Proteomic analysis of grapevine (Vitis vinifera L.) tissues subjected to herbicide stress

Stress response of lettuce (Lactuca sativa) to environmental contamination with selected pharmaceuticals: A proteomic study

Pharmaceutical compounds have been found in rivers and treated wastewaters. They often contaminate irrigation waters and consequently accumulate in edible vegetables, causing changes in plants metabolism. The main objective of this work is to understand how lettuce plants cope with the contamination from three selected pharmaceuticals using a label free proteomic analysis. A lettuce hydroponic culture, grown for 36 days, was exposed to metformin, acetaminophen and carbamazepine (at 1 mg/L), during 8 days, after which roots and leaves were sampled and analysed using a liquid chromatography-mass spectrometry proteomics-based approach. In roots, a total of 612 proteins showed differentially accumulation while in leaves 237 proteins were identified with significant differences over controls. Carbamazepine was the contaminant that most affected protein abundance in roots, while in leaves the highest number of differentially accumulated proteins was observed for acetaminophen. In roots under carbamazepine, stress related protein species such as catalase, superoxide dismutase and peroxidases presented higher abundance. Ascorbate peroxidase increased in roots under metformin. Cell respiration protein species were affected by the presence of the three pharmaceuticals suggesting possible dysregulation of the Krebs cycle. Acetaminophen caused the main differences in respiration pathways, with more emphasis in leaves. Lettuce plants revealed different tolerance levels when contaminants were compared, being more tolerant to metformin presence and less tolerant to carbamazepine. SIGNIFICANCE: The significant increase of emerging contaminants in ecosystems makes essential to understand how these compounds may affect the metabolism of different organisms. Our study contributes with a detailed approach of the main interactions that may occur in plant metabolism when subjected to the stress induced by three different pharmaceuticals (acetaminophen, carbamazepine and metformin).

How the Depletion in Mineral Major Elements Affects Grapevine (Vitis vinifera L.) Primary Cell Wall

The noteworthy fine remodeling that plant cell walls (CWs) undergo to adapt to developmental, physiological and environmental cues and the observation that its composition and dynamics differ between species represents an opportunity to couple crop species agronomic studies with research on CW modifications. Vitis vinifera is one of the most important crops from an economic point-of-view due to the high value of the fruit, predominantly for winemaking. The availability of some information related to this species' CWs allows researching its responses to imposed conditions that affect the plant's development. Mineral deficiency, in particular nitrogen, phosphorus, potassium and sulfur, strongly affects plant metabolism, reducing both growth and crop yield. Despite the importance of mineral nutrition in development, its influence on CW synthesis and modifications is still insufficiently documented. Addressing this knowledge gap, V. vinifera experimental models were used to study CW responses to imposed mineral depletion in unorganized (callus) and organized (shoots) tissues. The discussion of the obtained results is the main focus of this review. Callus and shoots submitted to mineral restriction are impaired in specific CW components, predominantly cellulose. Reorganization on structure and deposition of several other polymers, in particular the degree and pattern of pectin methyl-esterification and the amount of xyloglucan (XyG), arabinan and extensin, is also observed. In view of recently proposed CW models that consider biomechanical hotspots and direct linkages between pectins and XyG/cellulose, the outcome of these modifications in explaining maintenance of CW integrity through compensatory stiffening can be debated. Nutrient stresses do not affect evenly all tissues with undifferentiated callus tissues showing more pronounced responses, followed by shoot mature internodes, and then newly formed internodes. The impact of nitrogen depletion leads to more noticeable responses, supporting this nutrient's primary role in plant development and metabolism. The consequential compensatory mechanisms highlight the pivotal role of CW in rearranging under environmental stresses.

Molecular responses of genetically modified maize to abiotic stresses as determined through proteomic and metabolomic analyses

Some genetically modified (GM) plants have transgenes that confer tolerance to abiotic stressors. Meanwhile, other transgenes may interact with abiotic stressors, causing pleiotropic effects that will affect the plant physiology. Thus, physiological alteration might have an impact on the product safety. However, routine risk assessment (RA) analyses do not evaluate the response of GM plants exposed to different environmental conditions. Therefore, we here present a proteome profile of herbicide-tolerant maize, including the levels of phytohormones and related compounds, compared to its near-isogenic non-GM variety under drought and herbicide stresses. Twenty differentially abundant proteins were detected between GM and non-GM hybrids under different water deficiency conditions and herbicide sprays. Pathway enrichment analysis showed that most of these proteins are assigned to energetic/carbohydrate metabolic processes. Among phytohormones and related compounds, different levels of ABA, CA, JA, MeJA and SA were detected in the maize varieties and stress conditions analysed. In pathway and proteome analyses, environment was found to be the major source of variation followed by the genetic transformation factor. Nonetheless, differences were detected in the levels of JA, MeJA and CA and in the abundance of 11 proteins when comparing the GM plant and its non-GM near-isogenic variety under the same environmental conditions. Thus, these findings do support molecular studies in GM plants Risk Assessment analyses.

Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism

Grapes (Vitis vinifera) are a valuable fruit crop and wine production is a major industry. Global warming and expanded range of cultivation will expose grapes to more temperature stresses in future. Our study investigated protein level responses to abiotic stresses, with particular reference to proteomic changes induced by the impact of four different temperature stress regimes, including both hot and cold temperatures, on cultured grape cells. Cabernet Sauvignon cell suspension cultures grown at 26°C were subjected to 14 h of exposure to 34 and 42°C for heat stress, and 18 and 10°C for cold stress. Cells from the five temperatures were harvested in biological triplicates and label-free quantitative shotgun proteomic analysis was performed. A total of 2042 non-redundant proteins were identified from the five temperature points. Fifty-five proteins were only detected in extreme heat stress conditions (42°C) and 53 proteins were only detected at extreme cold stress conditions (10°C). Gene Ontology (GO) annotations of differentially expressed proteins provided insights into the metabolic pathways that are involved in temperature stress in grape cells. Sugar metabolism displayed switching between alternative and classical pathways during temperature stresses. Additionally, nine proteins involved in the phenylpropanoid pathway were greatly increased in abundance at extreme cold stress, and were thus found to be cold-responsive proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD000977 (http://proteomecentral.proteomexchange.org/dataset/PXD000977).

