Proteomic analysis of apricot fruit during ripening

Effects of Near-Freezing Temperature Combined with Jujube Polysaccharides Treatment on Proteomic Analysis of 'Diaogan' Apricot (Prunus armeniaca L.)

This study involved the extraction of polysaccharides from jujube for application in apricot storage. Although near-freezing temperature (NFT) storage is commonly employed for preserving fresh fruit, its effectiveness is somewhat limited. Incorporating jujube polysaccharides was proposed to augment the preservative effect on apricots. Our findings demonstrated that the combined use of NFT and jujube polysaccharides can maintain fruit color, and effectively inhibit decay. Additionally, Tandem Mass Tag (TMT) quantitative proteomic technology was utilized to analyze protein variations in 'Diaogan' apricots during storage. This dual approach not only markedly lowered the activity of polyphenol cell wall-degrading enzymes (p < 0.05) but also revealed 1054 differentially expressed proteins (DEPs), which are related to sugar and energy metabolism, stress response and defense, lipid metabolism, and cell wall degradation. The changes in DEPs indicated that the combined use of NFT and jujube polysaccharides could accelerate the conversion of malic acid to oxaloacetic acid and regulate antioxidant ability, potentially extending the storage lifespan of apricot fruit.

Transcriptome analysis reveals the mechanism of different fruit appearance between apricot (Armeniaca vulgaris Lam.) and its seedling

BACKGROUND

Apricot fruit has great economic value. In the process of apricot breeding using traditional breeding methods, we obtained a larger seedling (named Us) from the original variety (named U). And Us fruit is larger than U, taste better. Therefore, revealing its mechanism is very important for Apricot breeding.

METHODS

In this study, de novo assembly and transcriptome sequencing (RNA-Seq) was used to screen the differently expressed genes (DEGs) between U and Us at three development stages, including young fruits stage, mid-ripening stage and mature fruit stage.

RESULTS

The results showed that there were 6,753 DEGs at different sampling time. "Cellulose synthase (UDP-forming) activity" and "cellulose synthase activity" were the key GO terms enriched in GO, of which CESA and CSL family played a key role. "Photosynthesis-antenna proteins" and "Plant hormone signal transduction" were the candidate pathways and lhca, lhcb, Aux/IAA and SAUR were the main regulators.

CONCLUSION

The auxin signaling pathway was active in Us, of which Aux/IAAs and SAUR were the key fruit size regulators. The low level of lhca and lhcb in Us could reveal the low demand for exogenous carbon, but they increased at mature stage, which might be due to the role of aux, who was keeping the fruit growing. Aux and photosynthesis maight be the main causes of appearance formation of Us fruits. Interestingly, the higher expression of CESA and CSL proved that Us entered the hardening process earlier than U. The advanced developmental progress might also be due to the role of Aux.

Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation

Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.

Effects of Reactive Oxygen Levels on Chilling Injury and Storability in 21 Apricot Varieties from Different Production Areas in China

The key factors for resistance to chilling injury in apricot fruits were obtained by analyzing the low-temperature storage characteristics of 21 varieties of apricot fruits in the main producing areas of China. Twenty-one varieties of apricots from different production areas in China were stored at 0 °C for 50 d and then shelved at 25 °C. The storage quality, chilling injury, reactive oxygen species (ROS), antioxidant ability, and contents of bioactive substances of the apricots were measured and analyzed. The results showed that the 21 varieties of apricot fruits could be divided into two categories according to tolerance during low-temperature storage, where there was chilling tolerance and lack of chilling tolerance. Eleven varieties of apricots, of which Xiangbai and Yunbai are representative, suffered from severe chilling injury after cold storage and shelf life. After 50 d of storage at 0 °C, the levels of superoxide anions and hydrogen peroxide accumulated in the 11 varieties of apricots with a lack of chilling tolerance during storage were significantly higher than those in the remaining 10 varieties of apricots with chilling tolerance. In addition, the activities of ROS scavenging enzymes, represented by superoxide dismutase, catalase and peroxidase, were significantly decreased in 11 varieties of apricots with a lack of chilling tolerance during storage. The contents of bioactive substances with ROS scavenging ability, represented by ascorbic acid, total phenols, carotenoids, and total flavonoids, also significantly decreased. The 10 varieties of apricots, of which Akeximixi and Suanmao are representative, were less affected by chilling injury because the production and removal of ROS were maintained at normal levels, avoiding the damaging effects of ROS accumulation in the fruit. In addition, the 10 apricot varieties with chilling tolerance during storage had higher sugar and acid contents after harvest. This could supply energy for physiological metabolism during cold storage and provide carbon skeletons for secondary metabolism, thus enhancing the chilling tolerance of the fruits. Based on the results of cluster analysis combined with the geographical distribution of the 21 fruit varieties, it was found that apricot varieties with chilling tolerance during storage were all from the northwestern region of China where diurnal temperature differences and rapid climate changes occur. In conclusion, maintaining the balance of ROS production and removal in apricots during cold storage is a key factor to enhance the storage tolerance of apricots. Moreover, apricots with higher initial glycolic acid and bioactive substance contents are less susceptible to chilling injury.

Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.

The Fruit Proteome Response to the Ripening Stages in Three Tomato Genotypes

The tomato is a horticultural crop that appears in various colors as it ripens. Differences in the proteome expression abundance of a tomato depend on its genotype and ripening stage. Thus, this study aimed to confirm the differences in changes in the proteome according to four ripening stages (green, breaker, turning, and mature) of three tomato genotypes, i.e., yellow, black, and red tomatoes, using a gel-based proteomic technique. The number of protein spots shown as two-dimensional electrophoresis (2-DE) gels differed according to tomato genotype and ripening stage. A total of 286 variant proteins were determined using matrix-assisted laser desorption-time of flight (MALDI-TOF) mass spectrometry (MS) analysis, confirming 233 identified protein functions. In three tomato genotypes in each ripening stage, grouping according to the Munich Information Center for Protein Sequences (MIPS) functional categories confirmed the variant proteins involved in the following: energy processes (21%); metabolism (20%); protein fate (15%); protein synthesis (10%); a protein with a binding function or cofactor requirement (8%); cell rescue, defense, and virulence (8%); cellular transport, transport facilitation, and transport routes (6%); the biogenesis of cellular components (5%); cell cycle and DNA processing (2%); others (5%). Among the identified protein spots in the function category, two proteins related to metabolism, four related to energy, four related to protein synthesis, and two related to interaction with the cellular environment showed significantly different changes according to the fruit color by the ripening stage. This study reveals the physiological changes in different types of tomatoes according to their ripening stage and provides information on the proteome for further improvement.

SH3BGRL3 binds to myosin 1c in a calcium dependent manner and modulates migration in the MDA-MB-231 cell line

Background

The human SH3 domain Binding Glutamic acid Rich Like 3 (SH3BGRL3) gene is highly conserved in phylogeny and widely expressed in human tissues. However, its function is largely undetermined. The protein was found to be overexpressed in several tumors, and recent work suggested a possible relationship with EGFR family members.

We aimed at further highlighting on these issues and investigated SH3BGRL3 molecular interactions and its role in cellular migration ability.

Results

We first engineered the ErbB2-overexpressing SKBR3 cells to express exogenous SH3BGRL3, as well as wild type Myo1c or different deletion mutants. Confocal microscopy analysis indicated that SH3BGRL3 co-localized with Myo1c and ErbB2 at plasma membranes. However, co-immunoprecipitation assays and mass spectrometry demonstrated that SH3BGRL3 did not directly bind ErbB2, but specifically recognized Myo1c, on its IQ-bearing neck region. Importantly, the interaction with Myo1c was Ca²⁺-dependent.

A role for SH3BGRL3 in cell migration was also assessed, as RNA interference of SH3BGRL3 in MDA-MB-231 cells, used as a classical migration model, remarkably impaired the migration ability of these cells. On the other side, its over-expression increased cell motility.

Conclusion

The results of this study provide insights for the formulation of novel hypotheses on the putative role of SH3BGRL3 protein in the regulation of myosin-cytoskeleton dialog and in cell migration. It could be envisaged the SH3BGRL3-Myo1c interaction as a regulation mechanism for cytoskeleton dynamics. It is well known that, at low Ca²⁺ concentrations, the IQ domains of Myo1c are bound by calmodulin. Here we found that binding of Myo1c to SH3BGRL3 requires instead the presence of Ca²⁺. Thus, it could be hypothesized that Myo1c conformation may be modulated by Ca²⁺-driven mechanisms that involve alternative binding by calmodulin or SH3BGRL3, for the regulation of cytoskeletal activity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12860-021-00379-1.

Label-free quantitative proteomics analysis of jujube (Ziziphus jujuba Mill.) during different growth stages

Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

BACKGROUND

Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.

RESULTS

To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O'Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.

