Analysis of the dispersive Fourier transform dataset using dynamic mode decomposition: evidence of multiple vibrational modes and their interplay in a three-soliton molecule.

We demonstrate that the dynamic mode decomposition technique can effectively reduce the amount of noise in the dispersive Fourier transform dataset and allow for finer quantitative analysis of the experimental data. We therefore show that the oscillation pattern of a soliton molecule actually results from the interplay of several elementary vibration modes.

Superlocalization Reveals Long-Range Synchronization of Vibrating Soliton Molecules.

We implement a superlocalization method in the time domain that allows the observation of the external motion of soliton molecules in a fiber ring cavity laser with unprecedented accuracy. In particular, we demonstrate the synchronization of two oscillating soliton molecules separated by several nanoseconds, with intermolecular oscillations following the same pattern as the intramolecular motion of the individual molecules. These experimental findings indicate an interplay between the different interaction mechanisms that coexist inside the laser cavity, despite their very different characteristic ranges, timescales, strengths, and physical origins.

Overexpression of a grapevine R2R3-MYB factor in tomato affects vegetative development, flower morphology and flavonoid and terpenoid metabolism.

Although the terpenoid pathway constitutes, with the phenylpropanoid metabolism, the major pathway of secondary metabolism in plants, little is known about its regulation. Overexpression of a Vitis vinifera R2R3-MYB transcription factor (VvMYB5b) in tomato induced pleiotropic changes including dwarfism, modified leaf structure, alterations of floral morphology, pigmented and glossy fruits at the "green-mature" stage and impaired seed germination. Two main branches of secondary metabolism, which profoundly influence the organoleptic properties of the fruit, were affected in the opposite way by VvMYB5b overexpression. Phenylpropanoid metabolism was down regulated whereas the amount of beta-carotene was up regulated. This is the first example of the independent regulation of phenylpropanoid and carotenoid metabolism. The strongest modification concerns a decrease in beta-amyrin, the precursor of the oleanolic acid, which is the major component of grape waxes. Scanning electron microscopy analysis of fruits and leaves confirms the alteration of wax metabolism and a modification of cell size and shape. This may potentially impact resistance/tolerance to biotic and abiotic stresses. The results are compared with a similar approach using heterologous expression of VvMYB5b in tobacco.

[Identification and characterization of "rd22" dehydration responsive gene in grapevine (Vitis vinifera L.)]. / Identification et caractérisation d'un gène de réponse à la déshydratation "rd22" chez la vigne (Vitis vinifera L.).

To identify and isolate genes related to abiotic stresses (salinity and drought) tolerance in grapevine, a candidate gene approach was developed and allowed isolating a full-length cDNA of rd22 gene from the Cabernet Sauvignon variety. The latter, named Vvrd22, is a dehydration-responsive gene that is usually induced by the application of exogenous ABA. Details of the physicochemical parameters and structural properties (molecular mass, secondary structure, conserved domains and motives, putative post-translational modification sites...) of the encoded protein have also been elucidated. The expression study of Vvrd22 was carried out at the berry growth stages and at the level of plant organs and tissues as well as under both drought and salt stresses. The results showed that Vvrd22 is constitutively expressed at a low level in all analyzed tissues. Moreover, salt stress induced Vvrd22 expression, particularly for the tolerant variety (Razegui), contrary to the sensitive one (Syrah), which did not display any expression variation during the stress, which means that Vvrd22 is involved in salt stress response and that its expression level depends on regulatory mechanisms that are efficient only for the tolerant variety. On the other hand, under drought stress, Vvrd22 is induced in an identical manner for both tolerant and sensitive varieties. In addition, stress signal molecules such as ABA (lonely applied or in combination with sucrose) induced Vvrd22 expression, even at a low level. A minimal knowledge about the role and the functionality of this gene is necessary and constitutes a prerequisite condition before starting and including Vvrd22 in any program of improvement of grapevine's abiotic stress tolerance.

Effect of methyl jasmonate in combination with carbohydrates on gene expression of PR proteins, stilbene and anthocyanin accumulation in grapevine cell cultures.