Comparative proteomic analysis in pea treated with microbial consortia of beneficial microbes reveals changes in the protein network to enhance resistance against Sclerotinia sclerotiorum

Microbial consortia may provide protection against pathogenic ingress via enhancing plant defense responses. Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27 and Bacillus subtilis BHHU100 were used either singly or in consortia in the pea rhizosphere to observe proteome level changes upon Sclerotinia sclerotiorum challenge. Thirty proteins were found to increase or decrease differentially in 2-DE gels of pea leaves, out of which 25 were identified by MALDI-TOF MS or MS/MS. These proteins were classified into several functional categories including photosynthesis, respiration, phenylpropanoid metabolism, protein synthesis, stress regulation, carbohydrate and nitrogen metabolism and disease/defense-related processes. The respective homologue of each protein identified was trapped in Pisum sativum and a phylogenetic tree was constructed to check the ancestry. The proteomic view of the defense response to S. sclerotiorum in pea, in the presence of beneficial microbes, highlights the enhanced protection that can be provided by these microbes in challenged plants.

Isolation and characterization of a pathogenesis-related protein 10 gene (GmPR10) with induced expression in soybean (Glycine max) during infection with Phytophthora sojae

In previous study, a cDNA library enriched for mRNAs encoding ESTs that increased in abundance during infection with Phytophthora sojae was constructed by suppression subtractive hybridization from leaf tissues of a high resistant soybean, and an EST homologous to the class 10 of pathogenesis-related (PR) proteins was identified to be up-regulated by microarray and real-time PCR. Here, the full-length cDNA (termed GmPR10, GenBank accession number FJ960440; ADC31789.1) of the EST was isolated by rapid amplification of cDNA ends, and contains an open reading frame of 474 bp. The GmPR10 protein included a "P-loop'' motif. The constitutive transcript abundance of GmPR10 in soybean was the highest in leaves, followed by roots and stems. Further analysis showed that GmPR10 mRNA abundance was increased during infection with P. sojae following leaf treatments with gibberellin (GA3), hydrogen peroxide (H2O2), salicylic acid (SA), and abscisic acid (ABA). The dialytically renatured GmPR10 protein significantly inhibited P. sojae hyphal growth and exhibited RNase activity. Transgenic tobacco and soybean plants overexpressing GmPR10 showed increased resistance to P. nicotianae Breda and P. sojae, respectively. These results suggest that the GmPR10 protein plays an important role in host defense against P. sojae infection. To the best of our knowledge, this is the first report on the functional characterization of a PR10 protein from soybean in defense against P. sojae.

A pathogenesis related protein, VpPR-10.1, from Vitis pseudoreticulata: an insight of its mode of antifungal activity

Previously, VpPR-10.1 was isolated and characterized from a cDNA library of a fungus-resistant accession of Chinese wild grape (Vitis pseudoreticulata). We found that expression of VpPR-10.1 is affected by the fungal pathogen Erysiphe necator. To investigate the biochemical basis of the nuclease activity of VpPR-10.1 and its role in antifungal resistance, we generated recombinant VpPR-10.1 as well as site-directed mutations targeting three conserved amino acid residues among plant PR-10 s: Lys55, Glu149, and Tyr151. We showed that wild-type recombinant VpPR-10.1 exhibits both RNase and DNase activities. Mutant VpPR10.1-Y151H essentially retained all these activities. In contrast, VpPR10.1-K55N, where Lys55 in the P-loop region is mutated to Asn, and VpPR10.1-E149G, where Glu149 is mutated to Gly, lost their nuclease activity, indicating that both residues play a critical role in catalyzing RNA and DNA degradation. Furthermore, VpPR10.1 and VpPR10.1-Y151H inhibited the growth of the cultured fungal pathogen Alternaria alternate. Through transient expression in grapevine, we also demonstrated that VpPR10.1-K55N and VpPR10.1-E149G compromised resistance to E. necator. Finally, we further found that VpPR-10.1 can lead to programmed cell death and DNA degradation when incubated with tobacco BY-2 suspension cells. We show here that Lys55 and Glu149, but not Tyr151, are required for the RNase, DNase and antifungal activities of VpPR-10.1. The strong correlation between the level of VpPR-10.1 nuclease activity and its antifungal property indicates that the former is the biochemical basis for the latter. Taken together, our experiments revealed that VpPR-10.1 is critical in mediating fungal resistance in grape, potentially playing a dual role by degrading pathogen RNA and inducing programmed death of host cells.

Current perspectives in proteomic analysis of abiotic stress in Grapevines

Grapes are an important crop plant which forms the basis of a globally important industry. Grape and wine production is particularly vulnerable to environmental and climatic fluctuations, which makes it essential for us to develop a greater understanding of the molecular level responses of grape plants to various abiotic stresses. The completion of the initial grape genome sequence in 2007 has led to a significant increase in research on grapes using proteomics approaches. In this article, we discuss some of the current research on abiotic stress in grapevines, in the context of abiotic stress research in other plant species. We also highlight some of the current limitations in grapevine proteomics and identify areas with promising scope for potential future research.

Transgenic soybeans and soybean protein analysis: an overview

To meet the increasing global demand for soybeans for food and feed consumption, new high-yield varieties with improved quality traits are needed. To ensure the safety of the crop, it is important to determine the variation in seed proteins along with unintended changes that may occur in the crop as a result various stress stimuli, breeding, and genetic modification. Understanding the variation of seed proteins in the wild and cultivated soybean cultivars is useful for determining unintended protein expression in new varieties of soybeans. Proteomic technology is useful to analyze protein variation due to various stimuli. This short review discusses transgenic soybeans, different soybean proteins, and the approaches used for protein analysis. The characterization of soybean protein will be useful for researchers, nutrition professionals, and regulatory agencies dealing with soy-derived food products.

Proteomics profiling reveals novel proteins and functions of the plant stigma exudate

Proteomic analysis of the stigmatic exudate of Lilium longiflorum and Olea europaea led to the identification of 51 and 57 proteins, respectively, most of which are described for the first time in this secreted fluid. These results indicate that the stigmatic exudate is an extracellular environment metabolically active, participating in at least 80 different biological processes and 97 molecular functions. The stigma exudate showed a markedly catabolic profile and appeared to possess the enzyme machinery necessary to degrade large polysaccharides and lipids secreted by papillae to smaller units, allowing their incorporation into the pollen tube during pollination. It may also regulate pollen-tube growth in the pistil through the selective degradation of tube-wall components. Furthermore, some secreted proteins were involved in pollen-tube adhesion and orientation, as well as in programmed cell death of the papillae cells in response to either compatible pollination or incompatible pollen rejection. Finally, the results also revealed a putative cross-talk between genetic programmes regulating stress/defence and pollination responses in the stigma.

