during ripening. Furthermore, the spliceosome and proteasome were significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, suggesting that post-transcriptional and post-translational mechanisms might play important roles in regulation of fruit ripening-associated genes expression, which might account for the poor correlation between mRNAs and proteins during fruit ripening. Our comprehensive transcriptomic and proteomic data offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of fruit ripening.

Peroxisomal Proteome Mining of Sweet Pepper (Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis

Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.

Integrative Morphological, Physiological, Proteomics Analyses of Jujube Fruit Development Provide Insights Into Fruit Quality Domestication From Wild Jujube to Cultivated Jujube

Jujube (Ziziphus jujuba) was domesticated from wild jujube (Z. jujuba var. spinosa). Here, integrative physiological, metabolomic, and comparative proteomic analyses were performed to investigate the fruit expansion and fruit taste components in a jujube cultivar 'Junzao' and a wild jujube 'Qingjiansuanzao' with contrasting fruit size and taste. We revealed that the duration of cell division and expansion largely determined the final fruit size, while the intercellular space in the mesocarp dictated the ratio of mesocarp volume in mature fruits. The high levels of endogenous gibbereline3 (GA) and zeatin in the growing fruit of 'Junzao' were associated with their increased fruit expansion. Compared with 'Junzao,' wild jujube accumulated lower sugars and higher organic acids. Furthermore, several protein co-expression modules and important member proteins correlated with fruit expansion, sugar synthesis, and ascorbic acid metabolism were identified. Among them, GA20OX involved in GA biosynthesis was identified as a key protein regulating fruit expansion, whereas sucrose-6-phosphate synthase (SPS) and neutral invertase (NINV) were considered as key enzymes promoting sugar accumulation and as major factors regulating the ratio of sucrose to hexose in jujube fruits, respectively. Moreover, the increase of Nicotinamide adenine dinucleotide-Malate dehydrogenase (NAD-MDH) activity and protein abundance were associated with the malic acid accumulation, and the high accumulation of ascorbic acid in wild jujube was correlated with the elevated abundance of GalDH, ZjAPXs, and MDHAR1, which are involved in the ascorbic acid biosynthesis and recycling pathways. Overall, these results deepened the understanding of mechanisms regulating fruit expansion and sugar/acids metabolisms in jujube fruit.

The proteomic data of liver in mice with hyperlipidemia

Fructus Rosae Roxburghii (FRR) has been considered as edible and medicinal fruit possessing antiatherosclerotic effect [1], [2], [3], [4], [5], but the mechanism is still unclear. Hyperlipidemia (HLP) is the material basis for atherosclerosis (AS) formation [6,7]. In this study, total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), lower high-density lipoprotein (HDL) and atherosclerotic index (ASI) in mice were analyzed under the action of FRR juice. Then differentially expressed proteins in liver were further analyzed by using TMT labeling and LC-MS/MS for better understanding the effect and molecular mechanism of FRR on diet-induced hyperlipidemic mice [8]. After the protein extraction and trypsin digestion, TMT labeling proteomic analysis were performed. The functions and KEGG signaling pathways of differentially expressed proteins were analyzed by bioinformatics methods. Hence, the potential antiatherosclerotic mechanism of FRR regulating blood lipids from protein level has great significance to explore new drug targets for AS.

Why Consumers Prefer Green Friariello Pepper: Changes in the Protein and Metabolite Profiles Along the Ripening

Fruit ripening is a physiologically complex process altering texture, color, flavor, nutritional value, and aroma. However, some fruits are consumed at an early stage of ripening due to the very peculiar characteristics varying during ripening. An example is a particular ecotype of pepper, the Friariello pepper, among the most important representatives of Campania (Southern Italy) agro-alimentary culture. In this study, for the first time, the physiological variations during Friariello ripening (green, veraison, and fully ripe) were evaluated by hyphenated mass spectrometric techniques in a proteomic and metabolomic approach. We found that Lutein and Thaumatin are particularly abundant in the green Friariello. Friariello at an early stage of ripening, is rich in volatile compounds like butanol, 1 3 5-cycloheptatriene, dimethylheptane, α-pinene, furan-2-penthyl, ethylhexanol, 3-carene, detected by gas chromatography-mass spectrometry (GC-MS) analysis, which give it the peculiar fresh and pleasant taste. The detected features of Friariello may justify its preferential consumption in the early ripening stage and outline new knowledge aimed at preserving specific agro-cultural heritage.