CONCLUSIONS

Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles

The organoleptic qualities of watermelon fruit are defined by the sugar and organic acid contents, which undergo considerable variations during development and maturation. The molecular mechanisms underlying these variations remain unclear. In this study, we used transcriptome profiles to investigate the coexpression patterns of gene networks associated with sugar and organic acid metabolism. We identified 3 gene networks/modules containing 2443 genes highly correlated with sugars and organic acids. Within these modules, based on intramodular significance and Reverse Transcription Quantitative polymerase chain reaction (RT-qPCR), we identified 7 genes involved in the metabolism of sugars and organic acids. Among these genes, Cla97C01G000640, Cla97C05G087120 and Cla97C01G018840 (r² = 0.83 with glucose content) were identified as sugar transporters (SWEET, EDR6 and STP) and Cla97C03G064990 (r² = 0.92 with sucrose content) was identified as a sucrose synthase from information available for other crops. Similarly, Cla97C07G128420, Cla97C03G068240 and Cla97C01G008870, having strong correlations with malic (r² = 0.75) and citric acid (r² = 0.85), were annotated as malate and citrate transporters (ALMT7, CS, and ICDH). The expression profiles of these 7 genes in diverse watermelon genotypes revealed consistent patterns of expression variation in various types of watermelon. These findings add significantly to our existing knowledge of sugar and organic acid metabolism in watermelon.

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.

Comparative proteomic analysis of Prunella vulgaris L. spica ripening

Prunella vulgaris L., better known as 'self-heal', has been extensively used in the traditional system of medicines. To reveal the regulatory mechanism of its development, TMT-based quantitative proteome analysis was performed in the Prunella vulgaris L. spica before and during ripening (Group A and Group B, respectively). This analysis resulted in the identification of 7655 proteins, of which 1910 showed differential abundance between the two groups. Pronounced changes in the proteomic profile included the following: 1) Stress-responsive proteins involved in protecting cells and promoting fruit ripening and seed development were highly abundant during ripening. 2) The degradation of chlorophyll, inhibition of chlorophyll biosynthesis and increased abundance of transketolase occurred simultaneously in the spica of Prunella vulgaris L., resulting in the spica changing color from green to brownish red. 3) The abundance of protein species related to phenylpropanoid biosynthesis mainly increased during ripening, while flavonoid and terpenoid backbone biosynthesis mostly occurred before ripening. SIGNIFICANCE: This study establishes a link between protein profiles and mature phenotypes, which will help to improve our understanding of the molecular mechanisms involved in the maturation of Prunella vulgaris L. at the proteome level and reveal the scientific connotation for the best time to harvest Prunella vulgaris L. This work provides a scientific basis for the production of high-quality medicinal Prunella vulgaris L., as well as a typical demonstration of molecular research used for the harvest period of traditional Chinese medicine. BIOLOGICAL SIGNIFICANCE: This work provided a comprehensive overview on the functional protein profile changes of Prunella vulgaris L. spica at different growing stages, as well as the scientific rationale of Prunella vulgaris L. harvested in summer after brownish red, thus laid an intriguing stepping stone for elucidating the molecular mechanisms of quality development.

Effect of Trichoderma Bioactive Metabolite Treatments on the Production, Quality, and Protein Profile of Strawberry Fruits

Fungi of the genus Trichoderma produce secondary metabolites having several biological activities that affect plant metabolism. We examined the effect of three Trichoderma bioactive metabolites (BAMs), namely, 6-pentyl-α-pyrone (6PP), harzianic acid (HA), and hydrophobin 1 (HYTLO1), on yield, fruit quality, and protein representation of strawberry plants. In particular, 6PP and HA increased the plant yield and number of fruits, when compared to control, while HYTLO1 promoted the growth of the roots and increased the total soluble solids content up to 19% and the accumulation of ascorbic acid and cyanidin 3-O-glucoside in red ripened fruits. Proteomic analysis showed that BAMs influenced the representation of proteins associated with the protein metabolism, response to stress/external stimuli, vesicle trafficking, carbon/energy, and secondary metabolism. Results suggest that the application of Trichoderma BAMs affects strawberry plant productivity and fruit quality and integrate previous observations on deregulated molecular processes in roots and leaves of Trichoderma-treated plants with original data on fruits.

