Assessment of Prunus persica fruit softening using a proteomics approach

Formation mechanism of salted egg yolk mudding during storage: Protein oxidation, gel structure, and conformation

The aim of this study was to investigate the formation mechanism of salted egg yolk (SEY) mudding during storage. Results showed that the soluble protein, hardness, and intrinsic fluorescence intensity of SEY decreased significantly during storage, while total volatile basic nitrogen, sulfhydryl group, dityrosine, adhesiveness, and surface hydrophobicity increased significantly, and the intrinsic fluorescence peak position red-shifted at first and then blue-shifted. In addition, from the results of infrared and microstructure analyses, there was an obvious oxidation reaction between protein and lipid in the late storage stage; the structure of SEY was destroyed, many random coils were formed, and the degree of protein-lipid binding and the crystallinity of SEY protein decreased during storage. Finally, the heatmap analysis revealed that the protein and lipid oxidation and conformational changes might be the main reasons for SEY mudding. This study can provide theoretical guidance for the control of SEY mudding.

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.

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

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

Identification of the cell wall proteins associated with the softening of Lycium barbarum L. fruit by using iTRAQ technology

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This was the first proteomic study on the cell walls of Lycium barbarum L. during fruit softening.

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A total of 258 differentially expressed proteins (DEPs) from the cell walls were identified between pre- and post-climacteric stages.

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Softening of Lycium barbarum L. fruit was accompanied by degradation of cell wall materials.

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DEPs promote cell wall polysaccharide degradation by driving energy metabolism.

Excessive softening of Lycium barbarum L. (LBL) fruit can limit the storage and transportation of fresh fruit. To better understand the underlying molecular mechanisms of fruit softening in LBL, changes in the pre-climacteric (S1) and post-climacteric (S2) proteomes were investigated by iTRAQ methods. The 14-fold reduction in S2 fruit firmness compared to S1 was accompanied by increased espiratory intensity and degradation of cell wall components. A total of 258 differentially expressed proteins (DEPs) were identified, which were mainly associated with photosynthesis, carbohydrate, amino acids and fatty acids metabolism. From the functional proteomic analysis, enhanced energy metabolisms, such as glycolysis/gluconeogenesis and citrate cycle (TCA cycle) contributed to cell wall degradation and conversion to substrates for respiratory metabolism, leading to fruit softening. These findings have provided new insights into the molecular pathways associated with fruit softening in LBL and the bioinformatics analyses provided insightful information for further transcriptional studies.

Comparative Analysis of Akebia trifoliata Fruit Softening at Different Flesh Ripening Stages Using Tandem Mass Tag Technology

Owing to its medicinal and high nutritional values, Akebia trifoliata can be considered as a new type of medicinal and edible homologous resources, and it has begun to be widely cultivated in many areas of China. Over-softening of fruit would affect the sensorial quality, utilization rate, and consumer acceptance of the fruit postharvest. However, fruit softening has not been characterized and the molecular mechanism underlying A. trifoliata fruit softening during ripening remains unclear. A comparative proteomic analysis was performed on the fruit at three developmental stages using tandem mass tag technology. In total, 2,839 proteins and 302 differentially abundant proteins (DAPs) were identified. Bioinformatics analysis indicated that most DAPs were implicated in oxidoreductase activity, protein domain-specific binding and pyruvate metabolism. Moreover, 29 DAPs associated with cell wall metabolism, plant hormone, and stress and defense response pathways were validated using quantitative PCR. Notably, pectinesterase, pectate lyase, and β-galactosidase, which are involved in cell wall degradation, as well as gibberellin regulated protein, cysteine protease, thaumatin-like protein and heat shock proteins which is involved in plant hormone, and stress and defense response, were significantly up-regulated in softening fruit compared with the levels in non-softening fruit. This indicated that they might play key roles in A. trifoliata fruit softening. Our findings will provide new insights into potential genes influencing fruit softening traits of A. trifoliata, which will help to develop strategies to improve fruit quality and reduce softening-related losses.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Primary Metabolism in Avocado Fruit

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

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’.

Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]

Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. 'Venus' selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed 'Response to auxin' as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers.

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.

Proteome analysis of the almond kernel (Prunus dulcis)

BACKGROUND

Almond (Prunus dulcis) is a popular tree nut worldwide and offers many benefits to human health. However, the importance of almond kernel proteins in the nutrition and function in human health requires further evaluation. The present study presents a systematic evaluation of the proteins in the almond kernel using proteomic analysis.