Subcellular localization and functional analyses of a PR10 protein gene from Vitis pseudoreticulata in response to Plasmopara viticola infection

Downy mildew, caused by the oomycete Plasmopara viticola, is a serious fungal disease in the cultivated European grapevines (Vitis vinifera L.). The class 10 of pathogenesis-related (PR) genes in grapevine leaves was reported to be accumulated at mRNA level in response to P. viticola infection. To elucidate the functional roles of PR10 genes during plant-pathogen interactions, a PR10 gene from a fungal-resistant accession of Chinese wild Vitis pseudoreticulata (designated VpPR10.2) was isolated and showed high homology to PR10.2 from susceptible V. vinifera (designated VvPR10.2). Comparative analysis displayed that there were significant differences in the patterns of gene expression between the PR10 genes from the two host species. VpPR10.2 was induced with high level in leaves infected by P. viticola, while VvPR10.2 showed a low response to this inoculation. Recombinant VpPR10.2 protein showed DNase activity against host genomic DNA and RNase activity against yeast total RNA in vitro. Meanwhile, recombinant VpPR10.2 protein inhibited the growth of tobacco fungus Alternaria alternata and over-expression of VpPR10.2 in susceptible V. vinifera enhanced the host resistance to P. viticola. The results from subcellular localization analysis showed that VpPR10.2 proteins were distributed dynamically inside or outside of host cell. Moreover, they were found in haustorium of P. viticola and nucleus of host cell which was associated with a nucleus collapse at 10 days post-inoculation. Taken together, these results suggested that VpPR10.2 might play an important role in host plant defense against P. viticola infection.

Omics methods for probing the mode of action of natural and synthetic phytotoxins

For a little over a decade, omics methods (transcriptomics, proteomics, metabolomics, and physionomics) have been used to discover and probe the mode of action of both synthetic and natural phytotoxins. For mode of action discovery, the strategy for each of these approaches is to generate an omics profile for phytotoxins with known molecular targets and to compare this library of responses to the responses of compounds with unknown modes of action. Using more than one omics approach enhances the probability of success. Generally, compounds with the same mode of action generate similar responses with a particular omics method. Stress and detoxification responses to phytotoxins can be much clearer than effects directly related to the target site. Clues to new modes of action must be validated with in vitro enzyme effects or genetic approaches. Thus far, the only new phytotoxin target site discovered with omics approaches (metabolomics and physionomics) is that of cinmethylin and structurally related 5-benzyloxymethyl-1,2-isoxazolines. These omics approaches pointed to tyrosine amino-transferase as the target, which was verified by enzyme assays and genetic methods. In addition to being a useful tool of mode of action discovery, omics methods provide detailed information on genetic and biochemical impacts of phytotoxins. Such information can be useful in understanding the full impact of natural phytotoxins in both agricultural and natural ecosystems.

Expression and in situ localization of two major PR proteins of grapevine berries during development and after UV-C exposition

In grapevine Vitis vinifera L. cv Pinot noir, the Pathogenesis-Related (PR) proteins CHI4D and TL3 are among the most abundant extractable PR proteins of ripe berries and accumulate during berry ripening from véraison until full maturation. Evidence was supplied in favor of the involvement of these two protein families in plant defense mechanisms and plant development. In order to better understand CHI4D and TL3 function in grapevine, we analyzed their temporal and spatial pattern of expression during maturation and after an abiotic stress (UV-C) by in situ hybridization (ISH) and immunohistolocalization. In ripening berries, CHI4D and TL3 genes were mainly expressed in the exocarp and around vascular bundles of the mesocarp. In UV-C exposed berries, CHI4D and TL3 gene expression was strongly induced before véraison. Corresponding proteins localized in the exocarp and, to a lesser extent, around vascular bundles of the mesocarp. The spatial and temporal accumulation of the two PR proteins during berry maturation and after an abiotic stress is discussed in relation to their putative roles in plant defense.

Linking proteome responses with physiological and biochemical effects in herbicide-exposed Chlamydomonas reinhardtii

Exposure to a toxicant causes proteome alterations in an organism. In ecotoxicology, analysis of these changes may allow linking them to physiological and biochemical endpoints, providing insights into subcellular exposure effects and responses and, ultimately mechanisms of action. Based on this, useful protein markers of exposure can be identified. We investigated the proteome changes induced by the herbicides paraquat, diuron, and norflurazon in the green alga Chlamydomonas reinhardtii. Shotgun proteome profiling and spectral counting quantification in combination with G-test statistics revealed significant changes in protein abundance. Functional enrichment analysis identified protein groups that responded to the exposures. Significant changes were observed for 149-254 proteins involved in a variety of metabolic pathways. While some proteins and functional protein groups responded to several tested exposure conditions, others were affected only in specific cases. Expected as well as novel candidate markers of herbicide exposure were identified, the latter including the photosystem II subunit PsbR or the VIPP1 protein. We demonstrate that the proteome response to toxicants is generally more sensitive than the physiological and biochemical endpoints, and that it can be linked to effects on these levels. Thus, proteome profiling may serve as a useful tool for ecotoxicological investigations in green algae.

Proteomic response of wheat embryos to fosthiazate stress in a protected vegetable soil

A proteomic analysis of wheat defense response induced by the widely used organophosphorus nematicide fosthiazate is reported. Seed germination and two-dimensional gel electrophoresis (2-DE) experiments were performed using a Chinese wheat cultivar, Zhenmai No. 5. Root and shoot elongation decreased but thiobarbituric acid reactive substances (TBARS) content in embryos increased with increasing pesticide concentration. More than 1000 protein spots were reproducibly detected in each silver-stained gel. Thirty-seven protein spots with at least 2-fold changes were identified using MALDI-TOF MS/MS analysis. Of these, 24 spots were up-regulated and 13 were down-regulated. Proteins identified included some well-known classical stress responsive proteins under abiotic or biotic stresses as well as some unusual responsive proteins. Ten responsive proteins were reported for the first time at the proteomic level, including fatty acyl CoA reductase, dihydrodipicolinate synthase, DEAD-box ATPase-RNA-helicase, fimbriata-like protein, waxy B1, rust resistance kinase Lr10, putative In2.1 protein, retinoblastoma-related protein 1, pollen allergen-like protein and S-adenosyl-L-methionine:phosphoethanolamine N-methyltransferase. The proteins identified were involved in several processes such as metabolism, defense/detoxification, cell structure/cell growth, signal transduction/transcription, photosynthesis and energy. Seven candidate proteins were further analyzed at the mRNA level by RT-PCR to compare transcript and protein accumulation patterns, revealing that not all the genes were correlated well with the protein level. Identification of these responsive proteins may provide new insight into the molecular basis of the fosthiazate-stress response in the early developmental stages of plants and may be useful in stress monitoring or stress-tolerant crop breeding for environmentally friendly agricultural production.