Grapevine (Vitis vinifera L.) is subject to a number of diseases which affect yield and wine quality. After veraison, berries become strongly susceptible to pathogens due to different physiological changes including the accumulation of glucose and fructose, on the one hand, and to the decrease of anti-microbial compounds called stilbenes, on the other. To obtain berry protection, pesticides are excessively used leading to important cost to the grower and to undesirable environmental impact of the residues, especially in grape, soil and water. As a consequence, alternative strategies have to be developed. Exogenously applied biotic elicitors induce defense responses. We studied the effects of methyl jasmonate in combination with sucrose on defense-related gene expression, stilbene and anthocyanin production in grapevine cell suspensions. The methyl jasmonate/sucrose treatment was effective in stimulating phenylalanine ammonia lyase, chalcone synthase, stilbene synthase, UDP-glucose: flavonoid-O-glucosyltransferase, proteinase inhibitor and chitinase gene expression, and triggered accumulation of both piceids and anthocyanins in cells, and trans-resveratrol and piceids in the extracellular medium. Methyl jasmonate treatment might be an efficient natural strategy to protect grapevine berries in vineyard.

Isolation and characterization of a Vitis vinifera transcription factor, VvWRKY1, and its effect on responses to fungal pathogens in transgenic tobacco plants.

Pathogen attack represents a major problem for viticulture and for agriculture in general. At present, the use of phytochemicals is more and more restrictive, and therefore it is becoming essential to control disease by having a thorough knowledge of resistance mechanisms. The present work focused on the trans-regulatory proteins potentially involved in the control of the plant defence response, the WRKY proteins. A full-length cDNA, designated VvWRKY1, was isolated from a grape berry library (Vitis vinifera L. cv. Cabernet Sauvignon). It encodes a polypeptide of 151 amino acids whose structure is characteristic of group IIc WRKY proteins. VvWRKY1 gene expression in grape is regulated in a developmental manner in berries and leaves and by various signal molecules involved in defence such as salicylic acid, ethylene, and hydrogen peroxide. Biochemical analysis indicates that VvWRKY1 specifically interacts with the W-box in various nucleotidic contexts. Functional analysis of VvWRKY1 was performed by overexpression in tobacco, and transgenic plants exhibited reduced susceptibility to various fungi but not to viruses. These results are consistent with a possible role for VvWRKY1 in grapevine defence against fungal pathogens.

A grape berry (Vitis vinifera L.) cation/proton antiporter is associated with berry ripening.

We have cloned and characterized VvNHX1, a gene encoding a vacuolar cation/H(+) antiporter from Vitis vinifera cv. Cabernet Sauvignon. VvNHX1 belongs to the vacuolar NHX protein family and showed high similarity to other known vacuolar antiporters. The expression of VvNHX1 partially complements the salt- and hygromycin-sensitive phenotypes of an ena1-4 nhx1 yeast strain. Immunoblots of vacuoles of yeast expressing a VvNHX1, together with the expression of a VvNHX1-GFP (green fluorescent protein) chimera demonstrated that VvNHX1 localized to the vacuoles. VvNHX1 displayed low affinity K(+)/H(+) and Na(+)/H(+) exchange activities (12.8 and 40.2 mM, respectively). The high levels of expression of VvNHX1 during the véraison and post-véraison stages would indicate that the increase in vacuolar K(+) accumulation, mediated by VvNHX1, is needed for vacuolar expansion. This process, together with the rapid accumulation of reducing sugars, would drive water uptake to the berry and the concomitant berry size increase, typical of the post-véraison stage of growth.

Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis.

