Effect of post-harvest heat treatment on proteome change of peach fruit during ripening

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.

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

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

Heat shock treatment maintains the quality attributes of postharvest jujube fruits and delays their senescence process during cold storage

The effects of heat shock (HT), 1-methylcyclopropene (1-MCP), or their combination (HT + 1-MCP) on the quality of fresh jujube fruits during cold storage were studied. Among them, HT showed the best preservation effect on jujube fruits, which was more effective than others in inhibiting the increase of red index, decay incidence, and weight loss and delaying the decrease of firmness, soluble solids content (SSC), titratable acidity (TA), and ascorbic acid (AsA) content. Besides, it could delay the degradation rate of the cell wall to maintain the integrity of cell membrane, and keep the high activity of active oxygen scavenging enzymes. During cold storage, malondialdehyde (MDA) content and relative electrolyte leakage (REL) of the HT group were significantly lower than those of the control group, 1-MCP, and HT + 1-MCP group (p < .05), while superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities were significantly higher than those of other groups (p < .05). It was concluded that the postharvest HT treatment could effectively delay the senescence and decay of jujube fruits. PRACTICAL APPLICATIONS: Jujube fruits have high nutritional value used for food and medicine. However, they are not tolerant to storage after harvest, resulting in high economic losses. Therefore, it is of great significance to find a suitable method to maintain the quality of jujube fruits. Our results revealed the effect of HT, 1-MCP, and their combination on the quality maintenance of jujube fruits, and found that HT could effectively maintain the quality of them, which could be used as an effective method for keeping jujube fruits fresh.

Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants

In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.

Dynamic Changes of DNA Methylation Induced by Heat Treatment Were Involved in Ethylene Signal Transmission and Delayed the Postharvest Ripening of Tomato Fruit

Deoxyribonucleic acid (DNA) methylation plays an important role in fruit ripening and senescence. Here, the role of DNA methylation of the CpG island of SlACS10, LeCTR1, LeEIN3, LeERT10, and SlERF-A1 genes induced by heat treatment (37 °C) in postharvest ripening of tomato fruit was studied. After heat treatment, the firmness and vitamin C content showed higher levels, the loss of aldehydes in volatile components was delayed, and the activities of methylase and demethylase decreased in tomato fruit. Moreover, in heat-treated fruit, significant changes in DNA methylation of SlACS10, LeCTR1, LeEIN3, LeERT10, and SlERF-A1 were induced, the expression of LeERT10 and LeEIN3 was inhibited, the expression of SlERF-A1 was increased, by which ethylene signal transmission might be suppressed and the postharvest ripening of tomato fruit was delayed. The present study provided valuable information for understanding the essential role of DNA methylation in the postharvest ripening of tomato fruit.

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.

Effects of ozone postharvest treatment on physicochemical and qualitative traits of Actinidia chinensis 'Soreli' during cold storage

BACKGROUND

Ozone has been used for improving the postharvest life of fruits and vegetables. Ozonation, an alternative decontamination method, can be applied effectively to perishable commodities immediately after harvest. Kiwifruit is a subtropical climacteric fruit that is less able to acclimate and is susceptible to low temperatures. In this study, we investigated the influence of ozone and different storage temperatures on the physico-chemical and qualitative features in Actinidia chinensis 'Soreli'. The fruits were treated with a continuous flow of ozone in air (300 ppb), stored at 2 and 4 °C for 60 days, and sampled every 15 days.

RESULTS

It was found that ozone treatment induced the ripening process; this was evident at the end of the storage, with higher soluble solids content for ozone-treated fruits at 2 and 4 °C. Storage temperatures and gaseous ozone treatment influenced in a different manner the bioactive compounds, such as polyphenols, flavonoids, ascorbic acid, and carotenoids. Additionally, under gaseous ozone storage, microbial growth was delayed, improving the microbial quality index when the fruits were stored at the lowest storage temperature (2 °C). Principal component analysis highlighted that the effects of storage temperature on physico-chemical and bioactive compounds were greater than the postharvest treatment.

CONCLUSION

Storage temperature influenced the postharvest life of 'Soreli'. Storage at 2 °C and under 300 ppb gaseous ozone improved the yellow-fleshed fruit storage life. However, storage at 4 °C under 300 ppb gaseous ozone did not show advantages in preserving the fruit quality. © 2019 Society of Chemical Industry.