Physiological changes in green stems of Vitis vinifera L. cv. Chardonnay in response to esca proper and apoplexy revealed by proteomic and transcriptomic analyses

Among grapevine trunk diseases, esca proper and apoplexy commonly represent a threat for viticulture worldwide. To retrieve further information about the mechanisms activated in apoplectic and esca proper-affected plants, a two-dimensional gel electrophoresis (2-DE) based analysis was conducted on green stems from 26-year-old standing vines. Symptomatic and asymptomatic stems from both apoplectic (A) and esca proper-affected (E) plants compared to control (without visual symptom since 10 years) stems were studied. Thirty-three differentially expressed proteins were identified by nanoLC-MS/MS and included into three groups conceptually defined as proteins involved in (i) metabolism and energy, (ii) stress tolerance, and (iii) defense response. For nine of them, expression of the relative mRNA's was also monitored by qRT-PCR. Proteome variations were specifically related to apoplexy and esca proper but were more similar in asymptomatic stems than in the symptomatic ones. Remarkable quantitative differences were noted for several proteins in symptomatic stems according to the expressed form, A and E. Results further indicate that similar responses are likely activated in asymptomatic stems but a various quantitative expression is triggered upon onset of apoplexy or esca proper symptoms while both kind of plants are infected by the same pathogenic fungi.

Arbuscular mycorrhizal symbiosis elicits proteome responses opposite of P-starvation in SO4 grapevine rootstock upon root colonisation with two Glomus species

Although plant biotisation with arbuscular mycorrhizal fungi (AMF) is a promising strategy for improving plant health, a better knowledge regarding the molecular mechanisms involved is required. In this context, we sought to analyse the root proteome of grapevine rootstock Selection Oppenheim 4 (SO4) upon colonisation with two AMF. As expected, AMF colonisation stimulates plant biomass. At the proteome level, changes in protein amounts due to AMF colonisation resulted in 39 differentially accumulated two-dimensional electrophoresis spots in AMF roots relative to control. Out of them, 25 were co-identified in SO4 roots upon colonisation by Glomus irregulare and Glomus mosseae supporting the existence of conserved plant responses to AM symbiosis in a woody perennial species. Among the 18 proteins whose amount was reduced in AMF-colonised roots were proteins involved in glycolysis, protein synthesis and fate, defence and cell rescue, ethylene biosynthesis and purine and pyrimidine salvage degradation. The six co-identified proteins whose amount was increased had functions in energy production, signalling, protein synthesis and fate including proteases. Altogether these data confirmed that a part of the accommodation program of AMF previously characterized in annual plants is maintained within roots of the SO4 rootstock cuttings. Nonetheless, particular responses also occurred involving proteins of carbon metabolism, development and root architecture, defence and cell rescue, anthocyanin biosynthesis and P remobilization, previously reported as induced upon P-starvation. This suggests the occurrence of P reprioritization upon AMF colonization in a woody perennial plant species with agronomical interest.

Proteomics as an approach to the understanding of the molecular physiology of fruit development and ripening

Fruit ripening is a developmental complex process which occurs in higher plants and involves a number of stages displayed from immature to mature fruits that depend on the plant species and the environmental conditions. Nowadays, the importance of fruit ripening comes mainly from the link between this physiological process in plants and the economic repercussions as a result of one of the human activities, the agricultural industry. In most cases, fruit ripening is accompanied by colour changes due to different pigment content and increases in sugar levels, among others. Major physiological modifications that affect colour, texture, flavour, and aroma are under the control of both external (light and temperature) and internal (developmental gene regulation and hormonal control) factors. Due to the huge amount of metabolic changes that take place during ripening in fruits from higher plants, the accomplishment of new throughput methods which can provide a global evaluation of this process would be desirable. Differential proteomics of immature and mature fruits would be a useful tool to gain information on the molecular changes which occur during ripening, but also the investigation of fruits at different ripening stages will provide a dynamic picture of the whole transformation of fruits. This subject is furthermore of great interest as many fruits are essential for human nutrition. Thus far different maturation profiles have been reported specific for each crop species. In this work, a thorough review of the proteomic database from fruit development and maturation of important crop species will be updated to understand the molecular physiology of fruits at ripening stages.

Response of the Vitis vinifera L. cv. 'Nebbiolo' proteome to Flavescence dorée phytoplasma infection

Flavescence dorée is a serious phytoplasma disease affecting grapevine in several European countries. We studied the interaction of Flavescence dorée phytoplasma with its natural plant host by monitoring the effects of infection on the protein expression profile. Among the 576 analyzed spots, 33 proteins were differentially regulated in infected grapevines. Grouping into MIPS functional categories showed proteins involved in metabolism (21%), energy processes (9%), protein synthesis (3%), protein fate (18%), cellular transport and transport routes (6%), cell defense and virulence (42%). Among the differentially regulated proteins, we selected six targets (thaumatin I, thaumatin II, osmotin-like protein, plant basic secretory protein, AAA(+) Rubisco activase and proteasome α5 subunit) and we analyzed their expression by quantitative RT-PCR on samples collected in 2008 and 2009 in several vineyards in Piedmont region, Italy. There was a positive correlation between mRNA and protein expression for most of the genes in both the years. We discuss the involvement of these proteins in the specific response to phytoplasma infection. To our knowledge, this work is the first to investigate the response of the grapevine proteome to Flavescence dorée phytoplasma infection, and provides reference protein profiles for future comparative proteomic and genomic studies.