The nicotinamide adenine dinucleotide phosphate (NADPH)-dependent enzyme dihydroflavonol 4-reductase (DFR) catalyzes a late step in the biosynthesis of anthocyanins and condensed tannins, two flavonoid classes of importance to plant survival and human nutrition. This enzyme has been widely investigated in many plant species, but little is known about its structural and biochemical properties. To provide a basis for detailed structure-function studies, the crystal structure of Vitis vinifera DFR, heterologously expressed in Escherichia coli, has been determined at 1.8 A resolution. The 3D structure of the ternary complex obtained with the oxidized form of nicotinamide adenine dinucleotide phosphate and dihydroquercetin, one of the DFR substrates, presents common features with the short-chain dehydrogenase/reductase family, i.e., an N-terminal domain adopting a Rossmann fold and a variable C-terminal domain, which participates in substrate binding. The structure confirms the importance of the 131-156 region, which lines the substrate binding site and enlightens the role of a specific residue at position 133 (Asn or Asp), assumed to control substrate recognition. The activity of the wild-type enzyme and its variant N133D has been quantified in vitro, using dihydroquercetin or dihydrokaempferol. Our results demonstrate that position 133 cannot be solely responsible for the recognition of the B-ring hydroxylation pattern of dihydroflavonols.

Overexpression of VvWRKY2 in tobacco enhances broad resistance to necrotrophic fungal pathogens.

WRKY genes encode proteins belonging to a large family of transcription factors that are involved in various developmental and physiological processes and in plant responses to pathogen infections. In the present work, a full-length cDNA from a Vitis vinifera L. cv. Cabernet Sauvignon grape berry library was isolated and characterized. The cDNA, designated VvWRKY2, encodes a polypeptide of 536 amino acids that shows the structural features of group I of WRKY protein family. VvWRKY2 is expressed in the different organs of healthy grapevine plants. In leaves, VvWRKY2 is induced by wounding and after infection with Plasmopara viticola. Constitutive expression of VvWRKY2 in tobacco reduced the susceptibility of transgenic tobacco to three types of fungal pathogens infecting different parts of the plant: Botrytis cinerea (leaves), Pythium spp. (roots) and Alternaria tenuis (seeds). The results indicate that VvWRKY2 may be involved in the resistance of grapevine against the pathogens.

Molecular basis of ergosterol-induced protection of grape against botrytis cinerea: induction of type I LTP promoter activity, WRKY, and stilbene synthase gene expression.

Type I lipid transfer proteins (LTPs) are basic, 9-kDa cystein-rich proteins believed to be involved in plant defense mechanisms. A 2,100-bp fragment containing the coding region of Vitis vinifera lipid transfer protein 1 (VvLTP1) and 1,420-bp of its promoter region was isolated by screening a grape genomic library. In silico analysis revealed several putative, defense-related, cis-regulatory elements such as W- and MYB-boxes, involved in the binding of WRKY and MYB transcription factors, respectively. The 5'-truncated versions of the VvLTP1 promoter were generated, cloned in front of the beta-glucuronidase (GUS) reporter gene, and introduced in tobacco plants and grapevine cell suspensions using Agrobacterium spp. Single MYB- and the W-boxes identified on the 0.250-kbp fragment were sufficient to induce GUS activity in transgenic tobacco plants after transient expression of MYB and WRKY. Ergosterol, a nonspecific fungal elicitor, induced GUS activity in transgenic grapevine cell suspensions transformed with the 1,420- and 750-bp promoter containing a palindromic arrangement of two W-boxes but not the 650- or 250-bp fragment, where only one W-box was present. Moreover, ergosterol triggered WRKY, VvLTP1, and stilbene synthase gene expression in grape plantlets and enhanced protection against Botrytis cinerea. The molecular basis of ergosterol-induced protection is discussed.

Characterization of a grapevine R2R3-MYB transcription factor that regulates the phenylpropanoid pathway.