The Combination of Hot Air and Chitosan Treatments on Phytochemical Changes during Postharvest Storage of 'Sanhua' Plum Fruits

Plum fruits would become putrid quickly after harvest. In order to prolong postharvest life, 'Sanhua' plum fruits were treated by hot air combined with a chitosan coating, and stored at low temperature. Fruit firmness, total soluble solids, total phytochemical contents were evaluated along with total antioxidant activities and phytochemical components. Results showed that hot air treatment delayed softening process of plum fruit. The total phenolics and flavonoids accumulated and antioxidant activities increased in both control and treatment samples during storage. These values in the samples treated with hot air and chitosan were all higher than control and hot air treatments. Phytochemicals of epicatechin, cyanidin, pelargonidin, and hesperetin were all upregulated by hot air and chitosan treatment, especially epicatechin. This suggested that chitosan might play an important role in regulating phytochemical profiles of 'Sanhua' plum fruits during storage.

Investigating proteome and transcriptome response of Cryptococcus podzolicus Y3 to citrinin and the mechanisms involved in its degradation

Citrinin (CIT) contamination has been reported in agricultural foods and is known to be nephrotoxic to human and animals. In the present study, the proteomes and transcriptomes of C. podzolicus Y3 treated with or without 10 μg/mL CIT were compared by two-dimensional electrophoresis (2-DE) and RNA sequencing, respectively. The proteomics results showed that there were 23 differentially expressed proteins (DEPs), 8 DEPs were up-regulated and 15 DEPs were significantly down-regulated. Transcriptomic analysis showed that 1208 genes were differentially expressed, 551 (43.05%) DEGs were up regulated and 657 (56.95%) were down-regulated. These results showed that the CIT treatment caused DNA damage, oxidative stress and cell apoptosis in C. podzolicus Y3. CIT treatment also activated the defense response (DNA repair and drug resistance biological process, antioxidative activity and TCA cycle) as well as drug metabolism (synthesize the CIT-degrading enzymes) in yeast cells to respond to CIT stress and degrade CIT.

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.

Proteomics profile of Hanseniaspora uvarum enhanced with trehalose involved in the biocontrol efficacy of grape berry

This present study tested the extent to which 2% w/v trehalose enhanced the proteins expression profile of Hanseniaspora uvarum Y3. Furthermore, it explored the relative gene expression of stilbene synthase (StSy), one of the vital defense-related genes found in the skin of grapes. The proteomics profile revealed that 29 proteins were differentially expressed out of which 26 were significantly up-regulated and 3 were download-regulated. The pathogenesis related (PR) and other protein spots were visible at 97.4 kDa and 14.4 kDa. Peroxiredoxin TSA1 and superoxide dismutase were the main proteins involved in defense response and both proteins were significantly up-regulated. The carbohydrate and energy metabolism proteins were also significantly up-regulated. The results revealed that the treatments were associated with substantial increase in peroxidase activity compared to the control. StSy relative gene expression level was observed to increase by 2.5-fold in grapes treated with the pre-enhanced H. uvarum compared to the control.

Effects of chlorogenic acid on capacity of free radicals scavenging and proteomic changes in postharvest fruit of nectarine

To study how chlorogenic acid affects changes of reactive oxygen species (ROS) and the proteins involved in ROS scavenging of nectarine during storage time, the fruits were treated with chlorogenic acid (CHA) then stored at 25°C for further studies. The CHA-treatment significantly reduced O₂^-· production rate, H₂O₂ content, and membrane permeability of nectarine fruit during storage. The key proteins related the nectarine fruit senescence during storage were identified by two-dimensional electrophoresis and MALDI-TOF/TOF. Level and enzymatic activity of peroxidase were reduced, while both the protein levels and the enzymatic activities of superoxide dismutase, glutathione reductase, glutathione-s-transferase and monodehydroascorbate reductase were enhanced in nectarine fruit treated with CHA. In addition, levels of several pathogen-related proteins were also enhanced by CHA-treatment. Taking together, the present study showed that CHA could influence changes in defense related proteins and reduced oxidative damage in nectarine fruit during postharvest ripening.