Characterisation of the Vitis vinifera PR10 multigene family

BACKGROUND

Genes belonging to the pathogenesis related 10 (PR10) group have been studied in several plant species, where they form multigene families. Until now, such an analysis has not been performed in Vitis vinifera, although three different PR10 genes were found to be expressed under pathogen attack or abiotic stress, and during somatic embryogenesis induction. We used the complete genome sequence for characterising the whole V. vinifera PR10 gene family. The expression of candidate genes was studied in various non-treated tissues and following somatic embryogenesis induction by the auxin 2,4-D.

RESULTS

In addition to the three V. vinifera PR10 genes already described, namely VvPR10.1, VvPR10.2 and VvPR10.3, fourteen different PR10 related sequences were identified. Showing high similarity, they form a single cluster on the chromosome 5 comprising three pseudogenes. The expression of nine different genes was detected in various tissues. Although differentially expressed in non-treated plant organs, several genes were up-regulated in tissues treated with 2,4-D, as expected for PR genes.

CONCLUSIONS

PR10 genes form a multigene family in V. vinifera, as found in birch, apple or peach. Seventeen closely related PR10 sequences are arranged in a tandem array on the chromosome 5, probably reflecting small-scale duplications during evolution. Various expression patterns were found for nine studied genes, highlighting functional diversification. A phylogenetic comparison of deduced proteins with PR10 proteins of other plants showed a characteristic low intraspecific variability. Particularly, a group of seven close tandem duplicates including VvPR10.1, VvPR10.2 and VvPR10.3 showed a very high similarity, suggesting concerted evolution or/and recent duplications.

Differential proteomic response to heat stress in thermal Agrostis scabra and heat-sensitive Agrostis stolonifera

Knowledge of heat-responsive proteins is critical for further understanding of the molecular mechanisms of heat tolerance. The objective of this study was to compare proteins differentially expressed in two C(3) grass species contrasting in heat tolerance, heat-tolerant thermal Agrostis scabra and heat-sensitive Agrostis stolonifera L., and to identify heat-responsive proteins for short- and long-term responses. Plants were exposed to 20/15 degrees C (day/night, control) or 40/35 degrees C (day/night, heat stress) in growth chambers. Leaves were harvested at 2 and 10 days after temperature treatment. Proteins were extracted and separated by fluorescence difference gel electrophoresis (DIGE). Thermal A. scabra had superior heat tolerance than A. stolonifera, as indicated by the maintenance of higher chlorophyll content and photochemical efficiency under heat stress. The two-dimensional difference electrophoresis detected 68 heat-responsive proteins in the two species. Thermal A. scabra had more protein spots either down- or up-regulated at 2 days of heat stress, but fewer protein spots were altered at 10 days of heat stress compared with A. stolonifera. Many protein spots exhibited transient down-regulation in thermal A. scabra (only at 2 days of heat treatment), whereas down-regulation of many proteins was also found at 10 days of heat treatment in A. stolonifera, which suggested that protein metabolism in thermal A. scabra might acclimate to heat stress more rapidly than those in A. stolonifera. The sequences of 56 differentially expressed protein spots were identified using mass spectrometry. The results suggest that the maintenance or less severe down-regulation of proteins during long-term (10 days) heat stress may contribute to the superior heat tolerance in thermal A. scabra, including those involved in photosynthesis [RuBisCo, RuBisCo activase, chloroplastic glyceraldehydes-3-phosphate dehydrogenase (GAPDH), chloroplastic aldolase, oxygen-evolving complex, photosystem I subunits], dark respiration (cytosolic GAPDH, cytoplasmic aldolase, malate dehydrogenase, hydroxypyruvate reductase, sedoheptulose-1,7-bisphosphatase), photorespiration [(hydroxypyruvate reductase, alanine aminotransferase (AlaAT), hydroxymethyltransferase (SHMT), glycine decarboxylase (GDC)], as well as heat and oxidative stress protection [heat shock cognate (HSC) 70 and FtsH-like protein].

Heard it through the grapevine: proteomic perspective on grape and wine

Grapevine (Vitis ssp.) is currently considered as the most important fruit plant throughout the world, both due to its economic importance and to its role as a non climacteric model species. The relevance of the studies devoted to the dissection of grapevine biology and biochemistry underlines the great amount of attention that this plant has attracted over the last decade. The milestones among these studies are represented by the accomplishment of the genome sequencing programmes in 2007 [1,2]. Since then, the investigation of grape OMICS has been implemented, and the number of reports published on grape and wine protein investigations using proteomic techniques have significantly improved knowledge in the field.

Changes in the accumulation of alpha- and beta-tubulin during bud development in Vitis vinifera L

Microtubules play important roles during growth and morphogenesis of plant cells. Multiple isoforms of alpha- and beta-tubulin accumulate in higher plant cells and originate either by transcription of different genes or by post-translational modifications. The use of different tubulin isoforms involves the binding of microtubules to different associated proteins and therefore generates microtubules with different organizations and functions. Tubulin isoforms are differentially expressed in vegetative and reproductive structures according to the developmental program of plants. In grapevine (Vitis vinifera L.), vegetative and reproductive structures appear on the same stem, making this plant species an excellent model to study the accumulation of tubulin isoforms. Proteins were extracted from grapevine samples (buds, leaves, flowers and tendrils) using an optimized extraction protocol, separated by two-dimensional electrophoresis and analyzed by immunoblot with anti-tubulin antibodies. We identified eight alpha-tubulin and seven beta-tubulin isoforms with pI around 4.8-5 that group into separate clusters. More acidic alpha-tubulin isoforms were detected in buds, while more basic alpha-isoforms were prevalently found in tendrils and flowers. Similarly, more acidic beta-tubulin isoforms were used in the bud stage while a basic beta-tubulin isoform was essentially used in leaves and two central beta-tubulin isoforms were characteristically used in tendrils and flowers. Acetylated alpha-tubulin was not detected in any sample while tyrosinated alpha-tubulin was essentially found in large latent buds and in bursting buds in association with a distinct subset of tubulin isoforms. The implication of these data on the use of different tubulin isoforms during grapevine development is discussed.

VitisNet: "Omics" integration through grapevine molecular networks

Background

Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet).

Methodology/Principal Findings

The sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 “Metabolic”, 15 “Genetic Information Processing”, 12 “Environmental Information Processing”, 3 “Cellular Processes”, 21 “Transport”, and 80 “Transcription Factors”. The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment.

Conclusions/Significance

VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage) and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome location can be accessed and downloaded from the VitisNet tab at http://vitis-dormancy.sdstate.org.

Proteomic and selected metabolite analysis of grape berry tissues under well-watered and water-deficit stress conditions

In order to investigate the unique contribution of individual wine grape (Vitis vinifera) berry tissues and water-deficit to wine quality traits, a survey of tissue-specific differences in protein and selected metabolites was conducted using pericarp (skin and pulp) and seeds of berries from vines grown under well-watered and water-deficit stress conditions. Of 1047 proteins surveyed from pericarp by 2-D PAGE, 90 identified proteins showed differential expression between the skin and pulp. Of 695 proteins surveyed from seed tissue, 163 were identified and revealed that the seed and pericarp proteomes were nearly completely distinct from one another. Water-deficit stress altered the abundance of approximately 7% of pericarp proteins, but had little effect on seed protein expression. Comparison of protein and available mRNA expression patterns showed that 32% pericarp and 69% seed proteins exhibited similar quantitative expression patterns indicating that protein accumulation patterns are strongly influenced by post-transcriptional processes. About half of the 32 metabolites surveyed showed tissue-specific differences in abundance with water-deficit stress affecting the accumulation of seven of these compounds. These results provide novel insights into the likely tissue-specific origins and the influence of water-deficit stress on the accumulation of key flavor and aroma compounds in wine.

Differential regulation of SERK, LEC1-like and pathogenesis-related genes during indirect secondary somatic embryogenesis in grapevine

A culture model was developed in Vitis vinifera L., cultivar 'Chardonnay' for studying SE (Somatic Embryogenesis). The auxin 2,4-D (2,4-Dichlorophenoxyacetic acid) was used to induce indirect secondary embryogenesis at a high rate, starting from embryos derived from embryogenic cultures previously obtained. Cotyledonary embryos were shown to be more responsive to SE induction than embryos at the torpedo-stage and were used for molecular analyses. The expression of SERK (Somatic Embryogenesis Receptor Kinase), L1L (Leafy Cotyledon1 Like) and a set of PR (Pathogenesis-Related) genes was monitored during the whole SE process. VvSERK1, VvSERK2 and VvL1L were down-regulated by the 2,4-D treatment but expressed in embryonic tissues. On the contrary, VvPR1, VvPR8, VvPR10.1 and VvPR10.3 were strongly up-regulated by the 2,4-D treatment, and their transcripts were not or only weakly detected in clusters of secondary embryos. VvSERK3, VvPR3 and VvPR10.2 were more stably expressed in all tissues examined. The discussion deals with the putative role of the different genes in grapevine SE.

Chitosan treatment induces changes of protein expression profile and stilbene distribution in Vitis vinifera cell suspensions

Polyphenols, including stilbenes and flavonoids, are an essential part of human diet and constitute one of the most abundant and ubiquitous groups of plant secondary metabolites, and their level is inducible by stress, fungal attack or biotic and abiotic elicitors. Proteomic analysis of Vitis vinifera (L.) cultivar (cv.) Barbera grape cell suspensions, showed that the amount of 73 proteins consistently changed in 50 microg/mL chitosan-treated samples compared with controls, or between the two controls, of which 56 were identified by MS analyses. In particular, de-novo synthesis and/or accumulation of stilbene synthase proteins were promoted by chitosan which also stimulated trans-resveratrol endogenous accumulation and decreased its release into the culture medium. No influence was shown on cis-resveratrol. There was no effect on the accumulation of total resveratrol mono-glucosides (trans- and cis-piceid and trans- and cis-resveratroloside). Throughout the observation period the upregulation of phenylalanine ammonia lyase, chalcone synthase, chalcone-flavanone isomerase (CHI) transcript expression levels well correlated with CHI protein amount and with the accumulation of anthocyanins. Chitosan treatment strongly increased the expression of eleven proteins of the pathogenesis related protein-10 family, as well as their mRNA levels.

Low responsiveness of grapevine flowers and berries at fruit set to UV-C irradiation

In grapevine, stimulation of defence responses was evidenced in response to various types of abiotic stresses in both leaves and berries, as revealed by the increasing expression of genes encoding defence-related proteins or the stimulation of their corresponding activities. However, the capability of inflorescences to respond to abiotic stresses has never been investigated. Therefore, plant defence reactions in response to UV-C irradiation were followed in inflorescences and young clusters focusing on both bunchstems (peduncle and pedicels) and developing flowers/berries from separated floral buds stage [Biologische Bundesanstalt, Bundessortenamt and CHemical industry (BBCH) stage 57] to groat-sized berries stage (BBCH 73). For this purpose, the expression of various genes coding for pathogenesis-related (PR) proteins (class I and III chitinases, Chi1b and CH3; beta-1,3-glucanase, GLUC), an enzyme of the phenylpropanoid pathway (phenylalanine ammonia-lyase, PAL), and stilbene synthase (STS) was analysed in parallel with variations of chitinase activity and the accumulation of the phytoalexin resveratrol. Multiple defence responses were induced in bunchstems of both inflorescences and clusters following UV-C treatment. First, expression of genes encoding PR proteins was stimulated and chitinase activity was enhanced. Secondly, PAL and STS expression increased in association with resveratrol accumulation. Amazingly, none of the tested defence processes was induced in grapevine flowers following UV-C exposure, whatever the stage analysed. Similarly, in berries at fruit set, induction of gene expression was weak and neither an increase in chitinase activity nor resveratrol synthesis was noticed. However, in groat-sized berries, responsiveness to UV-C increased, as revealed by the induction of CH3, PAL, and STS expression, together with resveratrol accumulation. The differential responsiveness between bunchstems, flowers, and berries is discussed.

Generation of a predicted protein database from EST data and application to iTRAQ analyses in grape (Vitis vinifera cv. Cabernet Sauvignon) berries at ripening initiation

Background

iTRAQ is a proteomics technique that uses isobaric tags for relative and absolute quantitation of tryptic peptides. In proteomics experiments, the detection and high confidence annotation of proteins and the significance of corresponding expression differences can depend on the quality and the species specificity of the tryptic peptide map database used for analysis of the data. For species for which finished genome sequence data are not available, identification of proteins relies on similarity to proteins from other species using comprehensive peptide map databases such as the MSDB.

