Disclosing the molecular basis of salinity priming in olive trees using proteogenomic model discovery.

Plant responses to salinity are becoming increasingly understood, however, salt priming mechanisms remain unclear, especially in perennial fruit trees. Herein, we showed that low-salt pre-exposure primes olive (Olea europaea) plants against high salinity stress. We then performed a proteogenomic study to characterize priming responses in olive roots and leaves. Integration of transcriptomic and proteomic data along with metabolic data revealed robust salinity changes that exhibit distinct or overlapping patterns in olive tissues, among which we focused on sugar regulation. Using the multi-crossed -omics data set, we showed that major differences between primed and nonprimed tissues are mainly associated with hormone signaling and defense-related interactions. We identified multiple genes and proteins, including known and putative regulators, that reported significant proteomic and transcriptomic changes between primed and nonprimed plants. Evidence also supported the notion that protein post-translational modifications, notably phosphorylations, carbonylations and S-nitrosylations, promote salt priming. The proteome and transcriptome abundance atlas uncovered alterations between mRNA and protein quantities within tissues and salinity conditions. Proteogenomic-driven causal model discovery also unveiled key interaction networks involved in salt priming. Data generated in this study are important resources for understanding salt priming in olive tree and facilitating proteogenomic research in plant physiology.

The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome.

Genome-wide transcriptome analysis provides systems-level insights into plant biology. Due to the limited depth of quantitative proteomics our understanding of gene-protein-complex stoichiometry is largely unknown in plants. Recently, the complexity of the proteome and its cell-/tissue-specific distribution have boosted the research community to the integration of transcriptomics and proteomics landscapes in a proteogenomic approach. Herein, we generated a quantitative proteome and transcriptome abundance atlas of 15 major sweet cherry (Prunus avium L., cv 'Tragana Edessis') tissues represented by 29 247 genes and 7584 proteins. Additionally, 199 984 alternative splicing events, particularly exon skipping and alternative 3' splicing, were identified in 23 383 transcribed regions of the analyzed tissues. Common signatures as well as differences between mRNA and protein quantities, including genes encoding transcription factors and allergens, within and across the different tissues are reported. Using our integrated dataset, we identified key putative regulators of fruit development, notably genes involved in the biosynthesis of anthocyanins and flavonoids. We also provide proteogenomic-based evidence for the involvement of ethylene signaling and pectin degradation in cherry fruit ripening. Moreover, clusters of genes and proteins with similar and different expression and suppression trends across diverse tissues and developmental stages revealed a relatively low RNA abundance-to-protein correlation. The present proteogenomic analysis allows us to identify 17 novel sweet cherry proteins without prior protein-level annotation evidenced in the currently available databases. To facilitate use by the community, we also developed the Sweet Cherry Atlas Database (https://grcherrydb.com/) for viewing and data mining these resources. This work provides new insights into the proteogenomics workflow in plants and a rich knowledge resource for future investigation of gene and protein functions in Prunus species.

Boron stimulates fruit formation and reprograms developmental metabolism in sweet cherry.

Boron modulates a wide range of plant developmental processes; however, the regulation of early fruit development by boron remains poorly defined. We report here the physiological, anatomical, metabolic, and transcriptomic impact of pre-flowering boron supply on the sweet cherry fruit set and development (S1-S5 stages). Our findings revealed that endogenous boron content increased in early growth stages (S1 and S2 stages) following preflowering boron exogenous application. Boron treatment resulted in increased fruit set (S1 and S2 stages) and mesocarp cell enlargement (S2 stage). Various sugars (e.g., fructose and glucose), alcohols (e.g., myo-inositol and maltitol), organic acids (e.g., malic acid and citric acid), amino acids (e.g., valine and serine) accumulated in response to boron application during the various developmental stages (S1-S5 stages). Transcriptomic analysis at early growth (S1 and S2 stages) identified boron-responsive genes that are mainly related to secondary metabolism, amino acid metabolism, calcium-binding, ribosome biogenesis, sugar homeostasis and especially to photosynthesis. We found various boron-induced/repressed genes, including those specifically involved in growth. Several heat shock proteins displayed distinct patterns during the initial growth in boron-exposed fruit. Gene analysis also discovered several putative candidate genes like PavPIP5K9, PavWAT1, PavMIOX, PavCAD1, PavPAL1 and PavSNRK2.7, which could facilitate the investigation of the molecular rationale underlying boron function in early fruit growth. Substantial changes in the expression of numerous transcription factors, including PavbHLH25, PavATHB.12L, and PavZAT10.1,.2 were noticed in fruits exposed to boron. The current study provides a baseline of information for understanding the metabolic processes regulated by boron during sweet cherry fruit early growth and fruit development in general.