Identification of Compounds with Potential Therapeutic Uses from Sweet Pepper (Capsicum annuum L.) Fruits and Their Modulation by Nitric Oxide (NO)

Plant species are precursors of a wide variety of secondary metabolites that, besides being useful for themselves, can also be used by humans for their consumption and economic benefit. Pepper (Capsicum annuum L.) fruit is not only a common food and spice source, it also stands out for containing high amounts of antioxidants (such as vitamins C and A), polyphenols and capsaicinoids. Particular attention has been paid to capsaicin, whose anti-inflammatory, antiproliferative and analgesic activities have been reported in the literature. Due to the potential interest in pepper metabolites for human use, in this project, we carried out an investigation to identify new bioactive compounds of this crop. To achieve this, we applied a metabolomic approach, using an HPLC (high-performance liquid chromatography) separative technique coupled to metabolite identification by high resolution mass spectrometry (HRMS). After chromatographic analysis and data processing against metabolic databases, 12 differential bioactive compounds were identified in sweet pepper fruits, including quercetin and its derivatives, L-tryptophan, phytosphingosin, FAD, gingerglycolipid A, tetrahydropentoxylin, blumenol C glucoside, colnelenic acid and capsoside A. The abundance of these metabolites varied depending on the ripening stage of the fruits, either immature green or ripe red. We also studied the variation of these 12 metabolites upon treatment with exogenous nitric oxide (NO), a free radical gas involved in a good number of physiological processes in higher plants such as germination, growth, flowering, senescence, and fruit ripening, among others. Overall, it was found that the content of the analyzed metabolites depended on the ripening stage and on the presence of NO. The metabolic pattern followed by quercetin and its derivatives, as a consequence of the ripening stage and NO treatment, was also corroborated by transcriptomic analysis of genes involved in the synthesis of these compounds. This opens new research perspectives on the pepper fruit’s bioactive compounds with nutraceutical potentiality, where biotechnological strategies can be applied for optimizing the level of these beneficial compounds.

Impact of ripening on the health-promoting components from fruta-do-lobo (Solanum lycocarpum St. Hill)

Fruta-do-lobo (Solanum lycocarpum St. Hill) is an underutilized native fruit commonly found in the Brazilian Cerrado, very known due to the presence of glycoalkaloids. In this work we evaluated the biochemical changes on carbohydrates, phenolic and alkaloids during ripening of fruta-do-lobo using chromatographic and spectrometric techniques. During ripening, we observed an increase in glucose, fructose and sucrose, while oligosaccharides levels varied. Chlorogenic acid isomers represented 80% of the identified phenolic compounds in unripe stage, but they reduced during ripening, resulting in predominance of p-coumaroylquinic acid (peel and pulp) and 1-O-sinapoyl-glucoside (seeds). Statistical analysis shows that the unripe fractions were richer in alkaloids compounds, which were the most important for antioxidant activity. Molecular network analysis summarizes the compound changes during ripening, especially regarding the alkaloid compounds, with a reduction of around 85% of solamargine abundance. These data show that fruta-do-lobo can presents different chemical compositions due their ripening stage providing support for future research aimed to the application of these compounds in glycemia control or uses of their extracts with higher content of alkaloids compounds.

Proteomic Changes in Antioxidant System in Strawberry During Ripening

To investigate the strawberry antioxidant defense system during fruit ripening, a targeted quantitative proteomic approach using multiple reaction monitoring (MRM) was developed to investigate targeted proteins in the antioxidant enzyme system in strawberry fruit. We investigated 46 proteins and isoforms with 73 identified peptides which may be involved in this antioxidant enzyme system. Among the proteins that changed during ripening, aldo/keto reductase (AKR), superoxide dismutase (SOD) and glutathione transferase (GT) increased significantly, while dehydroascorbate reductase, 2-Cys peroxiredoxin, catalase (CAT), 1-Cys peroxiredoxin and L-ascorbate peroxidase (APX) decreased significantly. These results suggest that fruit ripening of strawberry activates the enzymes of an SOD/glutathione metabolism system. The methodologies used in this study will be useful for systematically characterizing the role of antioxidant enzymes in fruit ripening of other plants.

Comparative proteomic analysis of oil palm (Elaeis guineensis Jacq.) during early fruit development

To gain insights on protein changes in fruit setting and growth in oil palm, a comparative proteomic approach was undertaken to study proteome changes during its early development. The variations in the proteome at five early developmental stages were investigated via a gel-based proteomic technique. A total of 129 variant proteins were determined using mass spectrometric analysis, resulting in 80 identifications. The majority of the identified protein species were classified as energy and metabolism, stress response/defence and cell structure during early oil palm development representing potential candidates for the control of final fruit size and composition. Seven prominent protein species were then characterised using real-time polymerase chain reaction to validate the mRNA expression against the protein abundant profiles. Transcript and protein profiles were parallel across the developmental stages, but divergent expression was observed in one protein spot, indicative of possible post-transcriptional events. Our results revealed protein changes in early oil palm fruit development provide valuable information in the understanding of fruit growth and metabolism during early stages that may contribute towards improving agronomic traits. BIOLOGICAL SIGNIFICANCE: Two-dimensional gel electrophoresis coupled with mass spectrometry approach was used in this study to identify differentially expressed proteins during early oil palm fruit development. A total of 80 protein spots with significant change in abundance were successfully identified and selected genes were analysed using real time PCR to validate their expression. The dynamic changes in oil palm fruit proteome during early development were mostly active in primary and energy metabolism, stress responses, cell structure and protein metabolism. This study reveals the physiological processes during early oil palm fruit development and provides a reference proteome for further improvements in fruit quality traits.