RESULTS

The nutrient and amino acid content in almond kernels from Xinjiang is similar to that of American varieties; however, Xinjiang varieties have a higher protein content. Two-dimensional electrophoresis analysis demonstrated a wide distribution of molecular weights and isoelectric points of almond kernel proteins. A total of 434 proteins were identified by LC-MS/MS, and most were proteins that were experimentally confirmed for the first time. Gene ontology (GO) analysis of the 434 proteins indicated that proteins involved in primary biological processes including metabolic processes (67.5%), cellular processes (54.1%), and single-organism processes (43.4%), the main molecular function of almond kernel proteins are in catalytic activity (48.0%), binding (45.4%) and structural molecule activity (11.9%), and proteins are primarily distributed in cell (59.9%), organelle (44.9%), and membrane (22.8%).

CONCLUSION

Almond kernel is a source of a wide variety of proteins. This study provides important information contributing to the screening and identification of almond proteins, the understanding of almond protein function, and the development of almond protein products. © 2015 Society of Chemical Industry.

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.

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.

Proteomic analysis of a segregant population reveals candidate proteins linked to mealiness in peach

Peaches are stored at low temperatures to delay ripening and increase postharvest life. However some varieties are susceptible to chilling injury,which leads to fruit mealiness, browning and flesh bleeding. In order to identify potentialmarkers associated with chilling injury,we performed proteomic analyses on a segregating population with contrasting susceptibility to chilling-induced mealiness. Chilling-induced mealiness was assessed by measuring juiciness in fruits that have been stored in cold and then allowed to ripen. Fruitmesocarp and leaf proteome from contrasting segregants were analyzed using 2-DE gels. Comparison of protein abundance between segregants revealed 133 spots from fruit mesocarp and 36 from leaf. Thirty four fruit mesocarp proteins were identified from these spots. Most of these proteins were related to ethylene synthesis, ABA response and stress response. Leaf protein analyses identified 22 proteins, most of which related to energy metabolism. Some of the genes that code for these proteins have been previously correlated with chilling injury through transcript analyses and co-segregation with mealiness QTLs. The results from this study, further deciphers the molecular mechanisms associated with chilling response in peach fruit, and identifies candidate proteins linked to mealiness in peach which may be used as putative markers for this trait.

Transcriptomic analysis of fruit stored under cold conditions using controlled atmosphere in Prunus persica cv. "Red Pearl"

Cold storage (CS) can induce a physiological disorder known as chilling injury (CI) in nectarine fruits. The main symptom is mealiness that is perceived as non-juicy fruit by consumers. Postharvest treatments such as controlled atmosphere (CA; a high CO2 concentration and low O2) have been used under cold conditions to avoid this disorder. With the objective of exploring the mechanisms involved in the CA effect on mealiness prevention, we analyzed transcriptomic changes under six conditions of "Red Pearl" nectarines by RNA-Seq. Our analysis included just harvested nectarines, juicy non-stored fruits, fruits affected for CI after CS and fruits stored in a combination of CA plus CS without CI phenotype. Nectarines stored in cold conditions combined with CA treatment resulted in less mealiness; we obtained 21.6% of juice content compared with just CS fruits (7.7%; mealy flesh). RNA-Seq data analyses were carried out to study the gene expression for different conditions assayed. During ripening, we detected that nectarines exposed to CA treatment expressed a similar number of genes compared with fruits that were not exposed to cold conditions. Firm fruits have more differentially expressed genes than soft fruits, which suggest that most important changes occur during CS. On the other hand, gene ontology analysis revealed enrichment mainly in metabolic and cellular processes. Differentially expressed genes analysis showed that low O2 concentrations combined with cold conditions slows the metabolic processes more than just the cold storage, resulting mainly in the suppression of primary metabolism and cold stress response. This is a significant step toward unraveling the molecular mechanism that explains the effectiveness of CA as a tool to prevent CI development on fruits.