Probing the effects of sweet cherry (Prunus avium L.) extract on 2D and 3D human skin models.

BACKGROUND: Natural products are not only positioned in the heart of traditional medicine but also in modern medicine as many current drugs are coming from natural sources. Apart from the field of medicine and therapeutics, natural products are broadly used in other industrial fields such as nutrition, skincare products and nanotechnology. METHODS AND RESULTS: The aim of this study was to assess the effects of sweet cherry (Prunus avium L.) fruit extract from the Greek native cultivar 'Vasiliadi', on the human 2D and 3D in vitro models in order to investigate its potential impact on skin. We focused on 2D culture of primary normal human epidermal keratinocytes (NHEK) that were treated with sweet cherry fruit extract. In the first place, we targeted fruit extract potential cytotoxicity by determining ATP intracellular levels. Furthermore, we assessed its potential skin irritability by using 3D skin model. To better understand the bioactivity of sweet cherry fruit. extract, we used qPCR to study the expression of various genes that are implicated in the skin functions. Our experiments showed that sweet cherry fruit extract is non-toxic in 2D keratinocytes culture as well as non-irritant in 3D skin model. Our results revealed that the extract mediated important pathways for the optimum epidermis function such as cell proliferation, immune and inflammatory response. CONCLUSION: The sweet cherry fruit extracts possesses significant activity in epidermis function without any potential of cytotoxicity or skin irritability, which makes it a rather promising active agent for skincare.

Unraveling salt-responsive tissue-specific metabolic pathways in olive tree.

Salinity is a serious constraint that reduces olive crop productivity. Here, we defined metabolite and gene expression changes in various tissues of olive trees (cv. "Chondrolia Chalkidikis") exposed to 75 mM NaCl for 45 days. Results showed that salinity induced foliar symptoms and impaired growth and photosynthetic parameters. The content of Na+ and Cl- in roots, xylem, phloem and leaves increased, although the Na+ levels in old leaves and Cl- in young leaves remained unaffected. Mannitol was accumulated in roots and old leaves challenged by salinity. NaCl-treated trees have a decreased TCA-associated metabolites, such as citric and malic acid, as well as changes in phenylpropanoid-associated metabolites (i.e., pinoresinol and vanillic acid) and genes (OePLRTp2 and OeCA4H). Salt treatment resulted in hydroxyl-decarboxylmethyl eleuropein aglycone accumulation and OeGTF up-regulation in new leaves, possibly suggesting that oleuropein metabolism was modified by NaCl. Tyrosine metabolism, particularly verbascoside levels and OePPO and OehisC expressions, was modulated by salinity. Both genes (e.g., OeAtF3H and OeFNSII) and metabolites (e.g., apigenin and luteolin) involved in flavonoid biosynthesis were induced in old leaves exposed to NaCl. Based on these data, we constructed an interaction scheme of changes in metabolites and transcripts across olive tissues upon salinity. Particularly, several metabolites involved in carbohydrate metabolism were reduced in roots, while many sugars, carbohydrates and flavonoids were increased in leaves. This study provided a framework for better understanding the possible mechanisms that govern the tissue-specific response of olive tree to salinity stress, with insights into molecules that can be used for olive crop improvement projects.

