Proteomic analysis of changes in mitochondrial protein expression during peach fruit ripening and senescence

Mitochondrial Energy Homeostasis and Membrane Interaction Regulate the Rapid Growth of Moso Bamboo

The rapid growth of moso bamboo is primarily attributed to the swift elongation of its internodes. While mitochondria are known to provide energy for various cellular processes, the specific mechanisms by which they facilitate rapid growth in bamboo remain elusive. In this study, we optimised the procedures for mitochondria isolation and performed a comprehensive analysis of mitochondrial dynamics and proteomics from internodes at various growth stages, including the initial growth (IG) stage, the starting of cell division (SD), and the rapid elongation (RE). Confocal observation demonstrated that cells in the RE stage have a higher mitochondrial density and increased mitochondrial motility compared to other stages. Proteomic analysis of isolated mitochondria revealed an upregulation of the tricarboxylic acid cycle, along with a synchronous increase in both mitochondrial- and nuclear-encoded components of oxidative phosphorylation in RE cells. Moreover, the upregulation of various mitochondrial membrane transporters in RE cells suggests an enhanced exchange of metabolic intermediates and inorganic ions with the cytosol. Intriguingly, ultrastructural analysis and pharmacological treatments revealed membrane interactions between the endoplasmic reticulum (ER) and mitochondria in RE cells. In conclusion, our study provides novel insights into mitochondrial function and the intracellular dynamics that regulate the rapid growth of moso bamboo.

Effects of reactive oxygen species on fruit ripening and postharvest fruit quality

Reactive oxygen species (ROS) serve as important signaling molecule, involved in numerous biological processes, particularly in the physiological changes associated with fruit ripening and postharvest handing. This review explores ROS key role in plant fruit ripening and postharvest quality. The mechanism of ROS production and degradation in maintaining ROS homeostasis are analyzed in detail. Fruit ripening is a complex and highly coordinated process involving physiological and biochemical changes. Studies have observed that the content of ROS, mainly hydrogen peroxide (H2O2), dynamically changes in various types of fruits during ripening. Furthermore, ROS have significant effects on fruit softening, color change, and other ripening processes. In addition, in the postharvest stage, the abnormal accumulation of ROS isclosely related to the decline in fruit quality and the occurrence of decay browning, which seriously affects the market value and shelf life of fruit. Overall, this review demonstrates the crucial role of ROS in regulating the ripening process and postharvest quality of fruit.

Thymol application delays the decline of fruit quality in blueberries via regulation of cell wall, energy and membrane lipid metabolism

In this study, we evaluated the potential for exogenous thymol to slow this decline by measuring the effects of thymol application on cell wall, energy, and membrane lipid metabolism. The results showed that thymol application improved the preservation of the total soluble solids, titratable acidity, decay rate, and anthocyanin content, and effectively inhibited the accumulation of O2·-, H2O2, and malondialdehyde in blueberries during storage. Thymol application also effectively maintained fruit firmness, cell wall structure, and energy levels, while delaying the degradation of membrane phospholipids and unsaturated fatty acids during the storage of post-harvest blueberries. Therefore, exogenous thymol can maintain the quality of blueberry fruits by regulating energy and membrane lipid metabolism and reducing cell wall degradation. Thus, thymol-treatment could be a suitable biocontrol agent for maintaining blueberry quality and extending blueberry fruit storage life.

