Population FBA predicts metabolic phenotypes in yeast

• Published in: PLoS computational biology Vol. 13; no. 9; p. e1005728
• Main Authors: Labhsetwar, Piyush, Melo, Marcelo C R, Cole, John A, Luthey-Schulten, Zaida
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-09-2017; Public Library of Science (PLoS)
• Subjects: Acetic acid; Baking yeast; Biochemistry; Biology; Biology and Life Sciences; Biophysics; Cancer; Carbon; Cell Proliferation - physiology; Computer Simulation; Culture Media - metabolism; E coli; Electron transport; Enzymes; Ethanol; Ethanol - metabolism; Fermentation; Fluxes; Gene expression; Gene regulation; Genetic algorithms; Genetic aspects; Genomes; Glycerol; Glycine; Growth media; Growth rate; Mathematical models; Metabolic Flux Analysis; Metabolic Networks and Pathways - physiology; Metabolism; Mitochondria; Models, Biological; Observations; Parameter identification; Phenotypes; Physical Sciences; Physics; Population; Proteome - metabolism; Proteomics; Research and Analysis Methods; Respiration; Saccharomyces cerevisiae; Saccharomyces cerevisiae - physiology; Saccharomyces cerevisiae Proteins - metabolism; Secretion; Serine; Software; Vitamin B; Yeast; Yeasts (Fungi); United States > US; Illinois
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1005728

Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance analysis (Population FBA) successfully described metabolic heterogeneity in a population of independent Escherichia coli cells growing in a defined medium. We extend the methodology to account for correlations in protein expression arising from the co-regulation of genes and apply it to study the growth of independent Saccharomyces cerevisiae cells in two different growth media. We find the partitioning of flux between fermentation and respiration predicted by our model agrees with recent 13C fluxomics experiments, and that our model largely recovers the Crabtree effect (the experimentally known bias among certain yeast species toward fermentation with the production of ethanol even in the presence of oxygen), while FBA without proteomics constraints predicts respirative metabolism almost exclusively. The comparisons to the 13C study showed improvement upon inclusion of the correlations and motivated a technique to systematically identify inconsistent kinetic parameters in the literature. The minor secretion fluxes for glycerol and acetate are underestimated by our method, which indicate a need for further refinements to the metabolic model. For yeast cells grown in synthetic defined (SD) medium, the calculated broad distribution of growth rates matches experimental observations from single cell studies, and we characterize several metabolic phenotypes within our modeled populations that make use of diverse pathways. Fast growing yeast cells are predicted to perform significant amount of respiration, use serine-glycine cycle and produce ethanol in mitochondria as opposed to slow growing cells. We use a genetic algorithm to determine the proteomics constraints necessary to reproduce the growth rate distributions seen experimentally. We find that a core set of 51 constraints are essential but that additional constraints are still necessary to recover the observed growth rate distribution in SD medium.