Assessment of the native electrophoretic analysis of total grape must proteins for the characterization of Vitis vinifera L. cultivars

TaqMan® and HRM approaches for SNP genotyping in genetic traceability of musts and wines

The fight against fraud in the wine sector requires continuous improvements and validations of new technologies applicable to musts and wines. Starting from published data from the Vitis18kSNP array, a series of new specific single nucleotide polymorphism (SNP) markers have been identified for some important north-western Italian cultivars, such as Barbera, Dolcetto and Arneis (Vitis vinifera L.), used in the production of high-quality wines under Protected Denomination of Origin. A pair of new SNP markers for each grape variety were selected and validated using two real-time PCR techniques: TaqMan® genotyping assays and high-resolution melting analysis (HRM). The TaqMan® assay has proven to be more reliable and repeatable than HRM analysis because despite being an economical and versatile technique for the detection of different types of genomic mutations (SNPs, insertions or deletions), HRM has shown limitations in the presence of poor-quality DNA extracted from musts and wines. TaqMan® assays have successfully identified Barbera, Dolcetto and Arneis in their respective musts and experimental wines, and with good efficiency in commercial wines. Marked differences between genotypes were observed, varietal identification in Dolcetto-based musts/wines was more efficient than that in Arneis-based wines. Therefore, the TaqMan® assay has considerable potential for varietal identification in wines and the procedure described in the present work can be easily adapted to all wines with adequate setup of DNA extraction methods that should be adapted to different wines.

White Wine Protein Instability: Mechanism, Quality Control and Technological Alternatives for Wine Stabilisation—An Overview

Wine protein instability depends on several factors, but wine grape proteins are the main haze factors, being mainly caused by pathogenesis-related proteins (thaumatin-like proteins and chitinases) with a molecular weight between 10~40 kDa and an isoelectric point below six. Wine protein stability tests are needed for the routine control of this wine instability, and to select the best technological approach to remove the unstable proteins. The heat test is the most used, with good correlation with the natural proteins’ precipitations and because high temperatures are the main protein instability factor after wine bottling. Many products and technological solutions have been studied in recent years; however, sodium bentonite is still the most efficient and used treatment to remove unstable proteins from white wines. This overview resumes and discusses the different aspects involved in wine protein instability, from the wine protein instability mechanisms, the protein stability tests used, and technological alternatives available to stabilise wines with protein instability problems.

Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.

Experimental Review of DNA-Based Methods for Wine Traceability and Development of a Single-Nucleotide Polymorphism (SNP) Genotyping Assay for Quantitative Varietal Authentication

The genetic varietal authentication of wine was investigated according to DNA isolation procedures reported for enological matrices and also by testing 11 commercial extraction kits and various protocol modifications. Samples were collected at different stages of the winemaking process of renowned Italian wines Brunello di Montalcino, Lambruschi Modenesi, and Trento DOC. Results demonstrated not only that grape DNA loss is produced by the fermentation process but also that clarification and stabilization operations contribute to the reduction of double-stranded DNA content on wine. Despite the presence of inhibitors, downstream PCR genotyping yielded reliable nuclear and chloroplast SSR markers for must samples, whereas no amplification or inconsistent results were obtained at later stages of the vinification. In addition, a TaqMan genotyping assay based on cultivar-specific single-nucleotide polymorphisms (SNPs) was designed, which allowed assessment of grapevine DNA mixtures. Once the wine matrix limitations are overcome, this sensitive tool may be implemented for the relative quantification of cultivars used for blend wines or frauds.

A novel preparation technique of red (sparkling) wine for protein analysis

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A new protocol for preparation of proteins in red (sparkling) wine was developed.

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Dialysis, lyophilization, removal of phenolic compounds, protein precipitation.

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New protocol enables improved resolution in subsequent analysis.

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Applicability of the method for other beverages made of grapes is given.

Despite their low concentration, proteins can influence several key enological parameters such as foam stability or haze formation in (sparkling) wine. Most studies focus on white (sparkling) wine since the higher content of phenolic compounds in red wines impairs proteomic research. The aim of the study was the development of a method for the preparation of red (sparkling) wine proteins for proteomic analysis. Three methods of sample preparation were assessed on silver stained SDS-PAGE gels and with MALDI-TOF MS. Our new method was highly suitable for the preparation of proteins for the aforementioned applications. The results showed a substantial increase in signal intensity with a simultaneous decrease in background noise. The preparation protocol consists of (i) dialysis and freeze drying of the sample, (ii) removal of phenolic compounds by water-saturated phenol and (iii) protein precipitation by addition of ammonium acetate. Employment of this method followed by SDS-PAGE analysis allowed for silver stained gels with diminished background or streaking and clearly resolved protein bands. Analysis of spectra obtained from samples prepared according to the proposed protocol showed increased intensity and signal-to-noise ratio in MALDI-TOF MS. Furthermore it was demonstrated that this method can be applied to various kinds of grape products.

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.

Toward the authentication of wines of Nemea denomination of origin through cleaved amplified polymorphic sequence (CAPS)-based assay

In the present study, we developed a cleaved amplified polymorphic sequence (CAPS)-based assay as a first attempt to detect fraud in grapevine musts with a long-term objective to establish an analytical methodology to authenticate wines of Nemea denomination of origin (Agiorgitiko). The analytical assay makes use of a single nucleotide polymorphism that discriminates Agiorgitiko and Cabernet Sauvignon varieties. The latter grape variety is one of the major adulterants for Nemea wines. Agiorgitiko grapevine must was spiked with Cabernet Sauvignon in several ratios (v/v) from 50 down to 10%, and the subsequent mixes were subjected to alcoholic microfermentation. DNA was extracted from all mixture samples up to the end of the fermentation process and was subjected to the CAPS assay. Both standard agarose gel and lab-on-a-chip capillary electrophoresis illustrated the ability of the method to detect the presence of Cabernet Sauvignon down to 10% throughout the whole fermentation process.