The pleiotropic effects of Prunus avium L. extract against oxidative stress on human fibroblasts. An in vitro approach.

There is a persistent interest in innovative and multifunctional ingredients in biology research. With regards to this, natural sources have an important role due to their multiple benefits. Thus, this study aims to present the pleiotropic activity of Prunus avium L. extract on human primary fibroblasts for proving its efficacy in dermis-related processes. We focused on the safety and efficacy assessments based on cytotoxicity and gene expression analysis under oxidative stress. Specifically, Prunus avium L. extract was proved non-cytotoxic in human fibroblasts. The gene expression analysis unveiled that this extract has in vitro protective properties on human dermal fibroblasts under oxidative stress related to antioxidant activity, anti-inflammatory response, cell proliferation and cell- aging. Our study demonstrated for the very first time that the Prunus avium L. extract is a multifunctional ingredient as it mediates several human dermis-related in vitro processes highlighting its potential to be used as an active ingredient in skin care products.

Olive Fruit Development and Ripening: Break on through to the "-Omics" Side.

The olive tree (Olea europaea L. subsp. europaea) is the most important perennial crop in the Mediterranean region, producing table olives and oil, both appreciated for their nutraceutical value. Although olive oil quality traits have been extensively studied, much less attention has been paid to olive drupe. Olive drupe ripening is an extremely complex process involving numerous physiological and molecular changes that are unique in this fruit crop species. This review underlines the contribution of "-omics" techniques and of the recent advances in bioinformatics and analytical tools, notably next-generation sequencing and mass spectrometry, for the characterization of the olive ripening syndrome. The usage of high-dimensional datasets, such as transcriptomics, proteomics, and metabolomics, will provide a systematical description of the molecular-specific processes regulating olive fruit development and ripening. However, the incomplete sequence of the O. europaea L. reference genome has largely hampered the utilization of omics tools towards olive drupe research. Due to this disadvantage, the most reported -omics studies on fruit trees concern metabolomics and only a few transcriptomics and proteomics. In this review, up-to-date applications of -omics technologies towards olive drupe biology are addressed, and future perspectives in olive fruit research are highlighted.

Novel insights into the calcium action in cherry fruit development revealed by high-throughput mapping.

KEY MESSAGE: This work provides the first system-wide datasets concerning metabolic changes in calcium-treated fruits, which reveal that exogenously applied calcium may specifically reprogram sweet cherry development and ripening physiognomy. Calcium modulates a wide range of plant developmental processes; however, the regulation of fruit ripening by calcium remains largely uncharacterized. In this study, transcriptome, proteome and metabolome profiling was used to document the responses of sweet cherry fruit to external calcium application (0.5% CaCl2) at 15, 27 and 37 days after full blossom. Endogenous calcium loading in fruit across development following external calcium feeding was accompanied by a reduction in respiration rate. Calcium treatment strongly impaired water-induced fruit cracking tested by two different assays, and this effect depended on the fruit size, water temperature and light/dark conditions. Substantial changes in the levels of numerous polar/non-polar primary and secondary metabolites, including malic acid, glucose, cysteine, epicatechin and neochlorogenic acid were noticed in fruits exposed to calcium. At the onset of ripening, we identified various calcium-affected genes, including those involved in ubiquitin and cysteine signaling, that had not been associated previously with calcium function in fruit biology. Calcium specifically increased the abundance of a significant number of proteins that classified as oxidoreductases, transferases, hydrolases, lyases, and ligases. The overview of temporal changes in gene expression and corresponding protein abundance provided by interlinked analysis revealed that oxidative phosphorylation, hypersensitive response, DNA repair, stomata closure, biosynthesis of secondary metabolites, and proton-pump activity were mainly affected by calcium. This report provides the fullest characterization of expression patterns in calcium-responsive genes, proteins and metabolites currently available in fruit ripening and will serve as a blueprint for future biological endeavors.

An integrated metabolomic and gene expression analysis identifies heat and calcium metabolic networks underlying postharvest sweet cherry fruit senescence.