Biochemical and molecular changes in peach fruit exposed to cold stress conditions

Storage or transportation temperature is very important for preserving the quality of fruit. However, low temperature in sensitive fruit such as peach can induce loss of quality. Fruit exposed to a specific range of temperatures and for a longer period can show chilling injury (CI) symptoms. The susceptibility to CI at low temperature varies among cultivars and genetic backgrounds. Along with agronomic management, appropriate postharvest management can limit quality losses. The importance of correct temperature management during postharvest handling has been widely demonstrated. Nowadays, due to long-distance markets and complex logistics that require multiple actors, the management of storage/transportation conditions is crucial for the quality of products reaching the consumer.Peach fruit exposed to low temperatures activate a suite of physiological, metabolomic, and molecular changes that attempt to counteract the negative effects of chilling stress. In this review an overview of the factors involved, and plant responses is presented and critically discussed. Physiological disorders associated with CI generally only appear after the storage/transportation, hence early detection methods are needed to monitor quality and detect internal changes which will lead to CI development. CI detection tools are assessed: they need to be easy to use, and preferably non-destructive to avoid loss of products.

Isothermal Storage Delays the Senescence of Post-Harvest Apple Fruit through the Regulation of Antioxidant Activity and Energy Metabolism

The purpose of this work was to elucidate the influence of TF (5 ± 5 °C, and 5 ± 1 °C) and CT (5 ± 0.1 °C served as an isothermal state) storage environment on the antioxidant ability and energy metabolism in post-harvest apple fruit during storage. Specifically, compared with fruit in TFs groups, the quality attributes of apples in the CT group, including firmness, fresh weight, contents of SSC, and TA were maintained at a higher level. In addition, fruit stored in the CT environment revealed a suppressed respiration rate and EL, lower MDA, O₂·^-, and H₂O₂ accumulation but increased the activities of SOD, CAT, APX, and GR. At the end of storage, the SOD, CAT, APX, and GR activities of fruit in the CT group were 38.14%,48.04%, 115.29%, and 34.85% higher than that of the TF5 group, respectively. Fruit in the CT environment also revealed higher AsA, GSH, total phenols, and total flavonoid content. In addition, fruit stored in the CT environment maintained higher ATP content, EC, and more active H⁺-ATPase, Ca²⁺-ATPase, CCO, and SDH. At the end of storage, the SDH and CCO activities of fruit in the TF0.1 group were 1.74, and 2.59 times higher than that in the TF5 group, respectively. Taken together, we attributed the fact that a constant temperature storage environment can retard the fruit senescence to the enhancement of antioxidant capacities and maintaining of higher energy status in apple fruit.

Arsenic inhibits citric acid accumulation via downregulating vacuolar proton pump gene expression in citrus fruits

Citric acid content is a critical quality determinant in citrus (Citrus spp.) fruits. Although arsenic (As) can effectively reduce citric acid content to improve citrus fruit quality, it can have adverse environmental effects. The discovery of nontoxic substitutes is hampered by the incomplete elucidation of the underlying mechanisms of As action in citrus fruits. Metabolic, transcriptomic, and physiological analyses were employed to investigate As action on citric acid accumulation to discover the mechanisms of As action in citrus. The enzyme activity related to citrate biosynthesis was not inhibited and the content of the involved metabolites was not reduced in As-treated fruits. However, the proton pump genes CitPH5 and CitPH1 control the vacuolar citric acid accumulation and transcription factor genes CitTT8 and CitMYB5, which regulate CitPH5 and CitPH1, were downregulated. The oxidative stress-response genes were upregulated in As-treated fruits. The reactive oxygen species (ROS) treatment also downregulated CitTT8 and CitMYB5 in juice cells. The mitochondrial ROS production rate increased in As-treated fruits. As^III was more potent in stimulating isolated mitochondria to overproduce ROS compared to As^V. Our results indicate that the As inhibition of citric acid accumulation may be primarily due to the transcriptional downregulation of CitPH5, CitPH1, CitTT8, and CitMYB5. As-induced oxidative stress signaling may operate upstream to downregulate these acid regulator genes. Mitochondrial thiol proteins may be the principal targets of As action in citrus fruits.