Metabolomic and transcriptomic analyses highlight the influence of lipid changes on the post-harvest softening of Pyrus ussurian Max. 'Zaoshu Shanli'

How lipids influence post-harvest softening in pears is not well understood. LC-MS/MS (Liquid chromatography-tandem mass spectrometry) and RNA-Seq analyses of 'Zaoshu Shanli' (ZSSL) pears were conducted during post-harvest storage. This approach enabled the identification of 98 different metabolites that upregulated and 95 that downregulated at 18 days post-harvest in ZSSL fruits to day 0. Metabolites were significantly enriched in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways including glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis. When comparing fruits from day 18 to those from day 0 post-harvest, RNA-seq analyses further highlighted 6496 differentially expressed genes (DEGs) in ZSSL fruits that were significantly enriched in KEGG pathways including glycerophospholipid metabolism and fatty acid degradation. Overall, these results suggested that glycerophospholipid metabolism is closely related to the post-harvest softening of pears. Further research will be essential in order to fully explore the functional implications of and mechanistic basis for these findings.

Antioxidant Profile of Pepper (Capsicum annuum L.) Fruits Containing Diverse Levels of Capsaicinoids

Capsicum is the genus where a number of species and varieties have pungent features due to the exclusive content of capsaicinoids such as capsaicin and dihydrocapsaicin. In this work, the main enzymatic and non-enzymatic systems in pepper fruits from four varieties with different pungent capacity have been investigated at two ripening stages. Thus, a sweet pepper variety (Melchor) from California-type fruits and three autochthonous Spanish varieties which have different pungency levels were used, including Piquillo, Padrón and Alegría riojana. The capsaicinoids contents were determined in the pericarp and placenta from fruits, showing that these phenyl-propanoids were mainly localized in placenta. The activity profiles of catalase, total and isoenzymatic superoxide dismutase (SOD), the enzymes of the ascorbate–glutathione cycle (AGC) and four NADP-dehydrogenases indicate that some interaction with capsaicinoid metabolism seems to occur. Among the results obtained on enzymatic antioxidants, the role of Fe-SOD and the glutathione reductase from the AGC is highlighted. Additionally, it was found that ascorbate and glutathione contents were higher in those pepper fruits which displayed the greater contents of capsaicinoids. Taken together, all these data indicate that antioxidants may contribute to preserve capsaicinoids metabolism to maintain their functionality in a framework where NADPH is perhaps playing an essential role.

Proteomic analysis of liver in diet-induced Hyperlipidemic mice under Fructus Rosa roxburghii action

Fructus Rosae Roxburghii (FRR) has been considered as edible and medicinal fruit possessing antiatherosclerotic effect, but the mechanism is still unclear. HLP is material basis for AS formation. Under FRR action, TC, TG, LDL, HDL and ASI in serum were regulated to control level. Differentially expressed proteins in liver were analyzed by using TMT labeling and LC-MS/MS for better understanding the effect and molecular mechanism of FRR on diet-induced hyperlipidemic mice. In total, 4460 proteins were quantified, of which 469 proteins showed dramatic changes between each group. According to molecular functions, 25 differentially co-expressed proteins were divided into five categories: substance metabolism, energy transformation and signal transduction, transcription and translation, immune defense. 15 key proteins involved lipids metabolism, which were identified as Cyp7a1, Cyp3a11, Tm7sf2, COAT2, CSAD, RBP3, Lpin1, Dhrs4, Aldh1b1, GK, Acot 4, TSC22D1, PGFS, EHs, GSTM1. This suggested that FRR could maintain metabolic homeostasis by regulating the metabolism of fatty acids, biosynthesis of BAs and steroids, and production of LPOs. 20 oxidative lipids further confirmed their importance regulating lipids metabolism. It's first time potential antiatherosclerotic mechanism of FRR regulating blood lipids was explored from protein level, which is of great significance to explore new drug targets for AS. SIGNIFICANCE: Under the action of FRR juice, the blood lipids in mice were regulated to control level. By TMT proteomic analysis, the effect and molecular mechanism of FRR on diet-induced hyperlipidemic mice were further explored. 25 differentially co-expressed proteins obtained in three diet groups might cooperatively regulate the lipids metabolism and hepatic function of mice, thus maintaining the metabolism homeostasis. By lipidomics analysis, 20 oxidative lipids further confirmed the importance of ω-3 and ω-6 PUFAs in regulating the lipids metabolism. These findings provide an improved understanding for the regulation of FRR on the blood lipids and explores potential metabolic targets for AS prevention.

BJ-B11, an Hsp90 Inhibitor, Constrains the Proliferation and Invasion of Breast Cancer Cells

Breast cancer is the leading cause of cancer-related deaths in women; however, its underlying etiology remains largely unknown. In this study, we systematically analyzed breast cancer tissues using comprehensive iTRAQ labeled quantitative proteomics, identifying 841 differentially expressed proteins (474 and 367 significantly over- and under-expressed, respectively), which were annotated by protein domain analysis. All the heat shock proteins identified were upregulated in breast cancer tissues; Hsp90 upregulation was also validated by RT-qPCR and immunohistochemistry, and high Hsp90 protein levels correlated with poorer survival. Hsp90AA1 overexpression promoted MDA-MB-231 cell proliferation, whilst BJ-B11, an Hsp90 inhibitor, hampered their invasion, migration, and proliferation in a time and dose-dependent manner and induced cell cycle arrest and apoptosis. BJ-B11 inhibited the expression of epithelial-mesenchymal transition (EMT) marker in MDA-MB-231 cells, whereas Hsp90AA1 promoted its expression. Moreover, BJ-B11 inhibited tumor growth in xenograft model. Altogether, Hsp90 activation is a risk factor in breast cancer patients, and BJ-B11 could be used to treat breast cancer.