MAIN CONCLUSION: Ηeat and calcium treatments reprogram sweet cherry fruit metabolism during postharvest senescence as evidenced by changes in respiration, amino acid metabolism, sugars, and secondary metabolites shift. Heat and calcium treatments are used to improve postharvest fruit longevity; however, the exact mechanism remains poorly understood. To characterize the impact of these treatments on sweet cherries metabolism, 'Lapins' fruits were treated with heat or CaCl2 solutions and their combination and subsequently were exposed at room temperature, for up to 4 days, defined as senescence period. Single and combined heat and calcium treatments partially delayed fruit senescence, as evidenced by changes in fruit colour darkening, skin penetration force, and respiration activity. Calcium content was noticeably increased by heat in Ca-treated fruit. Several primary metabolites, including amino acids, organic acids, and alcohols, were decreased in response to both treatments, while many soluble sugars and secondary metabolites were increased within 1 day post-treatment. Changes of several metabolites in heat-treated fruits, especially esculetin, peonidin 3-O-glucoside and peonidin 3-O-galactoside, ribose, pyroglutamate, and isorhamnetin-3-O-rutinoside, were detected. The metabolome of fruit exposed to calcium also displayed substantial modulations, particularly in the levels of galactose, glycerate, aspartate, tryptophan, phospharate rutin, and peonidin 3-O-glucoside. The expression of several genes involved in TCA cycle (MDH1, IDH1, OGDH, SUCLA2, and SDH1-1), pectin degradation (ADPG1) as well as secondary (SK1, 4CL1, HCT, and BAN), amino acids (ALDH18A1, ALDH4A1, GS, GAD, GOT2, OPLAH, HSDH, and SDS), and sugar (PDHA1 and DLAT) metabolism were affected by both treatments. Pathway-specific analysis further revealed the regulation of fruit metabolic programming by heat and calcium. This work provides a comprehensive understanding of metabolic regulation in response to heat and calcium during fruit senescence.

Ozone-induced inhibition of kiwifruit ripening is amplified by 1-methylcyclopropene and reversed by exogenous ethylene.

BACKGROUND: Understanding the mechanisms involved in climacteric fruit ripening is key to improve fruit harvest quality and postharvest performance. Kiwifruit (Actinidia deliciosa cv. 'Hayward') ripening involves a series of metabolic changes regulated by ethylene. Although 1-methylcyclopropene (1-MCP, inhibitor of ethylene action) or ozone (O3) exposure suppresses ethylene-related kiwifruit ripening, how these molecules interact during ripening is unknown. RESULTS: Harvested 'Hayward' kiwifruits were treated with 1-MCP and exposed to ethylene-free cold storage (0 °C, RH 95%) with ambient atmosphere (control) or atmosphere enriched with O3 (0.3 µL L- 1) for up to 6 months. Their subsequent ripening performance at 20 °C (90% RH) was characterized. Treatment with either 1-MCP or O3 inhibited endogenous ethylene biosynthesis and delayed fruit ripening at 20 °C. 1-MCP and O3 in combination severely inhibited kiwifruit ripening, significantly extending fruit storage potential. To characterize ethylene sensitivity of kiwifruit following 1-MCP and O3 treatments, fruit were exposed to exogenous ethylene (100 µL L- 1, 24 h) upon transfer to 20 °C following 4 and 6 months of cold storage. Exogenous ethylene treatment restored ethylene biosynthesis in fruit previously exposed in an O3-enriched atmosphere. Comparative proteomics analysis showed separate kiwifruit ripening responses, unraveled common 1-MCP- and O3-dependent metabolic pathways and identified specific proteins associated with these different ripening behaviors. Protein components that were differentially expressed following exogenous ethylene exposure after 1-MCP or O3 treatment were identified and their protein-protein interaction networks were determined. The expression of several kiwifruit ripening related genes, such as 1-aminocyclopropane-1-carboxylic acid oxidase (ACO1), ethylene receptor (ETR1), lipoxygenase (LOX1), geranylgeranyl diphosphate synthase (GGP1), and expansin (EXP2), was strongly affected by O3, 1-MCP, their combination, and exogenously applied ethylene. CONCLUSIONS: Our findings suggest that the combination of 1-MCP and O3 functions as a robust repressive modulator of kiwifruit ripening and provide new insight into the metabolic events underlying ethylene-induced and ethylene-independent ripening outcomes.