NAC transcription factor TgNAP promotes tulip petal senescence

Petal senescence is a crucial determinant for ornamental quality and economic value of floral crops. Salicylic acid (SA) and reactive oxygen species (ROS) are two prominent factors involved in plant senescence regulation. In this study, tulip TgNAP (NAC-like, activated by APETALA3/PISTILLATA) was characterized as positively regulating tulip petal senescence through dually regulating SA biosynthesis and ROS detoxification pathways. TgNAP was upregulated in senescing petals of tulip while exogenous SA and H2O2 treatments substantially promoted petal senescence in tulip. Silencing of TgNAP by VIGS assay delayed SA and H2O2-induced petal senescence in tulip, whereas overexpression of TgNAP promoted the senescence process in Arabidopsis (Arabidopsis thaliana) plants. Additionally, inhibition of SA biosynthesis prolonged the lifespan of TgNAP-silenced petal discs. Further evidence indicated that TgNAP activates the transcriptions of two key SA biosynthetic genes ISOCHORISMATE SYNTHASE 1 (TgICS1) and PHENYLALANINE AMMONIA-LYASE 1 (TgPAL1) through directly binding to their promoter regions. Meanwhile, TgNAP repressed ROS scavenging by directly inhibiting PEROXIDASE 12 (POD12) and POD17 expression. Taken together, these results indicate that TgNAP enhances SA biosynthesis and ROS accumulation to positively regulate petal senescence in tulip.

Proteomic and metabolomic studies on chilling injury in peach and nectarine

Peaches and nectarines are temperate climate stone fruits, which should be stored at 0°C to prevent the ripening of these climacteric fruits. However, if stored for too long or if stored at a higher temperature (4 or 5°C), they develop chilling injury. Chilling injury damage includes (1) dry, mealy, wooly (lack of juice) fruits, (2) hard-textured fruits with no juice (leatheriness), (3) flesh browning, and (4) flesh bleeding or internal reddening. There are genetic components to these disorders in that early season fruits are generally more resistant than late season fruits, and white-fleshed fruits are more susceptible to internal browning than yellow-fleshed fruits. A recent review covered the recent research in genomic and transcriptomic studies, and this review examines findings from proteomic and metabolomics studies. Proteomic studies found that the ethylene synthesis proteins are decreased in cold compromised fruits, and this affects the processes initiated by ethylene including cell wall and volatile changes. Enzymes in metabolic pathways were both higher and lower in abundance in CI fruits, an indication of an imbalance in energy production. Stress proteins increased in both fruits with or without CI, but were higher in damaged fruits. Metabolomics showed the role of levels of sugars, sucrose, raffinose, galactinol, and glucose-6-phosphate in protection against chilling injury, along with other membrane stabilizers such as polyamines. Amino acid changes were inconsistent among the studies. Lipid species changes during storage could be correlated with sensitivity or resistance to CI, but more studies are needed.

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.

Reactive oxygen species-induced protein carbonylation promotes deterioration of physiological activity of wheat seeds

During the seed aging process, reactive oxygen species (ROS) can induce the carbonylation of proteins, which changes their functional properties and affects seed vigor. However, the impact and regulatory mechanisms of protein carbonylation on wheat seed vigor are still unclear. In this study, we investigated the changes in wheat seed vigor, carbonyl protein content, ROS content and embryo cell structure during an artificial aging process, and we analyzed the correlation between protein carbonylation and seed vigor. During the artificial wheat-seed aging process, the activity levels of antioxidant enzymes and the contents of non-enzyme antioxidants decreased, leading to the accumulation of ROS and an increase in the carbonyl protein content, which ultimately led to a decrease in seed vigor, and there was a significant negative correlation between seed vigor and carbonyl protein content. Moreover, transmission electron microscopy showed that the contents of protein bodies in the embryo cells decreased remarkably. We postulate that during the wheat seed aging process, an imbalance in ROS production and elimination in embryo cells leads to the carbonylation of proteins, which plays a negative role in wheat seed vigor.

