Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.

ABSTRACT: Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amin

SUBMITTER: Domenzain I 

PROVIDER: S-EPMC9246944 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature