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Metabolites 2015, 5(3), 521-535; doi:10.3390/metabo5030521

Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations

Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
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Author to whom correspondence should be addressed.
Academic Editor: Kazuyuki Shimizu
Received: 26 August 2015 / Accepted: 4 September 2015 / Published: 18 September 2015
(This article belongs to the Special Issue Metabolic Flux Analysis)
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Abstract

Recent advances in 13C-Metabolic flux analysis (13C-MFA) have increased its capability to accurately resolve fluxes using a genome-scale model with narrow confidence intervals without pre-judging the activity or inactivity of alternate metabolic pathways. However, the necessary precautions, computational challenges, and minimum data requirements for successful analysis remain poorly established. This review aims to establish the necessary guidelines for performing 13C-MFA at the genome-scale for a compartmentalized eukaryotic system such as yeast in terms of model and data requirements, while addressing key issues such as statistical analysis and network complexity. We describe the various approaches used to simplify the genome-scale model in the absence of sufficient experimental flux measurements, the availability and generation of reaction atom mapping information, and the experimental flux and metabolite labeling distribution measurements to ensure statistical validity of the obtained flux distribution. Organism-specific challenges such as the impact of compartmentalization of metabolism, variability of biomass composition, and the cell-cycle dependence of metabolism are discussed. Identification of errors arising from incorrect gene annotation and suggested alternate routes using MFA are also highlighted. View Full-Text
Keywords: genome-scale MFA; S. cerevisiae; challenges; requirements; considerations genome-scale MFA; S. cerevisiae; challenges; requirements; considerations
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Gopalakrishnan, S.; Maranas, C.D. Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations. Metabolites 2015, 5, 521-535.

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