Synergy of Nitric Oxide and 1-Methylcyclopropene Treatment in Prolong Ripening and Senescence of Peach Fruit

Peach is a putrescible fruit thus drastically restricting its postharvest storage life. In recent years, the application of 1-methylcyclopropene (1-MCP) and nitric oxide (NO) in postharvest fruit quality control has received considerable attention and investigative efforts due to the advantages of using relatively low concentrations and short-time treatment duration. In the present study, the effects of various 1-MCP and NO treatments on peach fruit (Prunus persica L. cv. Xiahui-8) stored at 25 °C were evaluated and compared. Results indicated that the combination treatment with both chemical agents (MN) was most effective in postponing peach ripening and preserving fruit quality, followed by 1-MCP and NO treatment alone. We also demonstrated that NO could delay fruit senescence mainly by stimulating antioxidant enzymes, while 1-MCP overly outperformed NO in the treatment of ‘Xiahui-8′ peach in slowing down respiration rate, inhibiting ethylene production, maintaining high firmness and reducing ROS content. NO treatment showed a greater influence on phenolic compounds than 1-MCP especially anthocyanins, flavanones and flavones according to LC/MS analysis. The phenolic change in MN group were highly associated to NO treatment. Through this study we provide informative physiological, biochemical and molecular evidence for the beneficial effects of the combined 1-MCP and NO treatment on peach fruit based on a functional synergy between these two chemical agents.

1-Methylcyclopropene (1-MCP) retards the senescence of Pteridium aquilinum var. latiusculum by regulating the cellular energy status and membrane lipid metabolism

1-MCP is an ethylene inhibitor which can delay the ripening and senescence of fruits and vegetables effectively. Pteridium aquilinum var. Latiusculum (PA) is one of the wild vegetables which is famous and nutrient in China. However, the mechanism of PA preservation treated with 1-MCP has not been reported. Consequently, the effects of postharvest 1-MCP treatment on the changes in quality, energy metabolism, and membrane lipid metabolism of PA were investigated in this study. The results indicated that 1-MCP treatment could effectively inhibit the decreases in firmness, titratable acid (TA) content and the increases in weight loss rate, malondialdehyde (MDA) content, membrane permeability, and membrane lipid metabolism-related enzymes in PA. The cellular energy charge (EC) and the levels of ATP, ATP/ADP, and ATP/AMP, the activities of energy metabolism-related enzymes, NAD+, and NADH were maintained, and the decreases in unsaturated fatty acids and the ratio of unsaturated-to-saturated fatty acids in the membrane of PA cells were effectively retarded by 1-MCP treatment. A positive correlation was observed between cellular ATP levels and the ratio of unsaturated-to-saturated fatty acids, while negative correlations were observed between the ratio of unsaturated-to-saturated fatty acids and both lipid peroxidation and membrane permeability. These results indicated that higher levels of energy status, unsaturated-to-saturated fatty acid ratios, and lipid metabolism in the membrane could preserve the membrane integrity of postharvest PA and effectively extend its shelf life.

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.

Isolation and comparative proteomic analysis of mitochondria from the pulp of ripening citrus fruit

Mitochondria are crucial for the production of primary and secondary metabolites, which largely determine the quality of fruit. However, a method for isolating high-quality mitochondria is currently not available in citrus fruit, preventing high-throughput characterization of mitochondrial functions. Here, based on differential and discontinuous Percoll density gradient centrifugation, we devised a universal protocol for isolating mitochondria from the pulp of four major citrus species, including satsuma mandarin, ponkan mandarin, sweet orange, and pummelo. Western blot analysis and microscopy confirmed the high purity and intactness of the isolated mitochondria. By using this protocol coupled with a label-free proteomic approach, a total of 3353 nonredundant proteins were identified. Comparison of the four mitochondrial proteomes revealed that the proteins commonly detected in all proteomes participate in several typical metabolic pathways (such as tricarboxylic acid cycle, pyruvate metabolism, and oxidative phosphorylation) and pathways closely related to fruit quality (such as γ-aminobutyric acid (GABA) shunt, ascorbate metabolism, and biosynthesis of secondary metabolites). In addition, differentially abundant proteins (DAPs) between different types of species were also identified; these were found to be mainly involved in fatty acid and amino acid metabolism and were further confirmed to be localized to the mitochondria by subcellular localization analysis. In summary, the proposed protocol for the isolation of highly pure mitochondria from different citrus fruits may be used to obtain high-coverage mitochondrial proteomes, which can help to establish the association between mitochondrial metabolism and fruit storability or quality characteristics of different species and lay the foundation for discovering novel functions of mitochondria in plants.