Screening of Deoxynivalenol Producing Strains and Elucidation of Possible Toxigenic Molecular Mechanism

In this study, seven strains of Fusarium graminearum were isolated from wheat, of which six were identified to produce deoxynivalenol and the production of deoxynivalenol was assessed. F. graminearum strain Fg1 was noted to produce 1.0 μg/g deoxynivalenol during the incubation period in the Czapek yeast broth, while none was detected in F. graminearum strain Fg2. Hence, the differences in proteomes and transcriptomes of Fg1 and Fg2 were compared to analyze the mechanism underlying deoxynivalenol production. Among the 66 significantly differentially expressed proteins in Fg1, 39 and 27 were more or less abundant expressed. Functional analysis suggested that the enzymes involved in the methylerythritol 4-phosphate and mevalonate pathways, which provide a substrate for biosynthesis of farnesyl pyrophosphate, a precursor of DON, were activated in Fg1. The transcriptomics data demonstrated that the expression level of a majority of genes, including trichothecene biosynthetic genes, protein kinases, and transcription factors, involved in trichothecene biosynthesis was higher in Fg1 than in Fg2. The results also revealed differential expression profiles of deoxynivalenol biosynthesis genes in strains Fg1 and Fg2, which emphasized their deoxynivalenol producing ability and the underlying mechanism.

Integration of transcriptome and proteome data reveals ochratoxin A biosynthesis regulated by pH in Penicillium citrinum

Proteomics and transcriptomics of P. citrinum under pH 5 (highest OTA-production) and pH 3 (not produce OTA) were analyzed to reveal the possible mechanism of OTA biosynthesis in P. citrinum.

The Possible Mechanisms Involved in Degradation of Patulin by Pichia caribbica

In this work, we examined the mechanisms involved in the degradation of patulin by Pichia caribbica. Our results indicate that cell-free filtrate of P. caribbica reduced patutlin content. The heat-killed cells could not degrade patulin. However, the live cells significantly reduced the concentration of the patulin. In furtherance to this, it was observed that patulin was not detected in the broken yeast cells and cell wall. The addition of cycloheximide to the P. caribbica cells decreased the capacity of degradation of patulin. Proteomics analyses revealed that patulin treatment resulted in an upregulated protein which was involved in metabolism and stress response processes. Our results suggested that the mechanism of degradation of patulin by P. caribbica was not absorption; the presence of patulin can induce P. caribbica to produce associated intracellular and extracellular enzymes, both of which have the ability to degrade patulin. The result provides a new possible method that used the enzymes produced by yeast to detoxify patulin in food and feed.

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

Ripening and senescence define the last step of fruit development, which directly affects its commercial value, and mitochondria play a crucial role in these processes. To better understand mitochondrial roles in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from peach tissues (Prunus persica. cv. Xiahui-8) stored at 4°C and 25°C, respectively, and their proteome was conducted using the method of 2-DE and MALDI-TOF/TOF. Twenty-four (24) differentially expressed proteins (2-fold, p≤0.01) were identified out of more than 300 spots and were divided into six categories by PIR and Uniprot, including oxidative stress (34%), carbon metabolism (29%), respiratory chain (17%), amino acid metabolism and protein biosynthesis (8%), heat shock protein (4%), ion channels (4%). Proteins involved in antioxidative systems, gluconeogenesis, glycolysis, ethanol fermentation were changed significantly in response to high temperature. Storage at 4°C dramatically delayed ripening and senescence processes by postponing the climacteric peak, slowing down carbon metabolism and degradation of cell structure. Besides, low temperature induced the expression of formate dehydrogenase and some amino acid metabolism proteins. Proteins classified in respiratory chain, ion channels showed high coherence with climacteric respiratory burst, and the antioxidative enzymes showed relatively important symptoms on ROS scavenging through orderly expressions.

SIGNIFICANCE

With the advent of proteomics and mass spectrometry (MS), it becomes possible to identify the specific functions of differentially abundant proteins in peach mitochondria. In the present study, a procedure to isolate mitochondria from peach fruits was established, and the mitochondrial proteome was systematically analyzed by 2-D gel electrophoresis procedures in combination with protein identification by mass spectrometry. Differentially expressed proteins in peach mitochondria during different stages of peach fruit ripening and senescence were characterized. Our data provide a great deal of information likely to enhance the understanding of the mitochondrial function in peach ripening and senescent process during storage.

