Label-free quantitative proteomics to investigate strawberry fruit proteome changes under controlled atmosphere and low temperature storage

Controlled atmosphere storage drive proteomic change in Chinese Daohuaxiang

Although the use of a controlled atmosphere is one of the most successful storage techniques, the mechanism thereof in rice storage remains unclear. We stored aromatic rice cultivar Daohuaxiang in a package filled with 98 % N2 and 35 % CO2 for 3 months. We investigated 2-acetyl-1-pyrroline loss, enzyme activities, and proteomics changes of rice during storage. The results showed that the content of 2-acetyl-1-pyrroline was reduced by 37.40 %, 25.65 %, and 43.89 % during storage using 98 % N2, 35 % CO2 controlled atmosphere storage, and conventional storage. Controlled atmosphere storage slowed down the increase of malondialdehyde content in Daohuaxiang. The results showed that 26S proteasome regulatory particle triple-A ATPase subunit 6, superoxide dismutase, glutathione transferase, and other key proteins were upregulated during 35 % CO2 regulation. This study provided a meaningful basis for exploring the regulation strategy of aromatic rice quality and strengthening the quality control of aromatic rice industry.

Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid

BACKGROUND

To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction.

RESULTS

Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups.

CONCLUSION

ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.

Comprehensive responses of aroma production in 'Benihoppe' strawberry to low oxygen associated with the changes of key gene expressions and energy levels

BACKGROUND

The influence of low oxygen on the biosynthesis of aroma-related esters and alcohols in strawberries has been well revealed. However, how low-oxygen conditions affect other volatile compounds, such as terpenes and furans, is still to be elucidated.

RESULTS

The effects of 2 kPa O₂ low oxygen on the biosynthesis of aroma in 'Benihoppe' strawberries were comprehensively investigated in this study. The results showed that, like esters, the accumulations of key terpene alcohols and furans in strawberries were also inhibited by 2 kPa O₂ low oxygen during storage and subsequent shelf life, which was associated with the down-regulation of expression of FaNES1 (nerolidol synthase) and FaOMT (O-methyltransferase). However, no anaerobic fermentation occurred in 'Benihoppe' strawberries since no ethanol and acetaldehyde were produced under the 2 kPa O₂ condition. As expected, the 2 kPa O₂ condition suppressed the respiratory intensity and lowered the energy charge to maintain the quality of strawberries. The negative effects of low-oxygen storage on aroma accumulations and the energy charge of strawberries were more pronounced when transferred to the period of shelf life.

CONCLUSION

The 2 kPa O₂ condition caused a full-scale loss of aroma in 'Benihoppe' strawberries, including esters and alcohols as well as terpenes and furans, which was mainly reflected in the reduction of aroma emissions rather than the production of off-flavor, probably due to the reduced expressions of related genes and energy charge. © 2022 Society of Chemical Industry.

Insights into the Mechanism of Flavor Loss in Strawberries Induced by Two Fungicides Integrating Transcriptome and Metabolome Analysis

Consumers have been complaining about the deterioration of the flavor of strawberries. The use of pesticides could have potential impacts on fruit flavor but the mechanisms are unclear. Here, we spayed boscalid and difenoconazole on the small green fruit of strawberries to investigate their effect on fruit flavor quality and the mechanism. The results indicated that both fungicides decreased the contents of soluble sugar and nutrients but increased acids in mature fruits, changed the levels of volatiles, and caused oxidative damage, which ultimately reduced the flavor quality of strawberries, and the negative effect of boscalid was greater. Combined with transcriptome and metabolome, boscalid altered the genes in sugar-acid metabolism (SUT, SPS, and INV), volatiles (FaQR, FaOMT, FaLOX, and FaAAT), and amino acid synthesis pathways and metabolites. This study elaborated on the effects of fungicides on the flavor quality of strawberries from physiological-biochemical and molecular levels and laid the foundation for improving the strawberry flavor quality.