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.

iTRAQ-based comparative proteomic analysis reveals high temperature accelerated leaf senescence of tobacco (Nicotiana tabacum L.) during flue-curing

Tobacco (Nicotiana tabacum) is extensively cultivated all over the world for its economic value. During curing and storage, senescence occurs, which is associated with physiological and biochemical changes in postharvest plant organs. However, the molecular mechanisms involved in accelerated senescence due to high temperatures in tobacco leaves during curing need further elaboration. We studied molecular mechanisms of senescence in tobacco leaves exposed to high temperature during curing (Fresh, 38 °C and 42 °C), revealed by isobaric tags for relative and absolute quantification (iTRAQ) for the proteomic profiles of cultivar Bi'na1. In total, 8903 proteins were identified, and 2034 (1150 up-regulated and 1074 down-regulated) differentially abundant proteins (DAPs) were obtained from tobacco leaf samples. These DAPs were mainly involved in posttranslational modification, protein turnover, energy production and conversion. Sugar- and energy-related metabolic biological processes and pathways might be critical regulators of tobacco leaves exposed to high temperature during senescence. High-temperature stress accelerated tobacco leaf senescence mainly by down-regulating photosynthesis-related pathways and degrading cellular constituents to maintain cell viability and nutrient recycling. Our findings provide a valuable inventory of novel proteins involved in senescence physiology and elucidate the protein regulatory network in postharvest organs exposed to high temperatures during flue-curing.

Metabolite Changes during Postharvest Storage: Effects on Fruit Quality Traits

Metabolic changes occurring in ripe or senescent fruits during postharvest storage lead to a general deterioration in quality attributes, including decreased flavor and ‘off-aroma’ compound generation. As a consequence, measures to reduce economic losses have to be taken by the fruit industry and have mostly consisted of storage at cold temperatures and the use of controlled atmospheres or ripening inhibitors. However, the biochemical pathways and molecular mechanisms underlying fruit senescence in commercial storage conditions are still poorly understood. In this sense, metabolomic platforms, enabling the profiling of key metabolites responsible for organoleptic and health-promoting traits, such as volatiles, sugars, acids, polyphenols and carotenoids, can be a powerful tool for further understanding the biochemical basis of postharvest physiology and have the potential to play a critical role in the identification of the pathways affected by fruit senescence. Here, we provide an overview of the metabolic changes during postharvest storage, with special attention to key metabolites related to fruit quality. The potential use of metabolomic approaches to yield metabolic markers useful for chemical phenotyping or even storage and marketing decisions is highlighted.

iTRAQ-based mitochondrial proteome analysis of the molecular mechanisms underlying postharvest senescence of Zizania latifolia