Characterization of ß-amino- and γ-amino butyric acid-induced citrus seeds germination under salinity using nanoLC-MS/MS analysis.

KEY MESSAGE: BABA or GABA induces salinity acclimation during citrus seeds germination via alternation of specific proteins (e.g., citrin). The impact of four elicitors, namely hydrogen peroxide (H2O2), ß-amino butyric acid (BABA), γ-amino butyric acid (GABA) and hydrogen sulfide (H2S) donor, sodium hydrosulfide (NaHS), in citrus seed germination under salinity (150 mM NaCl) was tested. The germination potential was adversely affected by NaCl-alone treatment. Pretreatment with H2O2 or the NaHS-H2S donor prior to salinity had no significant effect in germination process, however, BABA and GABA substantially improved seed acclimation to salinity, as evidenced by increased germination percentage and radicle length. Total soluble proteins of radicle and cotyledons were separated by 1DE SDS-PAGE and proteins zones were analyzed by mass spectrometry. In total, 27 and 3 proteins were identified in radicle and cotyledons, respectively. The identified proteins mainly include redox-regulated enzymes (i.e., glutathione S-transferase, dehydroascorbate reductase, Mn-superoxide dismutase, glutathione peroxidase), energy-related proteins (i.e., isocitrate lyase, malate synthase, pyruvate decarboxylase), stress proteins (i.e., stress-related protein, miraculin, thaumatin, disulfide isomerase), storage proteins (i.e., vicilin, Pis v 1 allergen 2S albumin) and transcriptional regulators (i.e., MarR family transcriptional regulator, MADS544 protein). Pretreatments with BABA or GABA altered the accumulation of protein zones exclusively corresponding to citrin, indicating that this protein may serve as a marker for salinity acclimation in citrus seeds.

Trichome patterning control involves TTG1 interaction with SPL transcription factors.

Epidermal cell differentiation is a paramount and conserved process among plants. In Arabidopsis, a ternary complex formed by MYB, bHLH transcription factors and TTG1 modulates unicellular trichome morphogenesis. The formation of multicellular glandular trichomes of the xerophytic shrub Cistus creticus that accumulate labdane-type diterpenes, has attained much attention renowned for its medicinal properties. Here, we show that C. creticus TTG1 (CcTTG1) interacts with the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPLA/B) proteins, putative homologs of AtSPL4/5 that in turn interact with AtTTG1. These interactions occur between proteins from evolutionarily distant species supporting the conserved function of TTG1-SPL complex. Overexpression of AtSPL4 and AtSPL5 decreased the expression of GLABRA2 (AtGL2), the major regulator of trichome morphogenesis, resulting in trichome reduction on the adaxial surface of cauline leaves, thereby illuminating the significance of TTG1-SPLs interactions in trichome formation control. AtGL2 and AtSPL4 have opposite expression patterns during early stages of leaf development. We postulate an antagonistic effect between SPLs and the heterogeneous MYB-bHLH factors binding to TTG1. Hence, the SPLs potentially rearrange the complex, attenuating its transcriptional activity to control trichome distribution.

Roles of sodium hydrosulfide and sodium nitroprusside as priming molecules during drought acclimation in citrus plants.