Results

We were interested in characterizing ripening initiation ('veraison') in grape berries at the protein level in order to better define the molecular control of this important process for grape growers and wine makers. We developed a bioinformatic pipeline for processing EST data in order to produce a predicted tryptic peptide database specifically targeted to the wine grape cultivar, Vitis vinifera cv. Cabernet Sauvignon, and lacking truncated N- and C-terminal fragments. By searching iTRAQ MS/MS data generated from berry exocarp and mesocarp samples at ripening initiation, we determined that implementation of the custom database afforded a large improvement in high confidence peptide annotation in comparison to the MSDB. We used iTRAQ MS/MS in conjunction with custom peptide db searches to quantitatively characterize several important pathway components for berry ripening previously described at the transcriptional level and confirmed expression patterns for these at the protein level.

Conclusion

We determined that a predicted peptide database for MS/MS applications can be derived from EST data using advanced clustering and trimming approaches and successfully implemented for quantitative proteome profiling. Quantitative shotgun proteome profiling holds great promise for characterizing biological processes such as fruit ripening initiation and may be further improved by employing preparative techniques and/or analytical equipment that increase peptide detection sensitivity via a shotgun approach.

Proteome analysis of soybean hypocotyl and root under salt stress

To evaluate the response of soybean to salt stress, the related changes in protein expression were investigated using the proteomic approach. Soybean plants were exposed to 0, 50, 100, and 200 mM NaCl. Especially at 200 mM, the length and fresh weight of the hypocotyl and root reduced under salt stress, while the proline content increased. Proteins from the hypocotyl and root treated with 100 mM NaCl were extracted and separated by two-dimensional polyacrylamide gel electrophoresis; 321 protein spots were detected. In response to salt stress, seven proteins were reproducibly found to be up- or down-regulated by two to sevenfold: late embryogenesis-abundant protein, beta-conglycinin, elicitor peptide three precursor, and basic/helix-loop-helix protein were up-regulated, while protease inhibitor, lectin, and stem 31-kDa glycoprotein precursor were down-regulated. These results indicate that salinity can change the expression level of some special proteins in the hypocotyl and root of soybean that may in turn play a role in the adaptation to saline conditions.

The herbicide flumioxazin stimulates pathogenesis-related gene expression and enzyme activities in Vitis vinifera

In this work, the capacity of the soil-applied herbicide flumioxazin (fmx) to trigger defence mechanisms was assessed using 6-week-old in vitro grown Vitis vinifera L. plantlets. Time-course studies demonstrated that the herbicide induced the expression of basic beta-1,3-glucanase (Vvglu), basic chitinase (Vvchit1b) and PR10 (VvPR10.3) genes encoding three pathogenesis-related (PR) proteins involved in grapevine defence against pathogens. Thus, all transcripts accumulated in grapevine tissues to reach maximum values after 24-72 h of herbicide exposure, except for VvPR10.3 gene expression, which was induced in roots and stems but not in leaves. Induction of PR genes was observed to a greater extent in roots and leaves, and its intensity diminished in the stems although still remained noteworthy. The activities of beta-1,3-glucanase and chitinase enzymes significantly increased in the whole plant after herbicide exposure and were still stimulated 21 days after the beginning of treatments. Similarly, the most remarkable effect occurred in roots. However, all enzyme activities tested were stimulated in the upper aerial tissues as well, indicating that fmx or a derived product acts systemically, likely via root uptake.

Proteome analysis of non-model plants: a challenging but powerful approach

Biological research has focused in the past on model organisms and most of the functional genomics studies in the field of plant sciences are still performed on model species or species that are characterized to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource. Some features and processes are unique to these plant species or families and cannot be approached via a model plant. The power of all proteomic and transcriptomic methods, that is, high-throughput identification of candidate gene products, tends to be lost in non-model species due to the lack of genomic information or due to the sequence divergence to a related model organism. Nevertheless, a proteomics approach has a great potential to study non-model species. This work reviews non-model plants from a proteomic angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-model organism. The review tackles problems associated with (i) sample preparation, (ii) the analysis and interpretation of a complex data set, (iii) the protein identification via MS, and (iv) data management and integration. We will illustrate the power of 2DE for non-model plants in combination with multivariate data analysis and MS/MS identification and will evaluate possible alternatives.

Grape berry plasma membrane proteome analysis and its differential expression during ripening

High purity berry plasma membranes (PMs) of Vitis vinifera L. cv. Cabernet Sauvignon were isolated by two-phase partitioning of microsome fractions at different stages of berry ripening. PM proteins resolvable by the detergent cocktail of CHAPS and ASB-14 were separated by two-dimensional electrophoresis. A total of 119 protein spots from pre-véraison berry PMs on 2-D gels detected with silver staining were subjected to MALDI-TOF mass spectrometry analysis. Sixty-two spots were identified as putative PM proteins, with 1-6 predicted transmembrane helices, including true PM proteins such as ATP synthase, ABC transporters, and GTP-binding proteins reported in plants. They were then grouped into eight functional categories, mainly involved in transport, metabolism, signal transduction, and protein synthesis. Another 11 spots were identified as proteins of unknown function. The véraison and post-véraison samples stained 98 and 86 spots on the gels, respectively. During the berry ripening process, total PM protein content gradually decreased. Among all identified proteins, 12 showed significant differences in terms of their relative abundance. Increasing ubiquitin proteolysis and cytoskeleton proteins were observed from pre-véraison to post-véraison. Zeatin O-glucosyltransferase peaked at véraison, while ubiquitin-conjugating enzyme E2-21 was down-regulated at this stage. This proteome research provides the first information on PM protein characterization during the grape berry ripening process.

Impact of solar ultraviolet-B on the proteome in soybean lines differing in flavonoid contents

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to systematically investigate the impact of solar ultraviolet-B (UV-B) radiation on the soybean leaf proteome. In order to investigate the protective role of flavonoids against UV-B, two isolines of the Clark cultivar (the standard line with moderate levels of flavonoids and the magenta line with reduced flavonoids) were grown in the field with or without natural levels of UV-B. The 12-day-old first trifoliates were harvested for proteomic analysis. More than 300 protein spots were reproducibly resolved and detected on each gel. Statistical analysis showed that 67 protein spots were significantly (P<0.05) affected by solar UV-B. Many more spots were altered by UV-B in the magenta line than in the standard line. Another 12 protein spots were not altered by UV-B but showed significantly (P<0.05) different accumulations between the two lines, and for most spots the line-specific differences were also observed under UV-B exclusion. Most of the differentially accumulated spots were identified by mass spectrometry. The proteins were quite diverse, and were involved in metabolism, energy, protein destination/storage, protein synthesis, disease/defense, transcription, and secondary metabolism. The results suggest that high levels of flavonoids lead to a reduction in UV-B sensitivity at the proteomic level.