To explore the molecular mechanisms underlying postharvest senescence of Zizania latifolia, the changes in the mitochondrial proteome of plants treated with or without (control) 1-methyleyelopropene and ethylene during storage at room temperature for 0, 3 and 6 days were investigated using isobaric tags for relative and absolute quantitation (iTRAQ) labeling combined with two-dimensional liquid chromatography-tandem mass spectrometry. A total of 1,390 proteins with two or more peptides were identified, of which 211 showed a significant (p < .05) change (at least twofold) in relative abundance. Monitoring the parallel reaction validated the reliability and accuracy of the iTRAQ results. Bioinformatics and functional analysis of these differentially expressed proteins (DEPs) revealed that postharvest senescence of Z. latifolia could be attributed to (a) strengthened pentose phosphate pathway, (b) imbalanced protein, amino acid, organic acid, and fatty acid metabolism, (c) disordered energy homeostasis, (d) exacerbated oxidative damage, (e) RNA degradation, (f) activation of the Ca²⁺ , mitogen-activated protein kinase, and jasmonic acid signaling pathways, (g) programed cell death, (h) excessive biosynthesis of secondary metabolites, or (i) degradation of cell structure. Our findings provide integrated insight into the molecular mechanisms of postharvest senescence during storage as well as the DEPs that show promise as targets for controlling senescence-induced quality deterioration of Z. latifolia. PRACTICAL APPLICATIONS: Postharvest senescence is the most important factor that causes fast quality deterioration of Zizania latifolia. The understanding of the processes leading to postharvest senescence of Z. latifolia is essential in enhancing the commercial value and extending the shelf life of the product. It is currently believed that the mitochondrial metabolism is closely related to postharvest senescence. For this, the changes of proteome in Z. latifolia mitochondria treated with or without (control) 1-MCP and ETH during storage at room temperature were investigated. Results showed that a variety of physiobiochemical responses occur during postharvest senescence of Z. latifolia. 1-MCP treatment significantly inhibited the changes of these physiobiochemical processes, finally, retarding the postharvest senescence of Z. latifolia. ETH treatment had opposite effects on proteome changes compared with 1-MCP treatment. Taken together, these results enrich the understanding of the molecular mechanisms of postharvest senescence of Z. latifolia.

Analysis of the molecular basis of fruit cracking susceptibility in Litchi chinensis cv. Baitangying by transcriptome and quantitative proteome profiling

Fruit cracking is a serious problem in Litchi chinensis cv. Baitangying orchards, but few advances have been made in understanding the molecular basis of cracking susceptibility in 'Baitangying'. In this work, we conducted transcriptome and quantitative proteome analyses of the pericarps of three kinds of litchi: noncracking 'Feizixiao' (cracking-resistant cultivar, F), noncracking 'Baitangying' (B), and cracking 'Baitangying' (CB). A total of 101 genes and 14 proteins with the same regulatory changes were found to overlap between CB vs. B and B vs. F, and we focused on these results to avoid the effects of passive progression after fruit cracking. The obtained data suggest that fruit cracking susceptibility in 'Baitangying' is related to pericarp photosynthetic characteristics and the oxidation of unsaturated fatty acids in this cultivar, which lead to changes in cuticle structure. Furthermore, differences in the pericarp hormone balance between 'Baitangying' and 'Feizixiao' may influence the susceptibility of 'Baitangying' to fruit cracking. This integrated analysis of transcriptomic and proteomic data indicates that susceptibility to fruit cracking in 'Baitangying' litchi is regulated both translationally and posttranslationally. Our results may help provide a new perspective for further study of the mechanisms that govern fruit cracking susceptibility in 'Baitangying' litchi and other fruits.

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.

Role of Mitochondria in Regulating Lutein and Chlorophyll Biosynthesis in Chlorella pyrenoidosa under Heterotrophic Conditions

The green alga Chlorella pyrenoidosa can accumulate lutein and chlorophyll under heterotrophic conditions. We propose that the mitochondrial respiratory electron transport chain (mRET) may be involved in this process. To verify this hypothesis, algal cells were treated with different mRET inhibitors. The biosynthesis of lutein and chlorophyll was found to be significantly stimulated by salicylhydroxamic acid (SHAM), whereas their contents substantially decreased after treatment with antimycin A and sodium azide (NaN₃). Proteomic studies revealed profound protein alterations related to the redox and energy states, and a network was proposed: The up-regulation of peroxiredoxin reduces oxidized glutathione (GSSG) to reduced glutathione (GSH); phosphoenolpyruvate carboxykinase (PEPCK) catalyzes the conversion of oxaloacetic acid to phosphoenolpyruvate, and after entering the methylerythritol phosphate (MEP) pathway, 4-hydroxy-3-methylbut-2-en-1yl diphosphate synthase reduces 2-C-methyl-d-erythritol-2,4-cyclodiphosphate (ME-Cpp) to 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (HMBPP), which is closely related to the synthesis of lutein; and coproporphyrinogen III oxidase and ChlI play important roles in the chlorophyll biosynthetic pathway. These results supported that for the heterotrophic C. pyrenoidosa, the signaling, oriented from mRET, may regulate the nuclear genes encoding the enzymes involved in photosynthetic pigment biosynthesis.