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

Soluble sugars and organic acids are the main determinants of fruit organoleptic quality. To investigate the genes responsible for the soluble sugar and organic acid contents of apple fruits, a label-free proteomic analysis involving liquid chromatography (LC)-mass spectrometry (MS)/MS was conducted with the fruits of two Malus species, M. sargentii and M. niedzwetzkyana, which exhibit significant differences in soluble sugar and organic acid contents. A total of 13,036 unique peptides and 1,079 differentially-expressed proteins were identified. To verify the LC-MS/MS results, five candidate proteins were further analyzed by parallel reaction monitoring. The results were consistent with the LC-MS/MS data, which confirmed the reliability of the LC-MS/MS analysis. The functional annotation of the differentially-expressed proteins, based on the gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, revealed that they were mainly related to biological processes and cellular components. Additionally, the main enriched KEGG pathways were related to metabolic processes. Moreover, 31 proteins involved in soluble sugar metabolism, organic acid metabolism, and H⁺-transport were identified. The results of this study may be useful for the comprehensive characterization of the complex mechanism regulating apple fruit-soluble sugar and organic acid contents.

Sweet Pepper (Capsicum annuum L.) Fruits Contain an Atypical Peroxisomal Catalase That is Modulated by Reactive Oxygen and Nitrogen Species

During the ripening of sweet pepper (Capsicum annuum L.) fruits, in a genetically controlled scenario, enormous metabolic changes occur that affect the physiology of most cell compartments. Peroxisomal catalase gene expression decreases after pepper fruit ripening, while the enzyme is also susceptible to undergo post-translational modifications (nitration, S-nitrosation, and oxidation) promoted by reactive oxygen and nitrogen species (ROS/RNS). Unlike most plant catalases, the pepper fruit enzyme acts as a homodimer, with an atypical native molecular mass of 125 to 135 kDa and an isoelectric point of 7.4, which is higher than that of most plant catalases. These data suggest that ROS/RNS could be essential to modulate the role of catalase in maintaining basic cellular peroxisomal functions during pepper fruit ripening when nitro-oxidative stress occurs. Using catalase from bovine liver as a model and biotin-switch labeling, in-gel trypsin digestion, and nanoliquid chromatography coupled with mass spectrometry, it was found that Cys377 from the bovine enzyme could potentially undergo S-nitrosation. To our knowledge, this is the first report of a cysteine residue from catalase that can be post-translationally modified by S-nitrosation, which makes it especially important to find the target points where the enzyme can be modulated under either physiological or adverse conditions.

Capsaicinoids, Polyphenols and Antioxidant Activities of Capsicum annuum: Comparative Study of the Effect of Ripening Stage and Cooking Methods

Peppers (Capsicum annuum L.) are an important crop usually consumed as food or spices. Peppers contain a wide range of phytochemicals, such as capsaicinoids, phenolics, ascorbic acid, and carotenoids. Capsaicinoids impart the characteristic pungent taste. The study analyzed capsaicinoids and other bioactive compounds in different pepper cultivars at both the mature green and red stages. The effect of roasting on their nutritional content was also investigated. In the cultivars tested, the levels of capsaicin ranged from 0 to 3636 µg/g in the mature green stage and from 0 to 4820 µg/g in the red/yellow stage. The concentration of dihydrocapsaicin ranged from 0 to 2148 µg/g in the mature green stage and from 0 to 2162 µg/g in the red/yellow stage. The levels of capsaicinoid compounds in mature green and red /yellow stages were either reduced or increased after roasting depending on the cultivar. The ranges of total phenolic and total flavonoids compounds were 2096 to 7689, and 204 to 962 µg/g, respectively, in the green and red/yellow mature stage pods. Ascorbic acid levels in the peppers ranged from 223 to 1025 mg/ 100 g Dry Weight (DW). Both raw and roasted peppers possessed strong antioxidant activity as determined by 2,2-diphenyl-1-picrylhydrazyl) reagent (DPPH, 61–87%) and 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS, 73–159 µg/g) assays. Ascorbic acid and antioxidant activity decreased after roasting in the mature green and red stages, whereas total phenolics and flavonoids increased except in the mature green stage of Sweet Delilah and yellow stage of Canrio.