Biodegradation of zearalenone by Saccharomyces cerevisiae: Possible involvement of ZEN responsive proteins of the yeast

The mycotoxin zearalenone, also known as F-2 mycotoxin or RAL is a potent estrogenic metabolite produced by some Gibberella and Fusarium species. It is a common contaminant of cereal crops, livestock and poultry products. However, detoxification of zearalenone (ZEN) remains a challenge. Recently, biological approach for ZEN detoxification is being explored. In this study, we investigated the biodegradation of ZEN by using Saccharomyces cerevisiae and the possible mechanisms involved. The findings revealed that, after 48h of incubation of S. cerevisiae in combination with ZEN, the ZEN was completely degraded by S. cerevisiae. On the contrary, heat-killed cells and cell-free culture filtrates of S. cerevisiae could not degrade ZEN. Furthermore, addition of cycloheximide to S. cerevisiae combined with ZEN at time 0h prevented ZEN degradation, while addition of cycloheximide at 12h significantly slowed down degradation. The results also indicated cellular proteomics of S. cerevisiae. Several differential proteins were identified, most of which were related to basic metabolism.

BIOLOGICAL SIGNIFICANCE

The findings revealed that, after 48h of incubating ZEN together with S. cerevisiae, ZEN was completely degraded by S. cerevisiae. The mechanisms involved in the degradation of ZEN by S. cerevisiae may be the production of associated intracellular and extracellular enzymes, which have the ability to degrade ZEN. In addition, there were some functional proteins produced by S. cerevisiae, indicating that the basic metabolism of S. cerevisiae was improved when ZEN was added. This novel discovery by the authors, will greatly contribute to the field of biodegradation of mycotoxin by antagonists. The authors also believed this innovation will open the grounds for further research and improvement of S. cerevisiae in the field of biodegradation.

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.

Comparative Physiological and Proteomic Analysis Reveal Distinct Regulation of Peach Skin Quality Traits by Altitude

The role of environment in fruit physiology has been established; however, knowledge regarding the effect of altitude in fruit quality traits is still lacking. Here, skin tissue quality characters were analyzed in peach fruit (cv. June Gold), harvested in 16 orchards located in low (71.5 m mean), or high (495 m mean) altitutes sites. Data indicated that soluble solids concentration and fruit firmness at commercial harvest stage were unaffected by alitute. Peach grown at high-altitude environment displayed higher levels of pigmentation and specific antioxidant-related activity in their skin at the commercial harvest stage. Skin extracts from distinct developmental stages and growing altitudes exhibited different antioxidant ability against DNA strand-scission. The effects of altitude on skin tissue were further studied using a proteomic approach. Protein expression analysis of the mature fruits depicted altered expression of 42 proteins that are mainly involved in the metabolic pathways of defense, primary metabolism, destination/storage and energy. The majority of these proteins were up-regulated at the low-altitude region. High-altitude environment increased the accumulation of several proteins, including chaperone ClpC, chaperone ClpB, pyruvate dehydrogenase E1, TCP domain class transcription factor, and lipoxygenase. We also discuss the altitude-affected protein variations, taking into account their potential role in peach ripening process. This study provides the first characterization of the peach skin proteome and helps to improve our understanding of peach's response to altitude.

Proteomics approach reveals mechanism underlying susceptibility of loquat fruit to sunburn during color changing period

The objective of this work was to investigate why loquat fruit peels are more sensitive to high temperature and strong sunlight, making them highly susceptible to sunburn, during the color changing period (CCP). Two dimensional gel electrophoresis (2-DE) of the fruit peel proteins was performed over three developmental periods, namely green fruit period (GFP), color changing period and yellow ripening period (YRP). Fifty-five protein spots with at least 2-fold differences in abundance were successfully identified by MALDI-TOF-TOF/MS. The identified proteins were divided into categories related to heat-shock response, stress response and defense, energy metabolism, photosynthesis and protein biosynthesis. The results showed that expression of proteins related to anaerobic respiration and photorespiration were increased while the proteins related to ROS scavenging, polyamine biosynthesis, defense pathogens and photosynthesis were decreased during CCP under heat stress. Our findings provide new insights into the molecular mechanism of loquat fruit susceptible to sunburn during CCP.