Post-Harvest Problems of Strawberry and Their Solutions

Strawberry is a fruit with a short season of harvest. Strawberry is well-known among people all over the world for its distinct flavour, nutritional value, and delicacy. While on the other hand, preserving strawberry and shelf life extension has been a huge difficulty due to their perishable nature. Making effective and sustainable use of already available food processing and preservation technology needs time. Researchers must use advanced techniques like a cool store, modified atmospheric packaging (MAP), cool store, controlled atmospheric storage (CA), various packaging methods, and a variety of chemical and physical treatments to retain commodities for a longer period due to strategic market sales following harvest. Except for the preserving techniques, there is some polysaccharide-based edible coating which has a crucial role in delaying fruit softening, fruit decay, maintaining the increased levels of ascorbic acid and phenols, enhancing the activities of antioxidant enzymes, and reducing membrane damage. During the postharvest stages, there are numerous threats to keep in view regarding the safety and quality of strawberries. In this chapter, we will discuss the benefits and drawbacks of some of the various preservation technologies, as well as how they might be utilised to preserve and a prolonged period of freshly harvested strawberries.

Effects of chitosan and nano-SiO2 concentrations on the quality of postharvest guavas (Psidium guajava L.)

Guava (Psidium guajava L.) is a perishable fruit susceptible to postharvest losses at tropical ambient temperature. Therefore, the development of green storage solution such as biodegradable film could be an alternative to increase guavas’ shelf life. The primary objective of the present work was to explore the effects of combining chitosan and nano-SiO2 coating at different concentrations on the external and internal quality parameters of guavas during 12-d storage at 15°C, and 8-d storage at 30°C. Weight loss, skin colour, firmness, ascorbic acid content, total soluble solids (TSS), decay incidence, and sensory taste score during storage were also analysed. Guavas coated with 2% chitosan and 0.02% nano-SiO2 film were economically optimum to maintain the tested postharvest quality parameters, including better skin colour, higher TSS, fruit firmness, ascorbic acid content, and good taste scores, while keeping lower weight loss and decay incidence when compared with those of other treatments at both tested temperatures. Therefore, chitosan and nano-SiO2 as a coating is a promising strategy for improving the postharvest quality of guavas.

Transcriptomic and metabolomic profiling of strawberry during postharvest cooling and heat storage

Temperature is one of the most important factors regarding fruit postharvest, however its effects in the strawberry fruits quality in postharvest remains to be evaluated. In this study, the effects of cold and heat storage temperature on fruit quality of 'Benihoppe' strawberry were performed. The results showed that different temperatures could affect the metabolism of hormone, anthocyanin, reactive oxygen species (ROS), and transcription level of responsive factors. The synthesis of terpenoids, amino acids, and phenylpropanoids in strawberries were also changed under different temperatures, which finally changed the quality characteristics of the fruit. We found HSF20 (YZ1)-overexpressed fruits were sensitive to cold and heat conditions but CBF/NF-Y (YZ9)-overexpressed fruits promoted coloring under cold treatment. This study clarified the effect of postharvest cooling and heat treatments on quality and transcriptional mechanism of strawberries fruits. Moreover, these results provided an experimental basis for further research on improving the quality of strawberry berries during postharvest periods.

Application of quantitative proteomics to investigate fruit ripening and eating quality

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

Comparative Proteomic Analysis of Rhizoctonia solani Isolates Identifies the Differentially Expressed Proteins with Roles in Virulence

Sheath blight of rice is a destructive disease that could be calamitous to rice cultivation. The significant objective of this study is to contemplate the proteomic analysis of the high virulent and less virulent isolate of Rhizoctonia solani using a quantitative LC-MS/MS-based proteomic approach to identify the differentially expressed proteins promoting higher virulence. Across several rice-growing regions in Odisha, Eastern India, 58 Rhizoctonia isolates were obtained. All the isolates varied in their pathogenicity. The isolate RS15 was found to be the most virulent and RS22 was identified as the least virulent. The PCR amplification confirmed that the RS15 and RS22 belonged to the Rhizoctonia subgroup of AG1-IA with a specific primer. The proteomic information generated has been deposited in the PRIDE database with PXD023430. The virulent isolate consisted of 48 differentially abundant proteins, out of which 27 proteins had higher abundance, while 21 proteins had lower abundance. The analyzed proteins acquired functionality in fungal development, sporulation, morphology, pathogenicity, detoxification, antifungal activity, essential metabolism and transcriptional activities, protein biosynthesis, glycolysis, phosphorylation and catalytic activities in fungi. A Quantitative Real-Time PCR (qRT-PCR) was used to validate changes in differentially expressed proteins at the mRNA level for selected genes. The abundances of proteins and transcripts were positively correlated. This study provides the role of the proteome in the pathogenicity of R. solani AG1-IA in rice and underpins the mechanism behind the pathogen’s virulence in causing sheath blight disease.