Nitric oxide in the physiology and quality of fleshy fruits

Fruits are unique to flowering plants and confer a selective advantage as they facilitate seed maturation and dispersal. In fleshy fruits, development and ripening are associated with numerous structural, biochemical, and physiological changes, including modifications in the general appearance, texture, flavor, and aroma, which ultimately convert the immature fruit into a considerably more attractive and palatable structure for seed dispersal by animals. Treatment with exogenous nitric oxide (NO) delays fruit ripening, prevents chilling damage, promotes disease resistance, and enhances the nutritional value. The ripening process is influenced by NO, which operates antagonistically to ethylene, but it also interacts with other regulatory molecules such as abscisic acid, auxin, jasmonic acid, salicylic acid, melatonin, and hydrogen sulfide. NO content progressively declines during fruit ripening, with concomitant increases in protein nitration and nitrosation, two post-translational modifications that are promoted by reactive nitrogen species. Dissecting the intimate interactions of NO with other ripening-associated factors, including reactive oxygen species, antioxidants, and the aforementioned phytohormones, remains a challenging subject of research. In this context, integrative 'omics' and gene-editing approaches may provide additional knowledge of the impact of NO in the regulatory processes involved in controlling physiology and quality traits in both climacteric and non-climacteric fruits.

Primary Metabolism in Avocado Fruit

Avocado (Persea americana Mill) is rich in a variety of essential nutrients and phytochemicals; thus, consumption has drastically increased in the last 10 years. Avocado unlike other fruit is characterized by oil accumulation during growth and development and presents a unique carbohydrate pattern. There are few previous and current studies related to primary metabolism. The fruit is also quite unique since it contains large amounts of C7 sugars (mannoheptulose and perseitol) acting as transportable and storage sugars and as potential regulators of fruit ripening. These C7 sugars play a central role during fruit growth and development, but still confirmation is needed regarding the biosynthetic routes and the physiological function during growth and development of avocado fruit. Relatively recent transcriptome studies on avocado mesocarp during development and ripening have revealed that most of the oil is synthesized during early stages of development and that oil synthesis is halted when the fruit is harvested (pre-climacteric stage). Most of the oil is accumulated in the form of triacylglycerol (TAG) representing 60-70% in dry basis of the mesocarp tissue. During early stages of fruit development, high expression of transcripts related to fatty acid and TAG biosynthesis has been reported and downregulation of same genes in more advanced stages but without cessation of the process until harvest. The increased expression of fatty acid key genes and regulators such as PaWRI1, PaACP4-2, and PapPK-β-1 has also been reported to be consistent with the total fatty acid increase and fatty acid composition during avocado fruit development. During postharvest, there is minimal change in the fatty acid composition of the fruit. Almost inexistent information regarding the role of organic acid and amino acid metabolism during growth, development, and ripening of avocado is available. Cell wall metabolism understanding in avocado, even though crucial in terms of fruit quality, still presents severe gaps regarding the interactions between cell wall remodeling, fruit development, and postharvest modifications.

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

BACKGROUND

Fig fruit are highly perishable at the tree-ripe (TR) stage. Commercial-ripe (CR) fruit, which are harvested before the TR stage for their postharvest transportability and shelf-life advantage, are inferior to TR fruit in size, color and sugar content. The succulent urn-shaped receptacle, serving as the protective structure and edible part of the fruit, determines fruit quality. Quantitative iTRAQ and RNA-Seq were performed to reveal the differential proteomic and transcriptomic traits of the receptacle at the two harvest stages.

RESULTS

We identified 1226 proteins, of which 84 differentially abundant proteins (DAPs) were recruited by criteria of abundance fold-change (FC) ≥1.3 and p < 0.05 in the TR/CR receptacle proteomic analysis. In addition, 2087 differentially expressed genes (DEGs) were screened by ≥2-fold expression change: 1274 were upregulated and 813 were downregulated in the TR vs. CR transcriptomic analysis. Ficin was the most abundant soluble protein in the fig receptacle. Sucrose synthase, sucrose-phosphate synthase and hexokinase were all actively upregulated at both the protein and transcriptional levels. Endoglucanase, expansin, beta-galactosidase, pectin esterase and aquaporins were upregulated from the CR to TR stage at the protein level. In hormonal synthesis and signaling pathways, high protein and transcriptional levels of aminocyclopropane-1-carboxylate oxidase were identified, together with a few diversely expressed ethylene-response factors, indicating the potential leading role of ethylene in the ripening process of fig receptacle, which has been recently reported as a non-climacteric tissue.

CONCLUSIONS

We present the first delineation of intra- and inter-omic changes in the expression of specific proteins and genes of TR vs. CR fig receptacle, providing valuable candidates for further study of fruit-quality formation control and fig cultivar innovation to accommodate market demand.

Mass spectrometry based proteomics for the molecular fingerprinting of Fiano, Greco and Falanghina cultivars

The official methodologies used for the identification and comparison of vine cultivars are ampelography and ampelometry. These methodologies are essentially based on qualitative assessments or biometric dependent morphological features of the plant. The heterogeneity of cultivars and consequently the increasing demand for a more detailed product typization, led to the introduction of new methodologies for the varietal characterization. In this scenario, proteomics has already proved to be a very useful discipline for the typization of many kinds of edible products. In this paper, we present a proteomic study carried out on three cultivars of Vitis vinifera peculiar of south Italy (Campania) used for white wine production (Fiano, Greco and Falanghina) by advanced biomolecular mass spectrometry approach. Our data highlight variations in the proteomic profiles during ripening for each cultivar and between analyzed cultivars, thus suggesting a new way to outline the biomolecular signature of vines.