Emerging evidence suggests that the gaseous molecules hydrogen sulfide (H2S) and nitric oxide (NO) enhances plant acclimation to stress; however, the underlying mechanism remains unclear. In this work, we explored if pretreatment of citrus roots with NaHS (a H2S donor) or sodium nitroprusside (SNP, a NO donor) for 2 days (d) could elicit long-lasting priming effects to subsequent exposure to PEG-associated drought stress for 21 d following a 5 d acclimation period. Detailed physiological study documented that both pretreatments primed plants against drought stress. Analysis of the level of nitrite, NOx, S-nitrosoglutahione reductase, Tyr-nitration and S-nitrosylation along with the expression of genes involved in NO-generation suggested that the nitrosative status of leaves and roots was altered by NaHS and SNP. Using a proteomic approach we characterized S-nitrosylated proteins in citrus leaves exposed to chemical treatments, including well known and novel S-nitrosylated targets. Mass spectrometry analysis also enabled the identification of 42 differentially expressed proteins in PEG alone-treated plants. Several PEG-responsive proteins were down-regulated, especially photosynthetic proteins. Finally, the identification of specific proteins that were regulated by NaHS and SNP under PEG conditions provides novel insight into long-term drought priming in plants and in a fruit crop such as citrus in particular.

The impact of sodium nitroprusside and ozone in kiwifruit ripening physiology: a combined gene and protein expression profiling approach.

BACKGROUND AND AIMS: Despite their importance in many aspects of plant physiology, information about the function of oxidative and, particularly, of nitrosative signalling in fruit biology is limited. This study examined the possible implications of O3 and sodium nitroprusside (SNP) in kiwifruit ripening, and their interacting effects. It also aimed to investigate changes in the kiwifruit proteome in response to SNP and O3 treatments, together with selected transcript analysis, as a way to enhance our understanding of the fruit ripening syndrome. METHODS: Kiwifruits following harvest were pre-treated with 100 µm SNP, then cold-stored (0 °C, relative humidity 95 %) for either 2 or 6 months in the absence or in the presence of O3 (0·3 µL L(-1)), and subsequently were allowed to ripen at 20 °C. The ripening behaviour of fruit was characterized using several approaches: together with ethylene production, several genes, enzymes and metabolites involved in ethylene biosynthesis were analysed. Kiwifruit proteins were identified using 2-D electrophoresis coupled with nanoliquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Expression patterns of kiwifruit ripening-related genes were also analysed using real-time quantitative reverse transcription-PCR (RT-qPCR). KEY RESULTS: O3 treatment markedly delayed fruit softening and depressed the ethylene biosynthetic mechanism. Although SNP alone was relatively ineffective in regulating ripening, SNP treatment prior to O3 exposure attenuated the O3-induced ripening inhibition. Proteomic analysis revealed a considerable overlap between proteins affected by both SNP and O3. Consistent with this, the temporal dynamics in the expression of selected kiwifruit ripening-related genes were noticeably different between individual O3 and combined SNP and O3 treatments. CONCLUSIONS: This study demonstrates that O3-induced ripening inhibition could be reversed by SNP and provides insights into the interaction between oxidative and nitrosative signalling in climacteric fruit ripening.

Leaf Age-Dependent Photoprotective and Antioxidative Response Mechanisms to Paraquat-Induced Oxidative Stress in Arabidopsis thaliana.

Exposure of Arabidopsis thaliana young and mature leaves to the herbicide paraquat (Pq) resulted in a localized increase of hydrogen peroxide (H2O2) in the leaf veins and the neighboring mesophyll cells, but this increase was not similar in the two leaf types. Increased H2O2 production was concomitant with closed reaction centers (qP). Thirty min after Pq exposure despite the induction of the photoprotective mechanism of non-photochemical quenching (NPQ) in mature leaves, H2O2 production was lower in young leaves mainly due to the higher increase activity of ascorbate peroxidase (APX). Later, 60 min after Pq exposure, the total antioxidant capacity of young leaves was not sufficient to scavenge the excess reactive oxygen species (ROS) that were formed, and thus, a higher H2O2 accumulation in young leaves occurred. The energy allocation of absorbed light in photosystem II (PSII) suggests the existence of a differential photoprotective regulatory mechanism in the two leaf types to the time-course Pq exposure accompanied by differential antioxidant protection mechanisms. It is concluded that tolerance to Pq-induced oxidative stress is related to the redox state of quinone A (QA).