The ripening of grape (Vitis vinifera) berry is characterized by dramatic changes in gene expression, enzymatic activities, and metabolism that lead to the production of compounds essential for berry quality. The phenylpropanoid metabolic pathway is one of the components involved in these changes. In this study, we describe the cloning and functional characterization of VvMYB5a, a cDNA isolated from a grape L. cv Cabernet Sauvignon berry library. VvMYB5a encodes a protein belonging to a small subfamily of R2R3-MYB transcription factors. Expression studies in grapevine indicate that the VvMYB5a gene is mainly expressed during the early steps of berry development in skin, flesh, and seeds. Overexpression of VvMYB5a in tobacco (Nicotiana tabacum) affects the expression of structural genes controlling the synthesis of phenylpropanoid and impacts on the metabolism of anthocyanins, flavonols, tannins, and lignins. Overexpressing VvMYB5a induces a strong accumulation of several phenolic compounds, including keracyanin (cyanidin-3-rhamnoglucoside) and quercetin-3-rhamnoglucoside, which are the main anthocyanin and flavonol compounds in tobacco. In addition, VvMYB5a overexpression increases the biosynthesis of condensed tannins and alters lignin metabolism. These findings suggest that VvMYB5a may be involved in the control of different branches of the phenylpropanoid pathway in grapevine.

Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development.

The transition from a green, hard, and acidic pericarp to a sweet, soft, coloured, and sugar-rich ripe fruit occurs in many unrelated fruit species. High throughput identification of differentially expressed genes in grape berry has been achieved by the use of 50-mers oligoarrays bearing a set of 3,200 Unigenes from Vitis vinifera to compare berry transcriptome at nine developmental stages. Analysis of transcript profiles revealed that most activations were triggered simultaneously with softening, occurring within only 24 h for an individual berry, just before any change in colouration or water, sugar, and acid content can be detected. Although most dramatically induced genes belong to unknown functional categories, numerous changes occur in the expression of isogenes involved in primary and secondary metabolism during ripening. Focusing on isogenes potentially significant in development regulation (hormonal control of transcription factor) revealed a possible role for several hormones (cytokinin, gibberellin, or jasmonic acid). Transcription factor analysis revealed the induction of RAP2 and WRKY genes at véraison, suggesting increasing biotic and abiotic stress conditions during ripening. This observation was strengthened by an increased expression of multiple transcripts involved in sugar metabolism and also described as induced in other plant organs during stress conditions. This approach permitted the identification of new isogenes as possible control points: a glutathione S-transferase exhibits the same expression profile as anthocyanin accumulation and a new putative sugar transporter is induced in parallel with sugar import.

Molecular characterization of recombinant T1, a non-allergenic periwinkle (Catharanthus roseus) protein, with sequence similarity to the Bet v 1 plant allergen family.

More than 25% of the population suffer from Type I allergy, an IgE-mediated hypersensitivity disease. Allergens with homology to the major birch ( Betula verrucosa ) pollen allergen, Bet v 1, belong to the most potent elicitors of IgE-mediated allergies. T1, a cytokinin-inducible cytoplasmic periwinkle ( Catharanthus roseus ) protein, with significant sequence similarity to members of the Bet v 1 plant allergen family, was expressed in Escherichia coli. Recombinant T1 (rT1) did not react with IgE antibodies from allergic patients, and failed to induce basophil histamine release and immediate-type skin reactions in Bet v 1-allergic patients. Antibodies raised against purified rT1 could be used for in situ localization of natural T1 by immunogold electron microscopy, but did not cross-react with most of the Bet v 1-related allergens. CD analysis showed significant differences regarding secondary structure and thermal denaturation behaviour between rT1 and recombinant Bet v 1, suggesting that these structural differences are responsible for the different allergenicity of the proteins. T1 represents a non-allergenic member of the Bet v 1 family that may be used to study structural requirements of allergenicity and to engineer hypo-allergenic plants by replacing Bet v 1-related allergens for primary prevention of allergy.

Distal regulatory regions restrict the expression of cis-linked genes to the tapetal cells.

The oleosin glycine-rich protein genes Atgrp-6, Atgrp-7, and Atgrp-8 occur in clusters in the Arabidopsis genome and are expressed specifically in the tapetum cells. The cis-regulatory regions involved in the tissue-specific gene expression were investigated by fusing different segments of the gene cluster to the uidA reporter gene. Common distal regulatory regions were identified that coordinate expression of the sequential genes. At least two of these genes were regulated spatially by proximal and distal sequences. The cis-acting elements (122 bp upstream of the transcriptional start point) drive the uidA expression to floral tissues, whereas distal 5' upstream regions restrict the gene activity to tapetal cells.