terclim by ICS banner
IVES 9 IVES Conference Series 9 Artificial intelligence (AI)-based protein modeling for the interpretation of grapevine genetic variants

Artificial intelligence (AI)-based protein modeling for the interpretation of grapevine genetic variants

Abstract

Genetic variants known to produce single residue missense mutations have been associated with phenotypic traits of commercial interest in grapevine. This is the case of the K284N substitution in VviDXS1 associated with muscat aroma, or the R197L in VviAGL11 causing stenospermocarpic seedless grapes. The impact of such mutations on protein structure, stability, dynamics, interactions, or functional mechanism can be studied by computational methods, including our pyDock scoring, previously developed. For this, knowledge on the 3D structure of the protein and its complexes with other proteins and biomolecules is required, but such knowledge is not available for virtually none of the proteins and complexes in grapevine. Fortunately, the possibility of modeling proteins and complex structures with Artificial Intelligence (AI)-based methods like AlphaFold2 and AlphaFold2-Multimer will facilitate the application of this approach to proteins and complexes without available structure. Moreover, we are developing new methods based on AI to combine AlphaFold models, molecular dynamics (MD), pyDock energy scoring, and CCharPPI descriptors to predict the impact of protein mutations at the molecular level. As a case study, we have modelled the impact of the R197L seedlessness-associated substitution in VviAGL11. This protein is a homo-dimeric transcription factor that interacts with VviMADS4 dimeric protein to form a functional hetero-tetramer. Structural modeling of this complex provides insights into the functional mechanism of this protein and the role of the mentioned mutation. This protein modeling approach could be extended for grapevine mutation analysis at the genomic level.

DOI:

Publication date: June 14, 2024

Issue: Open GPB 2024

Type: Poster

Authors

Luis Ángel Rodríguez-Lumbreras1, Víctor Monteagudo1, Pablo Carbonell-Bejerano1, Fabian Glaser2, Juan Fernández-Recio1*

1 Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-UR-Gobierno de La Rioja, Spain
2 Technion Institute of Technology, Israel

Contact the author*

Keywords

AI-based modeling, Seedless grapes, Protein-protein interactions, Mutation impact analysis, Protein structure

Tags

IVES Conference Series | Open GPB | Open GPB 2024

Citation

Related articles…

Influence of the carbonic maceration winemaking method on the colour features of Tempranillo red wines

During recent years, carbonic maceration (CM) wines are increasingly demanded by consumers. The Spanish Rioja Qualified Designation of Origin (D.O.Ca. Rioja) is a winemaking area

Chemical and sensory diversity of regional Cabernet-Sauvignon wines

AIM: To investigate chemical and sensory drivers of regional typicity of Cabernet Sauvignon from different geographical regions of Australia.

Study of the Interactions between High Molecular Weight Salivary Proteins and Red Wine Flavanols.

Astringency has been defined by the American Society for Testing Materials as “the complex of sensations due to shrinking, drawing or puckering of the epithelium as a result of exposure to substances such as alums or tannins”. Regarding the importance of astringency in wine consumer acceptance, elucidating the molecular mechanisms underpinning this complex sensation represents an important goal for scientists. Although different mechanisms have been described (Gibbins & Carpenter, 2013), the salivary protein precipitation is still the most accepted theory. According to this, wine astringency perceived in the oral cavity is originally attributed to the interaction and subsequence precipitation of salivary proteins by wine tannins –mainly flavanols–.

Using δ13C and hydroscapes as a tool for discriminating cultivar specific drought response

Measurement of carbon isotope discrimination in berry juice sugars at maturity (δ13C) provides an integrated assessment of water use efficiency (WUE) during the period of berry ripening, and when collected over multiple seasons can be used as an indication of drought stress response. Berry juice δ13C measurements were carried out on 48 different varieties planted in a common garden experiment in Bordeaux, France from 2014 through 2021 and were paired with midday and predawn leaf water potential measurements on the same vines in a subset of six varieties. The aim was to discriminate a large panel of varieties based on their stomatal behaviour and potentially identify hydraulic traits characterizing drought tolerance by comparing δ13C and hydroscapes (the visualisation of plant stomatal behaviour as a response to predawn water potential). Cluster analysis found that δ13C values are likely affected by the differing phenology of each variety, resulting in berry ripening of different varieties taking place under different stress conditions within the same year. We accounted for these phenological differences and found that cluster analysis based on specific δ13C metrics created a classification of varieties that corresponds well to our current empirical understanding of their relative drought tolerances. In addition, we analysed the water potential regulation of the subset of six varieties (using the hydroscape approach) and found that it was well correlated with some δ13C metrics. Surprisingly, a variety’s water potential regulation (specifically its minimum critical leaf water potential under water deficit) was strongly correlated to δ13C values under well-watered conditions, suggesting that base WUE may have a stronger impact on drought tolerance than WUE under water deficit. These results give strong insights on the innate WUE of a very large panel of varieties and suggest that studies of drought tolerance should include traits expressed under non-limiting conditions.

La valorisation des Terroirs Viticoles par les Indications géographiques et les appellations d’origine

Le sujet proposé dans le thème “l’environnement juridique” est plus économique que juridique, et constitue une sorte de complément au sujet qui l’a précédé : analyse des marchés, stratégies commerciales et terroirs”.