Thursday, December 19, 2024 - Thesis defense - Chloé Beaumont

Chloé BEAUMONT

Thesis presented to obtain the degree of Doctor of the University of Bordeaux - Specialization : Sciences Agronomiques

Team Metabolism (META)

Thursday, December 19, 2024 - 14:pm - Amphithéâtre Colette & Josy Bové - Campus INRAE Villenave d'Ornon
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Abstract : To overcome barriers related to improving plant production, a better understanding of the mechanisms underlying fruit development is essential, with protein metabolism at the core of these processes. Recent studies on protein turnover in tomato have highlighted the importance of protein synthesis in metabolic and physiological traits. Recent results from the laboratory also show that proteins play a key role in fruit growth, allowing for a good prediction of the relative growth rate (RGR) in a panel of nine species.
In this context, this thesis aims to study the stability of proteins in a panel of ten fleshy fruit species, selected for their genetic diversity and contrasting characteristics, such as the development duration, ranging from 30 to over 200 days. The objective is to identify generic and specific properties during growth. Multi-omics data (transcriptomics, proteomics, metabolomics) were acquired at ten stages of development, all expressed in absolute quantification.
We first compared the physiological growth data with fruit development rates and metabolic fluxes estimated by modeling. This highlighted the importance of nitrogen metabolism, particularly proteins, in the growth-defense trade-off.
Next, transcriptomic data were explored to predict fruit development characteristics (growth, RGR, total protein content). Generalized linear models showed reliable predictions, highlighting the central role of proteins and cell wall compounds in fruit growth.
The following chapter describes the comparative proteomic data obtained from the same samples of the nine fruit species. The analysis of proteins derived from multi-species orthologous genes reveals key biological functions shared between species, including roles in fruit maturation, energy metabolism regulation, and protein synthesis and degradation.
Finally, the last part compares protein turnovers calculated from transcriptomic and proteomic data. The synthesis rates are relatively stable across species, while the degradation rates vary according to the development duration, with more stable proteins in slow-developing fruits (trees) compared to fast-developing fruits (herbaceous plants). The analysis of orthogroups shows that protein stability depends on their function, with proteins involved in essential processes being more stable than those with regulatory functions, such as stress response. These results open up prospects for using advanced techniques, such as deep learning, to predict protein lifespan based on their sequences.

Direction : Mme Sophie Colombié

Jury members :

Mme. Christine DILLMANN Professeure des universités Université Paris-Saclay (Gif-sur-Yvette) Rapporteure
Mme. Anne GOELZER Ingénieure de recherche INRAE (Jouy en Josas) Rapporteure
Mme. Marie-Laure MARTIN-MAGNIETTE Directrice de recherche INRAE (Palaiseau) Examinatrice
M. Sébastien MONGRAND Directeur de recherche CNRS (Villenave d’Ornon) Examinateur