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

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

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

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

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 analysis of grapevine (Vitis vinifera L.) leaf changes induced by transition to autotrophy and exposure to high light irradiance

Using a proteomics approach, we evaluated the response of heterotrophic and autotrophic leaves of grapevine when exposed to high light irradiation. From a total of 572 protein spots detected on two-dimensional gels, 143 spots showed significant variation caused by changes in the trophic state. High light treatment caused variation in 90 spots, and 51 spots showed variation caused by the interaction between both factors. Regarding the trophic state of the leaf, most of the proteins detected in the heterotrophic stage decreased in abundance when the leaf reached the autotrophic stage. Major differences induced by high light were detected in autotrophic leaves. In the high-light-treated autotrophic leaves several proteins involved in the oxidative stress response were up-regulated. This pattern was not observed in the high-light-treated heterotrophic leaves. This indicates that in these types of leaves other mechanisms different to the protein antioxidant system are acting to protect young leaves against the excess of light. This also suggests that these protective mechanisms rely on other sets of proteins or non-enzymatic molecules, or that differences in protein dynamics between the heterotrophic and autotrophic stages makes the autotrophic leaves more prone to the accumulation of oxidative stress response proteins.

BIOLOGICAL SIGNIFICANCE

Transition from a heterotrophic to an autotrophic state is a key period during which the anatomical, physiological and molecular characteristics of a leaf are defined. In many aspects the right functioning of a leaf at its mature stage depends on the conditions under what this transition occurs. This because apart of the genetic control, environmental factors like mineral nutrition, temperature, water supply, light etc. are also important in its control. Many anatomical and physiological changes have been described in several plant species, however in grapevine molecular data regarding changes triggered by this transition or by light stress are still scarce. In this study, we identify that the transition from heterotrophic to autotrophic state in grapevine triggers major changes in the leaf proteome, which are mainly related to processes such as protein synthesis, protein folding and degradation, photosynthesis and chloroplast development. With the exception of proteins involved in carbon fixation, that increased in abundance, most of the proteins detected during the heterotrophic stage decreased in abundance when the leaf reached its autotrophic stage. This is most likely because leaves have reached their full size and from now they have to work as a carbon source for sink organs located in other parts of the plant. Despite the potential control of this transition by light, to date, no studies using a proteomics approach have been conducted to gain a broader view of the effects of short-term high light stress. Our results indicate that short-term high light exposure has a major impact on the proteome of the autotrophic leaves, and trigger a differential accumulation of several proteins involved in the oxidative stress response. Surprisingly, heterotrophic leaves do not display this pattern which can be attributed to a lower sensitivity of these leaves to high light stimulus. In fact we discovered that heterotrophic leaves are more tolerant to light stress than autotrophic leaves. This finding is of high biological significance because it helps to understand how young leaves are able to evolve to autotrophy in areas where high light intensities are predominant. This also reveals in this type of leaves the existence of alternative mechanisms to address this stressful condition. These observations provide new insights into the molecular changes occurring during transition of leaves to autotrophy particularly when this transition occurs under high light intensities. This for example occurs during the springtime when the grapevine buds burst and the young leaves are suddenly exposed to high light intensities.

ABA may promote or delay peach fruit ripening through modulation of ripening- and hormone-related gene expression depending on the developmental stage

Peach (Prunus persica laevis L. Batsch) was chosen as a model to further clarify the physiological role of ABA during fruit ripening. To this aim, branches bearing one fruit at mid-S3, S3/S4 and S4 stages of fruit development and characterized by a different ripening index (I(AD)), as revealed by a non-destructive device called a DA-meter, were treated with ABA (0.02 mM) for 1 and 5 days. Exogenously applied ABA interfered with the progression of ripening leading to less ripe or riper fruit depending on the physiological stage. To better understand the molecular basis of ABA interference with ripening, the time-course changes in the expression of ethylene-, cell wall-, and auxin-related genes as well as other genes (NCED, PIP, LOX, AOS and SOT) was evaluated in the fruit mesocarp. Real-time PCR analyses revealed that in mid-S3 fruit transcript levels of ethylene biosynthesis and signaling (ACS1, ACO1, ETR2, ERF2), cell wall softening-related (PG, PMEI, EXP1, EXP2) and auxin biosynthesis, conjugation, transport and perception (TRPB, IGPS, Aux/IAA, GH3, PIN1 and TIR1) genes were substantially down-regulated on day 5 indicating a ripening delay. On the contrary, in more advanced stages (S3/S4 and S4) the same genes were early (day 1) up-regulated suggesting an acceleration of ripening. Transcript profiling of other ripening-related genes revealed changes that were in accord with a ripening delay (mid-S3) or acceleration (S3/S4 and S4). Thus, in peach fruit, ABA appears to modulate ripening through interference not only with ethylene and cell wall but also with auxin-related genes.