1-Methylcyclopropene Treatment on Phenolics and the Antioxidant System in Postharvest Peach Combined with the Liquid Chromatography/Mass Spectrometry Technique

In the present study, the potential effect of 1-methylcyclopropene (1-MCP) treatment on phenolics and antioxidant capacity in postharvest peach was assessed. Peach fruit (cv. Xiahui-8) treated with 1-MCP or without treatment was stored in 25 °C for 2, 4, 6, and 8 days. The phenolic composition and change trend were evaluated by liquid chromatography/mass spectrometry. The reactive oxygen species production and scavenging capacity against DPPH, O₂^• -, and HO^• were determined. Gene expression of enzymes in the flavonoid biosynthetic pathway was assayed by quantitative reverse transcription polymerase chain reaction analysis. 1-MCP application inhibited the ethylene and CO₂ production and stimulated the total phenol and total flavonoid contents. Total anthocyanin formation may be influenced directly or indirectly by the level of ethylene. The scavenging capacities of DPPH, HO^•, and O₂^• - after 1-MCP treatment were enhanced. 1-MCP treatment affected the tissue color change, stimulated gene expression of PpaPAL, PpaCHS, PpaF3H, and PpaUFGT, and promoted the biosynthesis of flavonoids and stability of anthocyanin. PpaDFR and PpaUFGT played crucial roles in rapid color change stages. Kaempferol and kaempferol 3- O-galactoside increased distinctively during storage time.

Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria.

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants

The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.

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.

iTRAQ-based Protein Profiling and Fruit Quality Changes at Different Development Stages of Oriental Melon

BACKGROUND

Oriental melon is one of the most popular crops for its nutritional and flavour quality. Components that determine melon quality, such as sugar, colour, texture, flavour and aroma, among other factors, accumulate in different developmental stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in the oriental melon is very important for advancing our understanding of oriental melon quality in the ripening processes.

RESULTS

iTRAQ-based protein profiling was conducted on 'YuMeiren' oriental melon fruit at different developmental stages. Physiological quality indices, including firmness, rind colour, soluble solids content (SSC), ethylene production, sugar content and volatile compounds were also characterized during four maturity periods of the melon, including 5, 15, 25 and 35 days after anthesis (DAA). A principal component analysis (PCA) revealed that the aroma volatiles at 5 DAA and 15 DAA were similar and separated from that of 35 DAA. More than 5835 proteins were identified and quantified in the two biological repeats and divided into 4 clusters by hierarchical cluster analysis. A functional analysis was performed using Blast2GO software based on the enrichment of a GO analysis for biological process, molecular function and cellular components. The main KEGG pathways, such as glycolysis, α-linolenic acid and starch and sucrose metabolism, were analyzed. The gene family members corresponding to differentially expressed proteins, including lipoxygenase (CmLOX01-18) and alcohol acetyltransferase (CmAAT1-4) involved in the α-linolenic acid metabolic pathway, were verified with real-time qPCR. The results showed that the expression patterns of 64.7% of the genes were consistent with the expression patterns of the corresponding proteins.

CONCLUSIONS

This study combined the variation of the quality index and differentially expressed proteins of oriental melon at different developmental stages that laid the foundation for the subsequent protein and gene function validation.