Proteomics Reveals the Mechanism Underlying the Autolysis of Postharvest Coprinus comatus Fruiting Bodies

Autolysis occurs widely in edible mushroom fruiting bodies after harvest, but the mechanism is still unclear. In this study, quantitative proteomics and bioinformatics analyses have been applied for revealing the autolysis mechanism of postharvest Coprinus comatus fruiting bodies. The results indicated that the autolysis mechanism of postharvest C. comatus was complicated. Before pileus opening, the carbohydrate metabolism including cell wall hydrolysis and energy biosynthesis, which were probably regulated by the ribosome, was involved in mushroom autolysis, whereas after pileus opening, the autolysis mechanism was related to the accumulated reactive oxygen species (ROS) and activated mitogen-activated protein kinase (MAPK) signaling pathway based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Furthermore, the changes in cell wall components and hydrolases, along with the production of ROS and the activities of oxidoreductase in C. comatus, were also verified to confirm the proteomic analysis results.

Chilling injury mechanism of hardy kiwifruit (Actinidia arguta) was revealed by proteome of label-free techniques

Refrigeration is an important method to extend shelf life of hardy kiwifruit. However, the inappropriate storage temperature can lead to chilling injury in the fruit. We found that firmness, total soluble solids, and total polyphenolic content of the fruit exposed to 0℃ environment were apparently lower, and titratable acidity content, browning rate, weight loss rate, electrolyte leakage, proline content, and malondialdehyde content were higher obviously than 4℃. A total of 244 differentially expressed proteins were found result from differential temperatures, among which 113 were up-regulated and 131 were down-regulated. Subcellular localization results presented that the differentially expressed proteins which were affected by low temperature were located in cytoplasmic, chloroplast, nuclear, mitochondrial, plasma membrane, and extracellular. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed proteins were mainly participated in synthesis of citrate cycle, oxidative phosphorylation, fatty acid biosynthesis, and starch and sucrose metabolism. Protein-protein interaction results revealed that central proteins interaction points respectively are 30S ribosomal proteins, 30S ribosomal protein S7, chloroplastic, cell division cycle 5-like protein, 50S ribosomal protein, ribosomal protein, ribosomal protein L6 protein, and SRP54 subunit protein. The quality deviations of all identified peptides were mainly distributed within 10 ppm, and MS2 has an ideal andromeda score, with more than 87.82% peptide scores above 60 points, and the median peptide score of 99.28 points. Therefore, the results of this study provide important information for new gene revelation and gene interaction relationship in hardy kiwifruit of chilling injury. PRACTICAL APPLICATIONS: Inhibition of cold damage in hardy kiwifruit under low temperature is very important work for the development of its storage industry. However, many qualities of fruit will deteriorate after long-term cold storage and those biological activities of the fruits are regulated by proteins. It is, therefore, of great significance to reveal the key proteins caused cold damage in hardy kiwifruit. Moreover, the study results could provide a scientific information for the quality improvement and genetic modification of hardy kiwifruit.