Overexpression of an ABC transporter and mutations of GyrA, GyrB, and ParC in contributing to high-level ciprofloxacin resistance in Streptococcus suis type 2

Streptococcus suis is a pathogen of zoonotic diseases. Moreover, the emergence of fluoro-quinolones (FQs) resistance in this pathogen has severe consequences for pigs and human health. In this study, the molecular mechanism of FQs resistance in S. suis type 2 (SS2) sensitive strains isolated from pigs was assessed after in vitro induction of resistance against the most frequently used FQs: ciprofloxacin, norfloxacin, and enrofloxacin. Proteome analysis, sequencing and real-time RT-PCR results strongly established an overexpression of an ABC transporter protein (other than SatAB) and topoisomerase mutations in GyrA (Ser81Arg), GyrB (Glu354Lys), and ParC (Ser79Phe) in contributing to high level ciprofloxacin resistance in SS2. Due to the overexpression of the ABC transporter, intracellular ciprofloxacin concentrations were significantly lower in the resistant strains than those of sensitive strains after 20, 35, and 60 min exposures to ciprofloxacin (p < 0.05). It was concluded that improper use of FQs is one of the main causes of the emergence of this zoonotic pathogen as a multiresistant organism against commonly used antibiotics. The existence of an efflux-like protein is an incentive to find new drug targets to avoid the spread of FQs-resistant S. suis isolates in pigs and the human population.

Ascorbic acid enhances oxidative stress tolerance and biological control efficacy of Pichia caribbica against postharvest blue mold decay of apples

The effect of ascorbic acid (VC) on improving oxidative stress tolerance of Pichia caribbica and biocontrol efficacy against blue mold caused by Penicillium expansum on apples was investigated. P. caribbica showed susceptibility to the oxidative stress in vitro test, and 250 μg/mL VC treatment improved its oxidative stress tolerance. The higher viability exhibited by VC-treated yeast was associated with a lower intracellular ROS level. The activities of antioxidant enzymes of P. caribbica were improved by VC treatment, including catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPX). Additionally, VC-treated yeast exhibited greater biocontrol activity against P. expansum and faster growth when stored at 25 and 4 °C, respectively, compared to the performance of the non-VC-treated yeast. In response to the VC treatment under oxidative stress, several differentially expressed proteins were identified in P. caribbica, and most of the poteins were confirmed to be related to basic metabolism. Therefore, the application of ascorbic acid is a useful approach to improve oxidative stress tolerance of P. caribbica and its biocontrol efficacy on apples.

Fundamental aspects of postharvest heat treatments

Heat treatments have been investigated for use in many aspects of postharvest storage. They have been developed for insect control, prevention of fungal development and prevention of postharvest storage disorders including chilling injury. The treatment times and temperature range vary widely, from days at 35 °C to 39 °C in hot air, to up to 63 °C for less than a minute in hot water. Much of the research has been performed to develop solutions to a particular problem, and less investigation has been conducted on the responses of the commodity to the treatment. However, since the turn of the century, a number of groups have been active in examining the molecular responses and changes that occur in commodities during and after the heat treatment. This review examines the changes at the level of transcriptome, proteome and metabolome that occur in response to the different heat treatments.

Enhanced biocontrol activity of Rhodotorula mucilaginosa cultured in media containing chitosan against postharvest diseases in strawberries: possible mechanisms underlying the effect

The effect of Rhodotorula mucilaginosa cultured in media containing chitosan on its antogonistic activity against postharvest diseases of strawberries and the possible mechanisms involved are discussed. Two-dimensional gel electrophoresis were applied in the analysis of the proteins of R. mucilaginosa in response to chitosan. Compared with the application of R. mucilaginosa alone, the biocontrol efficacy of the yeast combined with 0.5% chitosan was enhanced greatly, with significant increase in chitinase activity of antagonistic yeast, polyphenoloxidase, peroxidase, phenylalanine ammonia lyase, chitinase and β-1,3-glucanase activity, and with an inhibition of lipid peroxidation of strawberries. The population of R. mucilaginosa harvested from NYDB amended with chitosan at 0.5% increased rapidly in strawberry wounds compared with those harvested from NYDB without chitosan. In the cellular proteome, several differentially expressed proteins were identified, most of which were related to basic metabolism.

