Petrizzelli MS, de Vienne D, Nidelet T, Noûs C, Dillmann C. Data integration uncovers the metabolic bases of phenotypic variation in yeast.
PLoS Comput Biol 2021;
17:e1009157. [PMID:
34264947 PMCID:
PMC8315545 DOI:
10.1371/journal.pcbi.1009157]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/27/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
The relationship between different levels of integration is a key feature for understanding the genotype-phenotype map. Here, we describe a novel method of integrated data analysis that incorporates protein abundance data into constraint-based modeling to elucidate the biological mechanisms underlying phenotypic variation. Specifically, we studied yeast genetic diversity at three levels of phenotypic complexity in a population of yeast obtained by pairwise crosses of eleven strains belonging to two species, Saccharomyces cerevisiae and S. uvarum. The data included protein abundances, integrated traits (life-history/fermentation) and computational estimates of metabolic fluxes. Results highlighted that the negative correlation between production traits such as population carrying capacity (K) and traits associated with growth and fermentation rates (Jmax) is explained by a differential usage of energy production pathways: a high K was associated with high TCA fluxes, while a high Jmax was associated with high glycolytic fluxes. Enrichment analysis of protein sets confirmed our results.
This powerful approach allowed us to identify the molecular and metabolic bases of integrated trait variation, and therefore has a broad applicability domain.
The integration of data at different levels of cellular organization is an important goal in computational biology for understanding the way the genotypic variation translates into phenotypic variation. Novel profiling technologies and accurate high-throughput phenotyping now allows genomic, transcriptomic, metabolic and proteomic characterization of a large number of individuals under various environmental conditions. However, the metabolic fluxes remain difficult to measure. In this work, we take advantage of recent advances in genome-scale functional annotation and constraint-based metabolic modeling to provide a mathematical framework that allows to estimate internal cellular fluxes from protein abundances and elucidate the biological mechanisms underlying phenotypic variation. Applied to yeast as a model system, this approach highlights that the negative correlation between production traits such as maximum population size and growth and fermentation traits is explained by a differential usage of energy production pathways. The ability to identify molecular and metabolic bases of the variation of integrated traits through population studies has a broad applicability domain.
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