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…

Optimization of aroma production in grape cell suspensions induced by chemical elicitor

Methyl-jasmonate (MeJA) induces the production of at least 25 compounds with sesquiterpene- like mass spectra in ‘Cabernet sauvignon’. Tost effective concentration of MeJA in stimulating the production of sesquiterpenes was found to be 500 µM if added when the cell suspensions had a PCV of 35 %, and 1000 if added when the cell suspensions had a PCV of 70 %.

Fractionation of copper and iron in wine: Assessment of potential macromolecule and sulfur binding agents

Copper and iron are known to substantially impact wine stability through oxidative, reductive or colloidal phenomena. However, the binding of metal ions to different wine components under wine conditions, and the impact of this binding on the ability of the metal ions to induce spoilage processes, is not well understood. This study surveyed a range of red and white wines for an understanding of the variability of broad metal categories within the wines. The techniques utilized included an electrochemical constant current stripping potentiometry technique (ccSP), and solid phase extraction (SPE) fractionation of wine with subsequent analysis of the metal content of each fraction by inductively coupled plasma – optical emission spectroscopy (ICP-OES).

The effect of cropload on the volatile aroma characteristics of ‘Beihong’ and ‘Beimei’ red wine

Beihong and Beimei were bred as winemaking cultivars released by Institute of Botany, the Chinese Academy of Sciences in 2008. The cultivars are selected from the population of ‘Muscat Hamburg’ (Vitis vinifera) ×V. amurensis. They are extended to most provinces in North of China because they have strong resistance to cold and disease and need not be buried in soil in winter. To better understand the effect of cropload on volatile compounds during wine-making, we surveyed volatiles composition and content of different cropload level in 3-years-old ‘Beihong’ and ‘Beimei’ vines which planted in east foot of Helan mountain of Ningxia (EHN).

Identification of arbuscular mycorrhizal fungi species preferentially associated with grapevine roots inoculated with commercial bioinoculants 

Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots and can help plants acquire nutrients from the soil in exchange for photosynthetic carbon. Commercial bioinoculants containing AMF are widely available and represent a potential opportunity to reduce the dependence of grapevines on agrochemicals. However, which commercially available AMF species colonize vine roots and affect vine growth remains unknown. The aim of this study was to identify the AMF species from commercial bioinoculants that colonize grapevine roots using high-throughput sequencing, and to evaluate the performance of five commercial bioinoculants and their effects on own-rooted Cabernet sauvignon.

Does foliar fertilization with Seaweed improve the productivity and quality of ‘Merlot’ grape must?

Developing technologies that help vines survive and produce in quantity and quality within current times is mandatory. In this sense, in the 2021/2022 agricultural harvest, the influence of the foliar application of seaweed – Laminaria japonica was studied, aiming at productivity and quality of the must in the ‘Merlot’ grape. In the city of “Santana do Livramento”, “Rio Grande do Sul” (RS), Brazil; in a 15-year-old commercial vineyard of ‘Merlot’ clone ENTAV-INRA® 347, grafted onto ‘SO4’ rootstock, the following treatments were applied on 6 occasions: No treatment (control) and; Foliar application of Laminaria japonica seaweed (commercial product: Exal (ALAS), 2 kg ha-1).