Trichoderma Applications on Strawberry Plants Modulate the Physiological Processes Positively Affecting Fruit Production and Quality

Many Trichoderma spp. are successful plant beneficial microbial inoculants due to their ability to act as biocontrol agents with direct antagonistic activities to phytopathogens, and as biostimulants capable of promoting plant growth. This work investigated the effects of treatments with three selected Trichoderma strains (T22, TH1, and GV41) to strawberry plants on the productivity, metabolites and proteome of the formed fruits. Trichoderma applications stimulated plant growth, increased strawberry fruit yield, and favored selective accumulation of anthocyanins and other antioxidants in red ripened fruits. Proteomic analysis of fruits harvested from the plants previously treated with Trichoderma demonstrated that the microbial inoculants highly affected the representation of proteins associated with responses to stress/external stimuli, nutrient uptake, protein metabolism, carbon/energy metabolism and secondary metabolism, also providing a possible explanation to the presence of specific metabolites in fruits. Bioinformatic analysis of these differential proteins revealed a central network of interacting molecular species, providing a rationale to the concomitant modulation of different plant physiological processes following the microbial inoculation. These findings indicated that the application of Trichoderma-based products exerts a positive impact on strawberry, integrating well with previous observations on the molecular mechanisms activated in roots and leaves of other tested plant species, demonstrating that the efficacy of using a biological approach with beneficial microbes on the maturing plant is also able to transfer advantages to the developing fruits.

Stone Fruits: Growth and Nitrogen and Organic Acid Metabolism in the Fruits and Seeds-A Review

Stone fruits of the Rosaceae family consist of several distinct parts, and these include the flesh, woody endocarp, and seed. To understand the metabolism of these fruits, it is necessary to have knowledge of both their structure and growth characteristics. The nitrogen metabolism of the different tissues of stone fruits is interlinked. For example, there is an import and storage of nitrogenous compounds in the endocarp that are then exported to the seed. Moreover, there are links between the metabolism of nitrogen and that of malic/citric acids. In this article, the structure and growth characteristics, together with the import/export, contents, metabolism, and functions of nitrogenous compounds and organic acids in the different parts of stone fruits and their seeds are reviewed.

Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp

The banana is one of the most important fruits in the world. Bananas undergo a rapid ripening process after harvest, resulting in a short shelf. In this study, the mechanism underlying pulp ripening of harvested bananas was investigated using integrated transcriptomic, proteomic, and metabolomic analysis. Ribonucleic acid sequencing (RNA-Seq) revealed that a great number of genes related to transcriptional regulation, signal transduction, cell wall modification, and secondary metabolism were up-regulated during pulp ripening. At the protein level, 84 proteins were differentially expressed during pulp ripening, most of which were associated with energy metabolism, oxidation-reduction, cell wall metabolism, and starch degradation. According to partial least squares discriminant analysis, 33 proteins were identified as potential markers for separating different ripening stages of the fruit. In addition to ethylene’s central role, auxin signal transduction might be involved in regulating pulp ripening. Moreover, secondary metabolism, energy metabolism, and the protein metabolic process also played an important role in pulp ripening. In all, this study provided a better understanding of pulp ripening of harvested bananas.

Integrated Transcriptomic, Proteomic, and Metabolomics Analysis Reveals Peel Ripening of Harvested Banana under Natural Condition

Harvested banana ripening is a complex physiological and biochemical process, and there are existing differences in the regulation of ripening between the pulp and peel. However, the underlying molecular mechanisms governing peel ripening are still not well understood. In this study, we performed a combination of transcriptomic, proteomic, and metabolomics analysis on peel during banana fruit ripening. It was found that 5784 genes, 94 proteins, and 133 metabolites were differentially expressed or accumulated in peel during banana ripening. Those genes and proteins were linked to ripening-related processes, including transcriptional regulation, hormone signaling, cell wall modification, aroma synthesis, protein modification, and energy metabolism. The differentially expressed transcriptional factors were mainly ethylene response factor (ERF) and basic helix-loop-helix (bHLH) family members. Moreover, a great number of auxin signaling-related genes were up-regulated, and exogenous 3-indoleacetic acid (IAA) treatment accelerated banana fruit ripening and up-regulated the expression of many ripening-related genes, suggesting that auxin participates in the regulation of banana peel ripening. In addition, xyloglucan endotransglucosylase/hydrolase (XTH) family members play an important role in peel softening. Both heat shock proteins (Hsps) mediated-protein modification, and ubiqutin-protesome system-mediated protein degradation was involved in peel ripening. Furthermore, anaerobic respiration might predominate in energy metabolism in peel during banana ripening. Taken together, our study highlights a better understanding of the mechanism underlying banana peel ripening and provides a new clue for further dissection of specific gene functions.

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.

Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening

BACKGROUND

Taste and aroma, which are important organoleptic qualities of apricot (Prunus armeniaca L.) fruit, undergo rapid and substantial changes during ripening. However, the associated molecular mechanisms remain unclear. The goal of this study was to identify candidate genes for flavor compound metabolism and to construct a regulatory transcriptional network.