Influence of Freezing and Different Drying Methods on Volatile Profiles of Strawberry and Analysis of Volatile Compounds of Strawberry Commercial Jams

Strawberry is the most consumed berry fruit worldwide due to its unique aroma and flavor. Drying fruits to produce a powder represents one of the possible conservation methods to extend their shelf-life. The aim of the present study was to compare the influence of freezing and different drying methods on the volatile profile of strawberry using the HS-SPME/GC–MS method, in addition to analysis of strawberry jam volatiles. A total of 165 compounds were identified, accounting for 85.03–96.88% of the total volatile compositions. Results and PCA showed that freezing and each drying process affected the volatile profile in a different way, and the most remarkable representative differential volatiles were ethyl hexanoate, hexyl acetate, (E)-2-hexenyl acetate, mesifurane, (E)-nerolidol, γ-decalactone, 1-hexanol, and acetoin. Shade air-dried, frozen, freeze-dried, and oven-dried 45 °C samples retained more of the fruity and sweet aromas of strawberry, representing more than 68% of the total aroma intensity according to the literature. In contrast, the microwave-drying method showed drastic loss of fruity esters. Strawberry jams demonstrated complete destruction of esters and alcohols in most jams, while terpenes were significantly increased. These findings help better understand the aroma of strawberry and provide a guide for the effects of drying, freezing, and jam processing.

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.

Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L

Citric acid (CA), as an organic chelator, plays a vital role in alleviating copper (Cu) stress-mediated oxidative damage, wherein a number of molecular mechanisms alter in plants. However, it remains largely unknown how CA regulates differentially abundant proteins (DAPs) in response to Cu stress in Brassica napus L. In the present study, we aimed to investigate the proteome changes in the leaves of B. L. seedlings in response to CA-mediated alleviation of Cu stress. Exposure of 21-day-old seedlings to Cu (25 and 50 μM) and CA (1.0 mM) for 7 days exhibited a dramatic inhibition of overall growth and considerable increase in the enzymatic activities (POD, SOD, CAT). Using a label-free proteome approach, a total of 6345 proteins were identified in differentially treated leaves, from which 426 proteins were differentially expressed among the treatment groups. Gene ontology (GO) and KEGG pathways analysis revealed that most of the differential abundance proteins were found to be involved in energy and carbohydrate metabolism, photosynthesis, protein metabolism, stress and defense, metal detoxification, and cell wall reorganization. Our results suggest that the downregulation of chlorophyll biosynthetic proteins involved in photosynthesis were consistent with reduced chlorophyll content. The increased abundance of proteins involved in stress and defense indicates that these DAPs might provide significant insights into the adaptation of Brassica seedlings to Cu stress. The abundances of key proteins were further verified by monitoring the mRNA expression level of the respective transcripts. Taken together, these findings provide a potential molecular mechanism towards Cu stress tolerance and open a new route in accelerating the phytoextraction of Cu through exogenous application of CA in B. napus.

Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)

Vacuolar H⁺-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence.

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.

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.

iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage

Background

Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis.

Results

The two kinds of commercial cultivars were exposed to a temperature of 0.5 °C for 0, 12 and 24 days. We found that the cold-sensitive cultivar (GE) suffered more severe damage as the length of the cold treatment increased. Proteomic analysis of both cultivars indicated that the number of differentially expressed proteins (DEPs) changed remarkably during the chilly treatment. JS expressed cold-responsive proteins more rapidly and mobilized more groups of proteins than GE. Furthermore, metabolic analysis revealed that more amino acids were up-regulated in JS during the early phases of low temperatures stress. The DEPs we found were mainly related to carbohydrate and energy metabolism, structural proteins, reactive oxygen species scavenging, amino acids metabolism and signal transduction. The consequences of phenotype assays, metabolic analysis and q-PCR validation confirm the findings of the iTRAQ analysis.

Conclusion

We found that the prompt response and mobilization of proteins in JS allowed it to maintain a higher level of cold tolerance than GE, and that the slower cold responses in GE may be a vital reason for the severe chilling injury commonly found in this cultivar. The candidate proteins we identified will form the basis of future studies and may improve our understanding of the mechanisms of cold tolerance in cantaloupe.

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.