Proteomic responses of fruits to environmental stresses

Fruits and vegetables are extremely susceptible to decay and easily lose commercial value after harvest. Different strategies have been developed to control postharvest decay and prevent quality deterioration during postharvest storage, including cold storage, controlled atmosphere (CA), and application of biotic and abiotic stimulus. In this review, mechanisms related to protein level responses of host side and pathogen side were characterized. Protein extraction protocols have been successfully developed for recalcitrant, low protein content fruit tissues. Comparative proteome profiling and functional analysis revealed that defense related proteins, energy metabolism, and antioxidant pathway played important roles in fruits in response to storage conditions and exogenous elicitor treatments. Secretome of pathogenic fungi has been well-investigated and the results indicated that hydrolytic enzymes were the key virulent factors for the pathogen infection. These protein level changes shed new light on interaction among fruits, pathogens, and environmental conditions. Potential postharvest strategies to reduce risk of fruit decay were further proposed based on currently available proteomic data.

Hypothesis: increase of the ratio singlet oxygen plus superoxide radical to hydrogen peroxide changes stress defense response to programmed leaf death

The level of reactive oxygen species (ROS) increases under different stresses and, by destroying cellular components, may cause cell death. In addition, ROS are part of the complex network of transduction signals that induce defense reactions against stress or, alternatively, trigger programmed cell death, and key questions are the levels of each ROS that, respectively determine defense and death responses of the cell. The answer to those questions is difficult because there are several patterns of cell death that frequently appear mixed and are hardly distinguishable. Moreover, although considerable progresses have been achieved in the determination of the levels of specific ROS, critical questions remain on the ROS level in specific cell compartments. By considering chloroplasts as the main source of ROS in photosynthetic tissues at light, a comparison of the levels in stress and senescence of the chloroplastic activities involved in the generation and scavenging of ROS suggests plausible differences in the levels of specific ROS between stress defense and death. In effect, the three activities of the chlororespiratory chain increase similarly in stress defense response. However, in senescence, superoxide dismutase (SOD), that converts superoxide anion radical ([Formula: see text]) to hydrogen peroxide (H2O2,) decreases, while the thylakoid Ndh complex, that favors the generation of singlet oxygen ((1)O2) and [Formula: see text], and peroxidase (PX), that consumes H2O2, increase. The obvious inference is that, in respect to defense response, the ratio ((1)O2 plus [Formula: see text])/H2O2 is increased in the senescence previous to cell death. We hypothesize that the different ROS ratios, probably through changes in the jasmonic acid/H2O2 ratio, could determine the activation of the defense network or the death network response of the cell.

Ethylene and auxin biosynthesis and signaling are impaired by methyl jasmonate leading to a transient slowing down of ripening in peach fruit

Peach (Prunus persica) was chosen as a model to further clarify the physiological role of jasmonates (JAs) during fruit ripening. To this aim, the effect of methyl jasmonate (MJ, 0.88 mM), applied at a late stage (S3) of fruit development under field conditions (in planta), on the time-course of fruit ripening over a 14-day period was evaluated. As revealed by a non-destructive device called a DA-meter, exogenously applied MJ impaired the progression of ripening leading to less ripe fruit at harvest. To better understand the molecular basis of MJ interference with ripening, the time-course changes in the expression of ethylene-, cell wall-, and auxin-related genes as well as other genes (LOX, AOS and bZIP) was evaluated in the fruit mesocarp. Real-time PCR analyses revealed that transcript levels of ethylene-related genes were strongly affected. In a first phase (days 2 and/or 7) of the MJ response, mRNAs of the ethylene biosynthetic genes ACO1, ACS1 and the receptor gene ETR2 were strongly but transiently down-regulated, and then returned to or above control levels in a second phase (days 11 and/or 14). Auxin biosynthetic, conjugating, transport and perception gene transcripts were also affected. While biosynthetic genes (TRPB and IGPS) were up-regulated, auxin-conjugating (GH3), perception (TIR1) and transport (PIN1) genes were transiently but strongly down-regulated in a first phase, but returned to control levels subsequently. Transcript levels of two JA-related genes (LOX, AOS) and a developmentally regulated transcription factor (bZIP) were also affected, suggesting a shift ahead of the ripening process. Thus, in peach fruit, the transient slowing down of ripening by exogenous MJ was associated with an interference not only with ethylene but also with auxin-related genes.