RESULTS

We characterized the transcriptome of the 'Jianali' apricot cultivar, which exhibits substantial changes in flavor during ripening, at 50 (turning), 73 (commercial maturation) and 91 (full ripe) days post anthesis (DPA) using RNA sequencing (RNA-Seq). A weighted gene co-expression network analysis (WGCNA) revealed that four of 19 modules correlated highly with flavor compound metabolism (P < 0.001). From them, we identified 1237 differentially expressed genes, with 16 intramodular hubs. A proposed pathway model for flavor compound biosynthesis is presented based on these genes. Two SUS1 genes, as well as SPS2 and INV1 were correlated with sugar biosynthesis, while NADP-ME4, two PK-like and mitochondrial energy metabolism exerted a noticeable effect on organic acid metabolism. CCD1 and FAD2 were identified as being involved in apocarotenoid aroma volatiles and lactone biosynthesis, respectively. Five sugar transporters (Sweet10, STP13, EDR6, STP5.1, STP5.2), one aluminum-activated malate transporter (ALMT9) and one ABCG transporter (ABCG11) were associated with the transport of sugars, organic acids and volatiles, respectively. Sixteen transcription factors were also highlighted that may also play regulatory roles in flavor quality development.

CONCLUSIONS

Apricot RNA-Seq data were obtained and used to generate an annotated set of predicted expressed genes, providing a platform for functional genomic research. Using network analysis and pathway mapping, putative molecular mechanisms for changes in apricot fruit taste and aroma during ripening were elucidated.

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’.

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.

Date Fruit Proteomics During Development and Ripening Stages

Gel-based comparative proteomics approach is a valuable technique for studying the changes in abundance of proteins in any given system. The combination of this technique with mass spectrometry has provided immense insight into protein dynamics during fruit development and ripening. This chapter describes, informatively, the procedures for carrying out comparative proteomics analysis of date palm (Phoenix dactylifera L.) fruits at different developmental stages using a combination of two-dimensional gel electrophoresis (2-DE) and mass spectrometry. A comparative proteomics approach provides an overview of protein abundances during fruit maturation and insights into proteins that play key roles during fruit maturation. Moreover, 2-DE technique enables the visualization of total protein distribution and abundance in addition to providing a comparative platform following separation of complex proteins based on their molecular weight and isoelectric point. Overall, this chapter describes methodologies for extraction of proteins from a high carbohydrate-containing fruit, protein quality assessment using one-dimensional gel electrophoresis (1-DE), separation using 2-DE, comparative analysis using Delta2D v4.6, processing of spots of interest, and protein identification using mass spectrometry. This protocol is important for studies aiming at comparative proteomics to gain insights into changes of protein abundances in tissues and organs in general and date palm fruits, in particular.

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.

iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis

BACKGROUND

Black rice (Oryza sativa L.), whose pericarp is rich in anthocyanins (ACNs), is considered as a healthier alternative to white rice. Molecular species of ACNs in black rice have been well documented in previous studies; however, information about the metabolic mechanisms underlying ACN biosynthesis during black rice grain development is unclear.

RESULTS

The aim of the present study was to determine changes in the metabolic pathways that are involved in the dynamic grain proteome during the development of black rice indica cultivar, (Oryza sativa L. indica var. SSP). Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS were employed to identify statistically significant alterations in the grain proteome. Approximately 928 proteins were detected, of which 230 were differentially expressed throughout 5 successive developmental stages, starting from 3 to 20 days after flowering (DAF). The greatest number of differentially expressed proteins was observed on 7 and 10 DAF, including 76 proteins that were upregulated and 39 that were downregulated. The biological process analysis of gene ontology revealed that the 230 differentially expressed proteins could be sorted into 14 functional groups. Proteins in the largest group were related to metabolic process, which could be integrated into multiple biochemical pathways. Specifically, proteins with a role in ACN biosynthesis, sugar synthesis, and the regulation of gene expression were upregulated, particularly from the onset of black rice grain development and during development. In contrast, the expression of proteins related to signal transduction, redox homeostasis, photosynthesis and N-metabolism decreased during grain maturation. Finally, 8 representative genes encoding different metabolic proteins were verified via quantitative real-time polymerase chain reaction (qRT-PCR) analysis, these genes had differed in transcriptional and translational expression during grain development.

CONCLUSIONS

Expression analyses of metabolism-related protein groups belonging to different functional categories and subcategories indicated that significantly upregulated proteins were related to flavonoid and starch synthesis. On the other hand, the downregulated proteins were determined to be related to nitrogen metabolism, as well as other functional categories and subcategories, including photosynthesis, redox homeostasis, tocopherol biosynthetic, and signal transduction. The results provide valuable new insights into the characterization and understanding of ACN pigment production in black rice.