Label-free quantitative proteomics to investigate the response of strawberry fruit after controlled ozone treatment

To elucidate postharvest senescence in strawberry (Fragaria ananassa Duch. var. 'JingTaoXiang') fruit in response to ozone treatment at different concentrations (0, 2.144, 6.432, and 10.72 mg m-3), a label-free quantitative proteomic investigation was performed. Postharvest physiological quality traits including respiration rate, firmness, titratable acid, and anthocyanin content were characterized. The observed protein expression profile after storage was related to delayed senescence in strawberries. A total of 2413 proteins were identified in differentially treated strawberry fruits, and 382 proteins were differentially expressed between the four treatments on day 7 and the initial value (blank 0). Proteins related to carbohydrate and energy metabolism and anthocyanin biosynthesis, cell stress response, and fruit firmness were characterized and quantified. Ozone treatment at the concentration of 10.72 mg m-3 effectively delayed the senescence of the strawberry. The proteomic profiles were linked to physiological traits of strawberry fruit senescence to provide new insights into possible molecular mechanisms.

Systematically quantitative proteomics and metabolite profiles offer insight into fruit ripening behavior in Fragaria × ananassa

Profound metabolic and proteomic changes involved in the primary and the secondary metabolism are required for the ripeness of fleshy fruit such as strawberries (Fragaria × ananassa). Here we present the quantitative proteomic profiling in parallel with metabolic and transcriptional profiling at five developmental stages of strawberry fruit ripening, and correlations between changes in representative metabolites and the abundance of related proteins were analyzed. Hierarchical clustering analysis of the quantitative proteomic profiling identified 143 proteins in strawberry fruit across five developmental stages. Meanwhile, both protein abundance and gene expression spanned a wide range of roles, such as the primary and the secondary metabolism, defense system, and response to stress stimuli. The decreased abundance of proteins contributed to the carbohydrate metabolism and the up-regulated expression of secondary biosynthetic proteins was found to be positively correlated with the accumulation of primary and secondary metabolites during strawberry development. Moreover, with the same annotations and high homology, the gene function of key genes involved in primary and secondary metabolism (FaTPI, FaPAL, FaMDH and FaME) was confirmed in Nicotiana via the transient expression assay, which provides further evidence for the role of those genes in metabolism of strawberry fruit. The results of the present study may serve as an important resource for the functional analysis of the proteome and offer new perspectives on regulation of fruit quality.

Proteome and metabolite profiles of fruit ripening behavior in Fragaria × ananassa Duch. ‘Benihoppe’.

Unveiling Kiwifruit Metabolite and Protein Changes in the Course of Postharvest Cold Storage

Actinidia deliciosa cv. Hayward fruit is renowned for its micro- and macronutrients, which vary in their levels during berry physiological development and postharvest processing. In this context, we have recently described metabolic pathways/molecular effectors in fruit outer endocarp characterizing the different stages of berry physiological maturation. Here, we report on the kiwifruit postharvest phase through an integrated approach consisting of pomological analysis combined with NMR/LC-UV/ESI-IT-MSⁿ- and 2D-DIGE/nanoLC-ESI-LIT-MS/MS-based proteometabolomic measurements. Kiwifruit samples stored under conventional, cold-based postharvest conditions not involving the use of dedicated chemicals were sampled at four stages (from fruit harvest to pre-commercialization) and analyzed in comparison for pomological features, and outer endocarp metabolite and protein content. About 42 metabolites were quantified, together with corresponding proteomic changes. Proteomics showed that proteins associated with disease/defense, energy, protein destination/storage, cell structure and metabolism functions were affected at precise fruit postharvest times, providing a justification to corresponding pomological/metabolite content characteristics. Bioinformatic analysis of variably represented proteins revealed a central network of interacting species, modulating metabolite level variations during postharvest fruit storage. Kiwifruit allergens were also quantified, demonstrating in some cases their highest levels at the fruit pre-commercialization stage. By lining up kiwifruit postharvest processing to a proteometabolomic depiction, this study integrates previous observations on metabolite and protein content in postharvest berries treated with specific chemical additives, and provides a reference framework for further studies on the optimization of fruit storage before its commercialization.