Polyamines reprogram oxidative and nitrosative status and the proteome of citrus plants exposed to salinity stress.

The interplay among polyamines (PAs) and reactive oxygen and nitrogen species (RNS and ROS) is emerging as a key issue in plant responses to salinity. To address this question, we analysed the impact of exogenous PAs [putrescine (Put), spermidine (Spd) and spermine (Spm)] on the oxidative and nitrosative status in citrus plants exposed to salinity. PAs partially reversed the NaCl-induced phenotypic and physiological disturbances. The expression of PA biosynthesis (ADC, SAMDC, SPDS and SPMS) and catabolism (DAO and PAO) genes was systematically up-regulated by PAs. In addition, PAs altered the oxidative status in salt-stressed plants as inferred by changes in ROS production and redox status accompanied by regulation of transcript expression and activities of various antioxidant enzymes. Furthermore, NaCl-induced up-regulation of NO-associated genes, such as NR, NADde, NOS-like and AOX, along with S-nitrosoglutathione reductase and nitrate reductase activities, was partially restored by PAs. Protein carbonylation and tyrosine nitration are depressed by specific PAs whereas protein S-nitrosylation was elicited by all PAs. Furthermore, we identified 271 S-nitrosylated proteins that were commonly or preferentially targeted by salinity and individual PAs. This work helps improve our knowledge on the plant's response to environmental challenge.

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.

Interplay between protein carbonylation and nitrosylation in plants.

ROS and reactive nitrogen species (RNS) are key regulators of redox homeostasis in living organisms including plants. As control of redox homeostasis plays a central function in plant biology, redox proteomics could help in characterizing the potential roles played by ROS/RNS-induced posttranslational modification in plant cells. In this review, we focus on two posttranslational modifications: protein carbonylation (a marker of protein oxidation) and protein S-nitrosylation, both of which having recently emerged as important regulatory mechanisms during numerous fundamental biological processes. Here, we describe the recent progress in proteomic analysis of carbonylated and nitrosylated proteins and highlight the achievements made in understanding the physiological basis of these oxy/nitro modifications in plants. In addition, we document the existence of a relationship between ROS-based carbonylation and RNS-based nitrosylation thus supporting the finding that crosstalk between cellular signaling stress pathways induced by ROS and RNS could be mediated by specific protein modifications.

Oxidative and nitrosative-based signaling and associated post-translational modifications orchestrate the acclimation of citrus plants to salinity stress.

Reactive oxygen and nitrogen species are involved in a plethora of cellular responses in plants; however, our knowledge on the outcomes of oxidative and nitrosative signaling is still unclear. To better understand how oxidative and nitrosative signals are integrated to regulate cellular adjustments to external conditions, local and systemic responses were investigated in the roots and leaves of sour orange plants (Citrus aurantium L.) after root treatment with hydrogen peroxide (H(2) O(2) ) or sodium nitroprusside (a nitric oxide donor), followed by NaCl stress for 8 days. Phenotypic and physiological data showed that pre-exposure to these treatments induced an acclimation to subsequent salinity stress that was accompanied by both local and systemic H(2) O(2) and nitric oxide (NO) accumulation. Combined histochemical and fluorescent probe approaches showed the existence of a vascular-driven long-distance reactive oxygen species and NO signaling pathway. Transcriptional analysis of genes diagnostic for H(2) O(2) and NO signaling just after treatments or after 8 days of salt stress revealed tissue- and time-specific mechanisms controlling internal H(2) O(2) and NO homeostasis. Furthermore, evidence is presented showing that protein carbonylation, nitration and S-nitrosylation are involved in acclimation to salinity stress. In addition, this work enabled characterization of potential carbonylated, nitrated and nitrosylated proteins with distinct or overlapping signatures. This work provides a framework to better understand the oxidative and nitrosative priming network in citrus plants subjected to salinity conditions.

A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes.

The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.