Proteomic Analysis of Differentially Expressed Proteins Involved in Peel Senescence in Harvested Mandarin Fruit

Mandarin (Citrus reticulata), a non-climacteric fruit, is an economically important fruit worldwide. The mechanism underlying senescence of non-climacteric fruit is poorly understood. In this study, a gel-based proteomic study followed by LC-ESI-MS/MS analysis was carried out to investigate the proteomic changes involved in peel senescence in harvested mandarin "Shatangju" fruit stored for 18 days. Over the course of the storage period, the fruit gradually senesced, accompanied by a decreased respiration rate and increased chlorophyll degradation and disruption of membrane integrity. Sixty-three proteins spots that showed significant differences in abundance were identified. The up-regulated proteins were mainly associated with cell wall degradation, lipid degradation, protein degradation, senescence-related transcription factors, and transcription-related proteins. In contrast, most proteins associated with ATP synthesis and scavenging of reactive oxygen species were significantly down-regulated during peel senescence. Three thioredoxin proteins and three Ca(2+) signaling-related proteins were significantly up-regulated during peel senescence. It is suggested that mandarin peel senescence is associated with energy supply efficiency, decreased antioxidant capability, and increased protein and lipid degradation. In addition, activation of Ca(2+) signaling and transcription factors might be involved in cell wall degradation and primary or secondary metabolism.

Proteomic Comparison of Fruit Ripening between 'Hedelfinger' Sweet Cherry (Prunus avium L.) and Its Somaclonal Variant 'HS'

The somaclonal variant HS, from sweet cherry (Prunus avium L.) 'Hedelfinger' (H), was previously selected for reduced tree vegetative vigor and lesser canopy density. In this work, we compared H and HS fruits at early unripe (green) and full ripe (dark red) stages by biochemical and proteomic approaches. The main biochemical parameters showed that fruit quality was not affected by somaclonal variation. The proteomic analysis identified 39 proteins differentially accumulated between H and HS fruits at the two ripening stages, embracing enzymes involved in several pathways, such as carbon metabolism, cell wall modification, stress response, and secondary metabolism. The evaluation of fruit phenolic composition by mass spectrometry showed that HS sweet cherries have higher levels of procyanidin, flavonol, and anthocyanin compounds. This work provides the first proteomic characterization of fruit ripening in sweet cherry, revealing new positive traits of the HS somaclonal variant.

Differentially Accumulated Proteins in Coffea arabica Seeds during Perisperm Tissue Development and Their Relationship to Coffee Grain Size

Coffee is one of the most important crops for developing countries. Coffee classification for trading is related to several factors, including grain size. Larger grains have higher market value then smaller ones. Coffee grain size is determined by the development of the perisperm, a transient tissue with a highly active metabolism, which is replaced by the endosperm during seed development. In this study, a proteomics approach was used to identify differentially accumulated proteins during perisperm development in two genotypes with regular (IPR59) and large grain sizes (IPR59-Graudo) in three developmental stages. Twenty-four spots were identified by MALDI-TOF/TOF-MS, corresponding to 15 proteins. We grouped them into categories as follows: storage (11S), methionine metabolism, cell division and elongation, metabolic processes (mainly redox), and energy. Our data enabled us to show that perisperm metabolism in IPR59 occurs at a higher rate than in IPR59-Graudo, which is supported by the accumulation of energy and detoxification-related proteins. We hypothesized that grain and fruit size divergences between the two coffee genotypes may be due to the comparatively earlier triggering of seed development processes in IPR59. We also demonstrated for the first time that the 11S protein is accumulated in the coffee perisperm.

Omics studies of citrus, grape and rosaceae fruit trees

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin-related verification in apple calli suggested that the regulation of MdMADS1 on anthocyanin biosynthesis was partially independent of fruit ripening process. Taken together, our findings provide insight into the mechanism how ALA regulates anthocyanin accumulation and add new information on transcriptase regulators of fruit coloration.

Proteome exploration to provide a resource for the investigation of Ganoderma lucidum

Ganoderma lucidum is a basidiomycete white rot fungus that has been used for medicinal purposes worldwide. Although information concerning its genome and transcriptome has recently been reported, relatively little information is available for G. lucidum at the proteomic level. In this study, protein fractions from G. lucidum at three developmental stages (16-day mycelia, and fruiting bodies at 60 and 90 days) were prepared and subjected to LC-MS/MS analysis. A search against the G. lucidum genome database identified 803 proteins. Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies. Fourteen TCA-cycle related proteins, 17 peptidases, two argonaute-like proteins, and two immunomodulatory proteins were also detected. A majority (470) of the 803 proteins had GO annotations and were classified into 36 GO terms, with "binding", "catalytic activity", and "hydrolase activity" having high percentages. Additionally, 357 out of the 803 proteins were assigned to at least one COG functional category and grouped into 22 COG classifications. Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity. In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.

