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…

Photoselective shade films affect grapevine berry secondary metabolism and wine composition

Grapevine physiology and production are challenged by forecasted increases in temperature and water deficits. Within this scenario, photoselective overhead shade films are promising tools in warm viticulture areas to overcome climate change related factors. The aim of this study was to evaluate the vulnerability of ‘Cabernet Sauvignon’ grape berry to solar radiation overexposure and optimize shade film use for berry integrity. A randomized complete block design field study was conducted across two years (2020-2021) in Oakville, Napa Valley, CA, with four shade films (D1, D3, D4, D5) differing in the percent of radiation spectra transmitted and compared to an uncovered control (C0). Integrals for gas exchange parameters and mid-day stem water potential were unaffected by the shade films in 2020 and 2021. By harvest, berries from uncovered and shaded vines did not differ in their size or primary metabolism in either year. Despite precipitation exclusion during the dormant season in the shaded treatments, yield did not differ between them and the control in either season. In 2020, total skin anthocyanins (mg/g fresh mass) in the shaded treatments was greater than C0 during berry ripening and at harvest. Conversely, flavonol concentrations in 2020 were reduced in shaded vines compared to C0. The 2020 growing season highlighted the impact of heat degradation on flavonoids. Flavonoid concentrations in 2021 increased until harvest while flavonoid degradation was apparent from veraison to harvest in 2020 across shaded and control vines. Wine analyses highlighted the importance of light spectra to modify wine composition. Wine color intensity, tonality and anthocyanin values were enhanced in D4 whereas antioxidant properties were enhanced in C0 and D5 wines. Altogether, our results highlighted the need of new approaches in warm viticulture areas given the impact that composition of light has on berry and wine quality.

Microbial consortia as a tool for sustainable vineyard management: A study on their acceptance among Veneto region’s grape-growers

In recent years, sustainability has become a key focus in agriculture, including viticulture.

Pierce’s disease of grapevines, a new threat to the wine industry in Southern Europe

Pierce’s disease (PD) is considered a potential threat to european viticulture (EPPO a2 list of pathogens since 1981). In the usa, infections caused by the vector-borne bacterium xylella fastidiosa have caused recurrent damage to vineyards in California and the southeastern states. However, vineyards in Europe have remained free of PD until recently, when it was first detected on the island of Mallorca in 2017. The reasons for the absence of PD in continental Europe have not been convincingly explained.

Nuove soluzioni e strumenti per l’agricoltura e la viticoltura di precisione

GEOSPHERA s. r. l. e TERR.A.IN. CNS, forti della grande esperienza dei loro collaboratori nell’ambito delle scienze naturali, della geologia, della geofisica e dell’informatica, garantiscono risposte innovative alle problematiche della moderna agricoltura rivolgendosi direttamente ai viticoltori, ai commercianti vinicoli ed ai liberi professionisti.

Volatile composition of base wines to obtain sparkling wines from seven autochthonous grape varieties from Castilla y León (Spain)

The aim of this work was to characterize the aromatic profile of white and rosé base wines for the elaboration of sparkling wines from seven autochthonous grape varieties of Castilla y León. The ‘Albarín’, ‘Godello’ and ‘Verdejo’ white grape cultivars contribute with more fruity notes than the ‘Viura’ and ‘Malvasía’ cultivars; and ‘Prieto picudo’ coloured grape cultivar has more fruity character than ‘Garnacha’.