A comprehensive evaluation of constraining amino acid biosynthesis in compartmented models for metabolic flux analysis
| Autor: | Lehnen, Mathias, Ebert, Birgitta Elisabeth, Blank, Lars Mathias |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
ILE
isoleucine Eukaryotes lcsh:Biotechnology S. cerevisiae LEU leucine Sdmin flux solution from a model with minimal constraints WP WoLF PSORT 13C-metabolic flux analysis Article Sf flux solution from an unconstrained model THR threonine ddc:570 lcsh:TP248.13-248.65 SER serine Compartmented metabolism lcsh:QH301-705.5 TP TargetP 1.1 Non-conventional yeast MFA metabolic flux analysis GLY glycine Sd flux solution from a fully constrained model lcsh:Biology (General) MDV mass distribution vector PYR pyruvate H. polymorpha ACCOA acetyl-CoA |
| Zdroj: | Metabolic Engineering Communications Metabolic Engineering Communications, Vol 5, Iss C, Pp 34-44 (2017) Metabolic engineering communications 5, 34-44 (2017). doi:10.1016/j.meteno.2017.07.001 |
| ISSN: | 2214-0301 |
| Popis: | Recent advances in the availability and applicability of genetic tools for non-conventional yeasts have raised high hopes regarding the industrial applications of such yeasts; however, quantitative physiological data on these yeasts, including intracellular flux distributions, are scarce and have rarely aided in the development of novel yeast applications. The compartmentation of eukaryotic cells adds to model complexity. Model constraints are ideally based on biochemical evidence, which is rarely available for non-conventional yeast and eukaryotic cells. A small-scale model for 13C-based metabolic flux analysis of central yeast carbon metabolism was developed that is universally valid and does not depend on localization information regarding amino acid anabolism. The variable compartmental origin of traced metabolites is a feature that allows application of the model to yeasts with uncertain genomic and transcriptional backgrounds. The presented test case includes the baker's yeast Saccharomyces cerevisiae and the methylotrophic yeast Hansenula polymorpha. Highly similar flux solutions were computed using either a model with undefined pathway localization or a model with constraints based on curated (S. cerevisiae) or computationally predicted (H. polymorpha) localization information, while false solutions were found with incorrect localization constraints. These results indicate a potentially adverse effect of universally assuming Saccharomyces-like constraints on amino acid biosynthesis for non-conventional yeasts and verify the validity of neglecting compartmentation constraints using a small-scale metabolic model. The model was specifically designed to investigate the intracellular metabolism of wild-type yeasts under various growth conditions but is also expected to be useful for computing fluxes of other eukaryotic cells. Highlights • Compartmentation influences computed intracellular fluxes. • Improper localization constraints potentially produce false flux solutions. • Minimal compartmentation constraints result in high-quality flux computations. |
| Databáze: | OpenAIRE |
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