An integrated proteomic and metabolomic study to evaluate the effect of nucleus-cytoplasm interaction in a diploid citrus cybrid between sweet orange and lemon

Our results provide a comprehensive overview how the alloplasmic condition might lead to a significant improvement in citrus plant breeding, developing varieties more adaptable to a wide range of conditions. Citrus cybrids resulting from somatic hybridization hold great potential in plant improvement. They represent effective products resulting from the transfer of organelle-encoded traits into cultivated varieties. In these cases, the plant coordinated array of physiological, biochemical, and molecular functions remains the result of integration among different signals, which derive from the compartmentalized genomes of nucleus, plastids and mitochondria. To dissect the effects of genome rearrangement into cybrids, a multidisciplinary study was conducted on a diploid cybrid (C2N), resulting from a breeding program aimed to improve interesting agronomical traits for lemon, the parental cultivars 'Valencia' sweet orange (V) and 'femminello' lemon (F), and the corresponding somatic allotetraploid hybrid (V + F). In particular, a differential proteomic analysis, based on 2D-DIGE and MS procedures, was carried out on leaf proteomes of C2N, V, F and V + F, using the C2N proteome as pivotal condition. This investigation revealed differentially represented protein patterns that can be associated with genome rearrangement and cell compartment interplay. Interestingly, most of the up-regulated proteins in the cybrid are involved in crucial biological processes such as photosynthesis, energy production and stress tolerance response. The cybrid differential proteome pattern was concomitant with a general increase of leaf gas exchange and content of volatile organic compounds, highlighting a stimulation of specific pathways that can be related to observed plant performances. Our results contribute to a better understanding how the alloplasmic condition might lead to a substantial improvement in plant breeding, opening new opportunities to develop varieties more adaptable to a wide range of conditions.

Endogenous hydrogen sulfide (H2S) is up-regulated during sweet pepper (Capsicum annuum L.) fruit ripening. In vitro analysis shows that NADP-dependent isocitrate dehydrogenase (ICDH) activity is inhibited by H2S and NO

Like nitric oxide (NO), hydrogen sulfide (H₂S) has been recognized as a new gasotransmitter which plays an important role as a signaling molecule in many physiological processes in higher plants. Although fruit ripening is a complex process associated with the metabolism of reactive oxygen species (ROS) and nitrogen oxygen species (RNS), little is known about the potential involvement of endogenous H₂S. Using sweet pepper (Capsicum annuum L.) as a model non-climacteric fruit during the green and red ripening stages, we studied endogenous H₂S content and cytosolic l-cysteine desulfhydrase (L-DES) activity which increased by 14% and 28%, respectively, in red pepper fruits. NADPH is a redox compound and key cofactor required for cell growth, proliferation and detoxification. We studied the NADPH-regenerating enzyme, NADP-isocitrate dehydrogenase (NADP-ICDH), whose activity decreased by 34% during ripening. To gain a better understanding of its potential regulation by H₂S, we obtained a 50-75% ammonium sulfate-enriched protein fraction containing the NADP-ICDH protein; with the aid of in vitro assays in the presence of H₂S, we observed that 2 and 10 mM NaHS used as H₂S donors resulted in a decrease of up to 36% and 45%, respectively, in NADP-ICDH activity, which was unaffected by reduced glutathione (GSH). On the other hand, peroxynitrite (ONOO^-), S-nitrosocyteine (CysNO) and DETA-NONOate, with the last two acting as NO donors, also inhibited NADP-ICDH activity. In silico analysis of the tertiary structure of sweet pepper NADP-ICDH activity (UniProtKB ID A0A2G2Y555) suggests that residues Cys133 and Tyr450 are the most likely potential targets for S-nitrosation and nitration, respectively. Taken together, the data reveal that the increase in the H₂S production capacity of red fruits is due to higher L-DES activity during non-climacteric pepper fruit ripening. In vitro assays appear to show that H₂S inhibits NADP-ICDH activity, thus suggesting that this enzyme may be regulated by persulfidation, as well as by S-nitrosation and nitration. NO and H₂S may therefore regulate NADPH production and consequently cellular redox status during pepper fruit ripening.

Nitro-oxidative metabolism during fruit ripening

Pepper (Capsicum annuum L.) and tomato (Solanum lycopersicum L.), which belong to the Solanaceae family, are among the most cultivated and consumed fleshy fruits worldwide and constitute excellent sources of many essential nutrients, such as vitamins A, C, and E, calcium, and carotenoids. While fruit ripening is a highly regulated and complex process, tomato and pepper have been classified as climacteric and non-climacteric fruits, respectively. These fruits differ greatly in shape, color composition, flavor, and several other features which undergo drastic changes during the ripening process. Such ripening-related metabolic and developmental changes require extensive alterations in many cellular and biochemical processes, which ultimately leads to fully ripe fruits with nutritional and organoleptic features that are attractive to both natural dispersers and human consumers. Recent data show that reactive oxygen and nitrogen species (ROS/RNS) are involved in fruit ripening, during which molecules, such as hydrogen peroxide (H2O2), NADPH, nitric oxide (NO), peroxynitrite (ONOO-), and S-nitrosothiols (SNOs), interact to regulate protein functions through post-translational modifications. In light of these recent discoveries, this review provides an update on the nitro-oxidative metabolism during the ripening of two of the most economically important fruits, discusses the signaling roles played by ROS/RNS in controlling this complex physiological process, and highlights the potential biotechnological applications of these substances to promote further improvements in fruit ripening regulation and nutritional quality. In addition, we suggest that the term 'nitro-oxidative eustress' with regard to fruit ripening would be more appropriate than nitro-oxidative stress, which ultimately favors the consolidation of the plant species.

The Plantain Proteome, a Focus on Allele Specific Proteins Obtained from Plantain Fruits

Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non-model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in-house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole-genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.