Impact of elevated O2 and CO2 atmospheres on chemical attributes and quality of strawberry (Fragaria × ananassa Duch.) during storage

Modified atmosphere has widely been evident to contribute to fruit quality maintenance, however the correlation among these quality traits was less known. To explore main factors of elevated atmosphere and reduce the detection indexes, we exposed strawberry to either high O₂ (80% O₂ + 20% N₂) or CO₂ (20% CO₂ + 20% O₂ + 60% N₂) atmosphere and compared quality characteristics. It was demonstrated that both atmospheres well maintained the fruit firmness, alleviated weight loss and decay rate. Elevated O₂ maintained the polyphenolic contents and cell integrity by significantly decreasing superoxide and hydrogen peroxide levels. PCA analysis implied that HO treatment mainly affected oxygen metabolism while HCO affected carbon metabolism more. Significantly positive correlation was observed between weight loss, anthocyanin content and decay rate in elevated O₂ and control groups. This study provided new insights into correlation and difference between impact of elevated O₂ and CO₂ to postharvest preservation.

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

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

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

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

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

The aroma volatile repertoire in strawberry fruit: a review

Aroma significantly contributes to flavor, which directly affects the commercial quality of strawberries. The strawberry aroma is complex as many kinds of volatile compounds are found in strawberries. In this review, we describe the current knowledge of the constituents and of the biosynthesis of strawberry volatile compounds, and the effect of postharvest treatments on aroma profiles. The characteristic strawberry volatile compounds consist of furanones, such as 2,5-dimethyl-4-hydroxy-3(2H)-furanone and 4-methoxy-2,5-dimethyl-3(2H)-furanone; esters, including ethyl butanoate, ethyl hexanoate, methyl butanoate, and methyl hexanoate; sulfur compounds such as methanethiol, and terpenoids including linalool and nerolidol. As for postharvest treatment, the present review discusses the overview of aroma volatiles in response to temperature, atmosphere, and exogenous hormones, as well as other treatments including ozone, edible coating, and ultraviolet radiation. The future prospects for strawberry volatile biosynthesis and metabolism are also presented. © 2018 Society of Chemical Industry.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

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.

Proteomic Response and Quality Maintenance in Postharvest Fruit of Strawberry (Fragaria × ananassa) to Exogenous Cytokinin

The limitations in current understanding of the molecular mechanisms underlying fruit response to the application of plant growth regulators have increasingly become major challenges in improvement of crop quality. This study aimed to evaluate the response of strawberry to the preharvest application of exogenous cytokinin known as forchlorfenuron (CPPU). Postharvest internal and physiological quality attributes were characterized following storage under different conditions. Hierarchical clustering analysis via a label-free proteomic quantitative approach identified a total of 124 proteins in strawberries across all treatments. The expression profiles of both proteins and genes spanned the ranged role of cytokinin involved in primary and secondary metabolism, stress response, and so on. Eighty-eight proteins and fifty-six proteins were significantly regulated immediately at harvest and after storage, respectively. In general, the glycolysis in strawberry was only regulated by CPPU before storage; in addition to the accelerated photosynthesis and acid metabolism, CPPU application maintained higher capacity of resistance in strawberry to stress stimuli after storage, in comparison to control. Nevertheless, the volatile biosynthesis in strawberry has been suppressed by exogenous CPPU. Novel cytokinin response proteins and processes were identified in addition to the main transcriptomic expression to gain insights into the phytohormone control of fruit postharvest quality.

Data in support of comparative analysis of strawberry proteome in response to controlled atmosphere and low temperature storage using a label-free quantification

To elucidate the mechanisms contributing to fruit responses to senescence and stressful environmental stimuli under low temperature (LT) and controlled atmosphere (CA) storage, a label-free quantitative proteomic investigation was conducted in strawberry (Fragaria ananassa, Duch. cv. ‘Akihime’). Postharvest volatile compounds were characterized following storage under different conditions. The observed post-storage protein expression profiles may be associated with delayed senescence features in strawberry [2]. A total of 454 proteins were identified in differentially treated strawberry fruits. Quantitative analysis, using normalized spectral counts, revealed 73 proteins common to all treatments, which formed three clusters in a hierarchical clustering analysis.