Proteomic analysis of eucalyptus leaves unveils putative mechanisms involved in the plant response to a real condition of soil contamination by multiple heavy metals in the presence or absence of mycorrhizal/rhizobacterial additives

Here we report on the growth, accumulation performances of, and leaf proteomic changes in Eucalyptus camaldulensis plants harvested for different periods of time in an industrial, heavy metals (HMs)-contaminated site in the presence or absence of soil microorganism (AMs/PGPRs) additives. Data were compared to those of control counterparts grown in a neighboring nonpolluted district. Plants harvested in the contaminated areas grew well and accumulated HMs in their leaves. The addition of AMs/PGPRs to the polluted soil determined plant growth and metal accumulation performances that surpassed those observed in the control. Comparative proteomics suggested molecular mechanisms underlying plant adaptation to the HMs challenge. Similarly to what was observed in laboratory-scale investigations on other metal hyperaccumulators but not on HMs-sensitive plants, eucalyptus grown in the contaminated areas showed an over-representation of enzymes involved in photosynthesis and the Calvin cycle. AMs/PGPRs addition to the soil increased the activation of these energetic pathways, suggesting the existence of signaling mechanisms that address the energy/reductive power requirement associated with augmented growth performances. HMs-exposed plants presented an over-representation of antioxidant enzymes, chaperones, and proteins involved in glutathione metabolism. While some antioxidant enzymes/chaperones returned to almost normal expression values in the presence of AMs/PGPRs or in plants exposed to HMs for prolonged periods, proteins guaranteeing elevated glutathione levels were constantly over-represented. These data suggest that glutathione (and related phytochelatins) could act as key molecules for ensuring the effective formation of HMs-chelating complexes that are possibly responsible for the observed plant tolerance to metal stresses. Overall, these results suggest potential genetic traits for further selection of phytoremediating plants based on dedicated cloning or breeding programs.

Identification and characterization of MOR-CP, a cysteine protease induced by ozone and developmental senescence in maize (Zea mays L.) leaves

Among the different classes of endoproteases, cysteine proteases are consistently associated with senescence, defense signaling pathways and cellular responses to abiotic stresses. The objectives of this work were to study the effects of various concentrations of ozone on gene expression and enzymatic activity for papain-like cysteine proteases (PLCPs), in the leaves of maize plants grown under field conditions. Leaves from ranks 12 and 10 (cob leaf) were harvested regularly over a long-term artificial ozone fumigation experiment (50 d). Tissues were tested for transcriptional and activity changes concerning cysteine proteases, using qRT-PCR for the newly identified ozone-responsive PLCP gene (Mor-CP) and synthetic oligopeptide Boc-Val-Leu-Lys-AMC as a PLCP-specific substrate, respectively. Results showed that developmental senescence induced a significant and progressive rise in CP activity, only in the older leaves 10 and had no effect on Mor-CP gene expression levels. On the other hand, ozone dramatically enhanced Mor-CP mRNA levels and global PLCP enzymatic activity in leaves 12 and 10, particularly toward the end of the treatment. Ozone impact was more pronounced in the older leaves 10. Together, these observations concurred to conclude that ozone stress enhances natural senescence processes, such as those related to proteolysis.

Proteomic analysis of 'Zaosu' pear (Pyrus bretschneideri Rehd.) and its early-maturing bud sport

Maturation of fruits involves a series of physiological, biochemical, and organoleptic changes that eventually make fleshy fruits attractive, palatable, and nutritional. In order to understand the mature mechanism of the early-maturing bud sport of 'Zaosu' pear, we analyzed the differences of proteome expression between the both pears in different mature stages by the methods of a combination of two-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Seventy-five differential expressed protein spots (p<0.05) were obtained between 'Zaosu' pear and its early-maturing bud sport, but only sixty-eight were demonstratively identified in the database of NCBI and uniprot. The majority of proteins were linked to metabolism, energy, stress response/defense and cell structure. Additionally, our data confirmed an increase of proteins related to cell-wall modification, oxidative stress and pentose phosphate metabolism and a decrease of proteins related to photosynthesis and glycolysis during the development process of both pears, but all these proteins increased or decreased faster in the early-maturing bud sport. This comparative analysis between both pears showed that these proteins were closely associated with maturation and could provide more detailed characteristics of the maturation process of both pears.