Study of anoxic and oxic cholesterol metabolism by Sterolibacterium denitrificans

The initial enzymes and genes involved in the anoxic metabolism of cholesterol were studied in the denitrifying bacterium Sterolibacterium denitrificans Chol-1S(T). The second enzyme of the proposed pathway, cholest-4-en-3-one-Delta1-dehydrogenase (AcmB), was partially purified. Based on amino acid sequence analysis, a gene probe was derived to screen a cosmid library of chromosomal DNA for the acmB gene. A positive clone comprising a 43-kbp DNA insert was sequenced. In addition to the acmB gene, the DNA fragment harbored the acmA gene, which encodes the first enzyme of the pathway, cholesterol dehydrogenase/isomerase. The acmA gene was overexpressed, and the recombinant dehydrogenase/isomerase was purified. This enzyme catalyzes the predicted transformation of cholesterol to cholest-4-en-3-one. S. denitrificans cells grown aerobically with cholesterol exhibited the same pattern of soluble proteins and cell extracts formed the same 14C-labeled products from [14C]cholesterol as cells that were grown under anoxic, denitrifying conditions. This is especially remarkable for the late products that are formed by anaerobic hydroxylation of the cholesterol side chain with water as the oxygen donor. Hence, this facultative anaerobic bacterium may use the anoxic pathway lacking any oxygenase-dependent reaction also under oxic conditions. This confers metabolic flexibility to such facultative anaerobic bacteria.

Proteomic analysis of Tunisian grapevine cultivar Razegui under salt stress

Salt stress is one of the major abiotic stresses in agriculture worldwide, especially in the Mediterranean area. We report here a proteomic approach to investigate the salt stress-responsive proteins in grapevine (Vitis vinifera). Two-dimensional electrophoresis (2-DE) was used to analyze the proteome of the salt-tolerant Tunisian grapevine cultivar Razegui, subjected to a supply of 100mm NaCl over 15d. Analysis of 2-DE gels derived from stressed plants revealed more than 800 reproducibly detected protein spots, with 48 proteins displaying a differential expression pattern, including 32 up-regulated, 9 down-regulated and 7 new protein spots induced after salt treatment. The presence of stress-responsive proteins in the different plant organs suggests that salt spreads systemically. Edman degradation analysis and database searching aided us in identifying a major protein GP. Database analysis revealed that this peptide has a 98% sequence similarity with a pathogenesis-related (PR) protein 10 (V. vinifera). A full-length cDNA encoding the GP protein was isolated from grapevine salt-stressed leaves and sequenced. The predicted protein contained 158 amino acids and showed 98% identity with PR10 protein of of V. vinifera (accession no. Cac16165).

A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs

The construction of a dense genetic map for Vitis vinifera and its anchoring to a BAC-based physical map is described: it includes 994 loci mapped onto 19 linkage groups, corresponding to the basic chromosome number of Vitis. Spanning 1245 cM with an average distance of 1.3 cM between adjacent markers, the map was generated from the segregation of 483 single-nucleotide polymorphism (SNP)-based genetic markers, 132 simple sequence repeats (SSRs), and 379 AFLP markers in a mapping population of 94 F(1) individuals derived from a V. vinifera cross of the cultivars Syrah and Pinot Noir. Of these markers, 623 were anchored to 367 contigs that are included in a physical map produced from the same clone of Pinot Noir and covering 352 Mbp. On the basis of contigs containing two or more genetically mapped markers, region-dependent estimations of physical and recombinational distances are presented. The markers used in this study include 118 SSRs common to an integrated map derived from five segregating populations of V. vinifera. The positions of these SSR markers in the two maps are conserved across all Vitis linkage groups. The addition of SNP-based markers introduces polymorphisms that are easy to database, are useful for evolutionary studies, and significantly increase the density of the map. The map provides the most comprehensive view of the Vitis genome reported to date and will be relevant for future studies on structural and functional genomics and genetic improvement.

Crop proteomics: Aim at sustainable agriculture of tomorrow

The advent of proteomics has made it possible to identify a broad spectrum of proteins in living systems. This capability is especially useful for crops as it may give clues not only about nutritional value, but also about yield and how these factors are affected by adverse conditions. In this review, we describe the recent progress in crop proteomics and highlight the achievements made in understanding the proteomes of major crops. The major emphasis will be on crop responses to abiotic stresses. Rigorous genetic testing of the role of possibly important proteins can be conducted. The increasing ease with the DNA, mRNA and protein levels can be conducted and connected suggests that proteomics data will not be difficult to apply to practical crop breeding.

Proteome changes in leaves from grapevine (Vitis vinifera L.) transformed for alcohol dehydrogenase activity

A proteomic approach has been used to study changes in leaf protein content from plants transformed for alcohol dehydrogenase (ADH) activity. Individual quantitative analysis of 190-436 spots separated by two-dimensional electrophoresis was performed, and spots displaying significant quantitative changes between control (C), sense (S), and antisense (R) transformants were selected using Student's t test. Of the 14 spots selected and further analyzed after trypsic digestion, 9 could be identified by MS analysis and 5 by LC-MS/MS. Identified proteins had mainly a chloroplastic origin: four rubisco large subunits, one rubisco binding protein, two glutamine synthetases, one elongation factor Tu, one ATP synthase beta subunit, and one plastidic aldolase. Proteins with other localization were also identified, such as a UDP-glucose pyrophosphorylase, a mitochondrial aminomethyltransferase, a linalool synthase, which comigrated with the protein identified as elongation factor Tu, an enolase comigrating with a glyceraldehyde 3-phosphate dehydrogenase, and a mixture of eight proteins among which were a dehydroascorbate reductase, a chalcone isomerase, and a rubisco activase. The results emphasize the changes in carbon metabolism-associated proteins linked to the alteration in ADH activity of grapevine transformant leaves.