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.

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.

Proteomic analysis and qRT-PCR verification of temperature response to Arthrospira (Spirulina) platensis

Arthrospira (Spirulina) platensis (ASP) is a representative filamentous, non-N2-fixing cyanobacterium that has great potential to enhance the food supply and possesses several valuable physiological features. ASP tolerates high and low temperatures along with highly alkaline and salty environments, and can strongly resist oxidation and irradiation. Based on genomic sequencing of ASP, we compared the protein expression profiles of this organism under different temperature conditions (15°C, 35°Cand 45°C) using 2-DE and peptide mass fingerprinting techniques. A total of 122 proteins having a significant differential expression response to temperature were retrieved. Of the positively expressed proteins, the homologies of 116 ASP proteins were found in Arthrospira (81 proteins in Arthrospira platensis str. Paraca and 35 in Arthrospira maxima CS-328). The other 6 proteins have high homology with other microorganisms. We classified the 122 differentially expressed positive proteins into 14 functions using the COG database, and characterized their respective KEGG metabolism pathways. The results demonstrated that these differentially expressed proteins are mainly involved in post-translational modification (protein turnover, chaperones), energy metabolism (photosynthesis, respiratory electron transport), translation (ribosomal structure and biogenesis) and carbohydrate transport and metabolism. Others proteins were related to amino acid transport and metabolism, cell envelope biogenesis, coenzyme metabolism and signal transduction mechanisms. Results implied that these proteins can perform predictable roles in rendering ASP resistance against low and high temperatures. Subsequently, we determined the transcription level of 38 genes in vivo in response to temperature and identified them by qRT-PCR. We found that the 26 differentially expressed proteins, representing 68.4% of the total target genes, maintained consistency between transcription and translation levels. The remaining 12 genes showed inconsistent protein expression with transcription level and accounted for 31.6% of the total target genes.

Antioxidant Defenses in Plants with Attention to Prunus and Citrus spp

This short review briefly introduces the formation of reactive oxygen species (ROS) as by-products of oxidation/reduction (redox) reactions, and the ways in which the antioxidant defense machinery is involved directly or indirectly in ROS scavenging. Major antioxidants, both enzymatic and non enzymatic, that protect higher plant cells from oxidative stress damage are described. Biochemical and molecular features of the antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) are discussed because they play crucial roles in scavenging ROS in the different cell compartments and in response to stress conditions. Among the non enzymatic defenses, particular attention is paid to ascorbic acid, glutathione, flavonoids, carotenoids, and tocopherols. The operation of ROS scavenging systems during the seasonal cycle and specific developmental events, such as fruit ripening and senescence, are discussed in relation to the intense ROS formation during these processes that impact fruit quality. Particular attention is paid to Prunus and Citrus species because of the nutritional and antioxidant properties contained in these commonly consumed fruits.

Proteomic changes in different growth periods of ginseng roots

For the first time, proteomics and biochemical variables have been employed to unravel the growth strategies for the different root growth periods of ginseng (Panax ginseng CA May., Araliaceae). Enzymatic activities and cellular contents, except for starch, related to defence and metabolism were significantly increased in the slow-growth period but decreased in the fast-growth period. Proteomic characterisation by two-dimensional gel electrophoresis (2DE) showed 83 differentially expressed spots; 62 spots were up-regulated and 21 spots were down-regulated in the slow-growth period when compared to the fast-growth period. The identification of these spots indicated that the major groups of differential proteins were associated with energy metabolism (37%) and defence (17%), which was consistent with the changes observed in the biochemical measurements. These results clearly demonstrate that ginseng stores energy during its fast-growth period to promote root elongation, whereas it expends energy to improve the synthesis of secondary metabolites and stress resistance during its slow-growth period. The levels of many proteins were changed during the conversion period from fast to slow growth, providing new insights into ginseng proteome evolution. The proposed hypothetical model explains the interaction of metabolic proteins associated with the growth strategies of ginseng.

Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics

Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.