Proteomics in the fruit tree science arena: new insights into fruit defense, development, and ripening

Fruit tree crops are agricultural commodities of high economic importance, while fruits also represent one of the most vital components of the human diet. Therefore, a great effort has been made to understand the molecular mechanisms covering fundamental biological processes in fruit tree physiology and fruit biology. Thanks to the development of cutting-edge "omics" technologies such as proteomic analysis, scientists now have powerful tools to support traditional fruit tree research. Such proteomic analyses are establishing high-density 2DE reference maps and peptide mass fingerprint databases that can lead fruit science into a new postgenomic research era. Here, an overview of the application of proteomics in key aspects of fruit tree physiology as well as in fruit biology, including defense responses to abiotic and biotic stress factors, is presented. A panoramic view of ripening-related proteins is also discussed, as an example of proteomic application in fruit science.

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE-based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).

Dynamic changes in the date palm fruit proteome during development and ripening

Date palm (Phoenix dactylifera) is an economically important fruit tree in the Middle East and North Africa and is characterized by large cultivar diversity, making it a good model for studies on fruit development and other important traits. Here in gel comparative proteomics combined with tandem mass spectrometry were used to study date fruit development and ripening. Total proteins were extracted using a phenol-based protocol. A total of 189 protein spots were differentially regulated (p≤0.05). The identified proteins were classified into 14 functional categories. The categories with the most proteins were 'disease and defense' (16.5%) and 'metabolism' (15.4%). Twenty-nine proteins have not previously been identified in other fleshy fruits and 64 showed contrasting expression patterns in other fruits. Abundance of most proteins with a role in abiotic stress responses increased during ripening with the exception of heat shock proteins. Proteins with a role in anthocyanin biosynthesis, glycolysis, tricarboxylic acid cycle and cell wall degradation were upregulated particularly from the onset of ripening and during ripening. In contrast, expression of pentose phosphate- and photosynthesis-related proteins decreased during fruit maturation. Although date palm is considered a climacteric species, the analysis revealed downregulation of two enzymes involved in ethylene biosynthesis, suggesting an ethylene-independent ripening of 'Barhi' fruits. In summary, this proteomics study provides insights into physiological processes during date fruit development and ripening at the systems level and offers a reference proteome for the study of regulatory mechanisms that can inform molecular and biotechnological approaches to further improvements of horticultural traits including fruit quality and yield.

Dynamic changes in proteins during apple (Malus x domestica) fruit ripening and storage

A proteomic study, using two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight, was conducted in apple fruit (cv. 'Golden Delicious') starting at 10 days prior to harvest through 50 days in storage. Total protein was extracted using a phenol/sodium dodecyl sulfate protocol. More than 400 protein spots were detected in each gel and 55 differentially expressed proteins (p<0.05) were subjected to matrix-assisted laser desorption/ionization time-of-flight/time-of-flight analysis. Fifty-three of these proteins were finally identified using an apple expressed sequence tag database downloaded from Genome Database for Rosaceae and placed into six categories. The categories and the percentage of proteins placed in each category were stress response and defense (49.0%), energy and metabolism (34.0%), fruit ripening and senescence (5.6%), signal transduction (3.8%), cell structure (3.8%) and protein synthesis (3.8%). Proteins involved in several multiple metabolic pathways, including glycolysis, pentose-phosphate pathway, anti-oxidative systems, photosynthesis and cell wall synthesis, were downregulated, especially during the climacteric burst in respiration and during the senescent stages of fruit development. Proteins classified as allergens or involved in cell wall degradation were upregulated during the ripening process. Some protein spots exhibited a mixed pattern (increasing to maximal abundance followed by a decrease), such as 1-aminocyclopropane-1-carboxylate oxidase, L-ascorbate peroxidase and abscisic acid response proteins. The identification of differentially expressed proteins associated with physiological processes identified in the current study provides a baseline of information for understanding the metabolic processes and regulatory mechanisms that occur in climacteric apple fruit during ripening and senescence.

Understanding development and ripening of fruit crops in an 'omics' era

Next generation sequencing has revolutionized plant biology. Not only has our understanding of plant metabolism advanced using model systems and modern chromatography, but application of 'omics'-based technology has been widely extended to non-model systems as costs have plummeted and efficiency increased. As a result, important fundamental questions relating to important horticultural crops are being answered, and novel approaches with application to industry are in progress. Here we review recent research advances on development and ripening of fruit crops, how next generation sequencing approaches are driving this advance and the emerging future landscape.