title: MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis.
abstract: Understanding cellular adaptation to environmental changes is one of the major challenges in systems biology. To understand how cellular systems react towards perturbations of their steady state, the metabolic dynamics have to be described. Dynamic properties can be studied with kinetic models but development of such models is hampered by limited in vivo information, especially kinetic parameters. Therefore, there is a need for mathematical frameworks that use a minimal amount of kinetic information. One of these frameworks is dynamic flux balance analysis (DFBA), a method based on the assumption that cellular metabolism has evolved towards optimal changes to perturbations. However, DFBA has some limitations. It is less suitable for larger systems because of the high number of parameters to estimate and the computational complexity. In this paper, we propose MetDFBA, a modification of DFBA, that incorporates measured time series of both intracellular and extracellular metabolite concentrations, in order to reduce both the number of parameters to estimate and the computational complexity. MetDFBA can be used to estimate dynamic flux profiles and, in addition, test hypotheses about metabolic regulation. In a first case study, we demonstrate the validity of our method by comparing our results to flux estimations based on dynamic 13C MFA measurements, which we considered as experimental reference. For these estimations time-resolved metabolomics data from a feast-famine experiment with Penicillium chrysogenum was used. In a second case study, we used time-resolved metabolomics data from glucose pulse experiments during aerobic growth of Saccharomyces cerevisiae to test various metabolic objectives.
authors.affiliation: Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academical Medical Centre, Amsterdam, The Netherlands.
authors.forename: A Marcel
authors.initials: AM
authors.lastname: Willemsen
authors.forename: Diana M
authors.initials: DM
authors.lastname: Hendrickx
authors.forename: Huub C J
authors.initials: HC
authors.lastname: Hoefsloot
authors.forename: Margriet M W B
authors.initials: MM
authors.lastname: Hendriks
authors.forename: S Aljoscha
authors.initials: SA
authors.lastname: Wahl
authors.forename: Bas
authors.initials: B
authors.lastname: Teusink
authors.forename: Age K
authors.initials: AK
authors.lastname: Smilde
authors.forename: Antoine H C
authors.initials: AH
authors.lastname: van Kampen
mesh_terms: D000465:Algorithms; D005110:Extracellular Space / Q000378:metabolism; D005947:Glucose / Q000378:metabolism; D042541:Intracellular Space / Q000378:metabolism; D055432:Metabolomics / Q000379:methods*; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D049490:Systems Biology / Q000379:methods
chemical_list: D005947:Glucose