Characterization and quantification of grape variety by means of shikimic acid concentration and protein fingerprint in still white wines

Protein profiles, obtained by high-performance capillary electrophoresis (HPCE) on white wines previously dialyzed, combined with shikimic acid concentration and multivariate analysis, were used for the determination of grape variety composition of a still white wine. Six varieties were studied through monovarietal wines elaborated in the laboratory: Chardonnay (24 samples), Chenin (24), Petit Manseng (7), Sauvignon (37), Semillon (24), and Ugni Blanc (9). Homemade mixtures were elaborated from authentic monovarietal wines according to a Plackett-Burman sampling plan. After protein peak area normalization, a matrix was elaborated containing protein results of wines (mixtures and monovarietal). Partial least-squares processing was applied to this matrix allowing the elaboration of a model that provided a varietal quantification precision of around 20% for most of the grape varieties studied. The model was applied to commercial samples from various geographical origins, providing encouraging results for control purposes.

Novel preparation method of template DNAs from wine for PCR to differentiate grape (Vitis vinifera L.) cultivar

Template DNAs were extracted from wine and purified for use as samples for PCR to differentiate grape cultivars. It has been pointed out that the authentication of grape material by PCR using wine as a material is very difficult. The problems are (1) decomposition of DNAs during fermentation; (2) contamination of DNAs from microorganisms such as yeast; (3) interference of DNA extraction by polysaccharides and polypeptides in the beverages; and (4) coexistence of PCR inhibitors, such as polyphenols. For this study was developed a novel preparation method of template DNA from wine to differentiate grape cultivars using PCR by (1) lyophilizing and pulverizing the fermented beverage to concentrate the DNAs; (2) decomposition of polysaccharides and proteins so as not to inhibit DNA extraction using heat-resistant amylase and proteinase K without DNA damage by endogenous DNase; and (3) separation of the template DNAs for PCR from PCR inhibitors, such as polyphenols, by purification using 70% EtOH extraction and isopropyl alcohol precipitation. To prevent the amplification of microorganisms' DNAs during PCR, suitable PCR primers closely related to the specific plant DNAs, such as chloroplast DNA and mitochondrial DNA, were selected. The sequences of the amplified DNAs by PCR were ascertained to be the same as those of grape materials.

The diversity of pathogenesis-related proteins decreases during grape maturation

It was recently shown that wines contain typically a huge diversity of structurally similar polypeptides that exhibit a high degree of homology to pathogenesis-related (PR) proteins. This observation suggested the existence of one or a few precursors in mature grapes, common to most or all the wine PR proteins. Limited proteolysis and chemical modification of the precursor(s) during fruit ripening and winemaking could then generate the large number of distinct wine polypeptides. However, the patterns of PR proteins extracted from grape berries regularly harvested from the onset of development until maturity did not confirm the previous hypothesis. Two different methodologies, involving 2-D immunoblotting and a combination of FPLC cation/anion exchange chromatographies with 1-D immunoblotting, indicate that the total concentration of PR proteins is increased but its diversity is reduced from the early stages of berry development until maturity. These results indicate that PR proteins are synthesized in a wide variety of forms from the early stages of grape development, eliminating the hypothesis previously formulated on the existence of one or few precursors common to the wine proteins.

Grape berry biochemistry revisited upon proteomic analysis of the mesocarp

Major soluble proteins of grapevine ripe berries were extracted from six different cultivars including non vinifera, with trichloroacetic acid acetone and resolved in two-dimensional electrophoresis (2-DE) gels. About three hundred spots were detected on the 2-DE map after colloidal blue staining. From 2-DE map of cv. Gamay mesocarp, 67 proteins were identified (p > 0.95) using matrix-assisted laser desorption/ionization-mass spectrometry analysis. About 34%, 19%, and 13% of identified proteins play, respectively, a role in energy metabolism, defense, and stress response and primary metabolism. 2-DE analysis revealed considerable accumulation of dehydrin, invertase, and a putative transcription factor in the ripe fruit, in addition to pathogenesis-related proteins such as chitinase and thaumatin-like proteins previously documented as prevalent proteins in ripe berries. Actual translation of redundant transcripts of unclear function such as Grip31, Grip32, and Grip61 recently cloned in ripe grape berries was confirmed. The relative abundance of UDP-glucose pyrophosphorylase and vacuolar invertase strongly supported a key role of the apoplastic pathway of sugar loading during ripening. Comparative analysis shows that differences between cultivars were low, but different isoforms of alcohol dehydrogenase and of a transcription factor of hexose transporter were obvious in the six cultivars. Peptide mass fingerprinting suggests that the Adh isoforms would be Adh2/Adh6 or Adh2/Adh7 dimers and unambiguously shows that considerable deletion/insertion inside Adh7 are not cloning artifacts.

Electrophoretic methods in the analysis of beverages

A review of the applications of electrophoresis to the determination of various compounds in beverage samples, namely beer, hard drinks, juice, milk, soft drinks, tea and wine, is presented.