The Proteome of Fruit Peroxisomes: Sweet Pepper (Capsicum annuum L.) as a Model

Despite of their economical and nutritional interest, the biology of fruits is still little studied in comparison with reports of other plant organs such as leaves and roots. Accordingly, research at subcellular and molecular levels is necessary not only to understand the physiology of fruits, but also to improve crop qualities. Efforts addressed to gain knowledge of the peroxisome proteome and how it interacts with the overall metabolism of fruits will provide tools to be used in breeding strategies of agricultural species with added value. In this work, special attention will be paid to peroxisomal proteins involved in the metabolism of reactive oxygen species (ROS) due to the relevant role of these compounds at fruit ripening. The proteome of peroxisomes purified from sweet pepper (Capsicum annuum L.) fruit is reported, where an iron-superoxide dismutase (Fe-SOD) was localized in these organelles, besides other antioxidant enzymes such as catalase and a Mn-SOD, as well as enzymes involved in the metabolism of carbohydrates, malate, lipids and fatty acids, amino acids, the glyoxylate cycle and in the potential organelles' movements.

Assimilation of 'omics' strategies to study the cuticle layer and suberin lamellae in plants

The assembly of the lipophilic cuticle layer and suberin lamellae, approximately 450 million years ago, was a major evolutionary development that enabled plants to colonize terrestrial habitats. The cuticle layer is composed of cutin polyester and embedded cuticular waxes, whereas the suberin lamellae consist of very long chain fatty acid derivatives, glycerol, and phenolics cross-linked with alkyl ferulate-embedded waxes. Due to their substantial biological roles in plant life, the mechanisms underlying the assembly of these structures have been extensively investigated. In the last decade, the introduction of 'omics' approaches, including genomics, transcriptomics, proteomics, and metabolomics, have been key in the identification of novel genetic and chemical elements involved in the formation and function of the cuticle layer and suberin lamellae. This review summarizes contemporary studies that utilized various large-scale, 'omics' strategies in combination with novel technologies to unravel how building blocks and polymers of these lipophilic barriers are made, and moreover linking structure to function along developmental programs and stress responses. We anticipate that the studies discussed here will inspire scientists studying lipophilic barriers to integrate complementary 'omics' approaches in their efforts to tackle as yet unresolved questions and engage the main challenges of the field to date.

Proteomic analysis of pear (Pyrus pyrifolia) ripening process provides new evidence for the sugar/acid metabolism difference between core and mesocarp

Pears are one of the most popular nutrient-rich fruits in the world. The pear core and mesocarp have significantly different metabolism, although they display similar profiles. Most strikingly, the core is more acidic in taste. Our results showed that there is more titrated acid but lower total soluble solids in the core compared to the mesocarp, and the content of citric acid was more than 17-fold higher in the core compared to the mesocarp at the ripening stage. Proteomics was used to investigate the difference between core and mesocarp tissues during "Cuiguan" pear ripening. Fifty-four different protein expression patterns were identified in the core and mesocarp. In general, common variably expressed proteins between the core and mesocarp were associated with important physiological processes, such as glycolysis, pyruvate metabolic processes, and oxidative stress. Further, protein level associated qRT-PCR verification revealed a higher abundance of fructose-bisphosphate aldolase and NADP-dependent malic enzymes, which may play a role in the low acid content in the mesocarp, whereas a higher abundance of disulfide isomerase-like 2-2 and calcium-dependent lipid-binding in the core may explain why it is less prone to accumulate sugar. The different levels of a few typical ROS scavenger enzymes suggested that oxidative stress is higher in the core than in the mesocarp. This study provides the first characterization of the pear core proteome and a description of its variation compared to the mesocarp during ripening.

Somatic Embryogenesis in Coffee: The Evolution of Biotechnology and the Integration of Omics Technologies Offer Great Opportunities

One of the most important crops cultivated around the world is coffee. There are two main cultivated species, Coffea arabica and C. canephora. Both species are difficult to improve through conventional breeding, taking at least 20 years to produce a new cultivar. Biotechnological tools such as genetic transformation, micropropagation and somatic embryogenesis (SE) have been extensively studied in order to provide practical results for coffee improvement. While genetic transformation got many attention in the past and is booming with the CRISPR technology, micropropagation and SE are still the major bottle neck and urgently need more attention. The methodologies to induce SE and the further development of the embryos are genotype-dependent, what leads to an almost empirical development of specific protocols for each cultivar or clone. This is a serious limitation and excludes a general comprehensive understanding of the process as a whole. The aim of this review is to provide an overview of which achievements and molecular insights have been gained in (coffee) somatic embryogenesis and encourage researchers to invest further in the in vitro technology and combine it with the latest omics techniques (genomics, transcriptomics, proteomics, metabolomics, and phenomics). We conclude that the evolution of biotechnology and the integration of omics technologies offer great opportunities to (i) optimize the production process of SE and the subsequent conversion into rooted plantlets and (ii) to screen for possible somaclonal variation. However, currently the usage of the latest biotechnology did not pass the stage beyond proof of potential and needs to further improve.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.