Dataset Information

Saa2016 - Mammalian methionine cycle - approximate bayesian computation

ABSTRACT: Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach Pedro A. Saa, Lars K. Nielsen* Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia *Corresponding author Email: lars.nielsen@uq.edu.au Reference methionine cycle model (i.e., true model) used for parameter estimation. This model is almost entirely based on the kinetic reconstruction of Korendyaseva et al. (2008). Korendyaseva TK, Kuvatov DN, Volkov Va, Martinov MV, Vitvitsky VM, Banerjee R, Ataullakhanov FI (2008) An allosteric mechanism for switching between parallel tracks in mammalian sulfur metabolism. Plos Comput Biol 4: e1000076

SUBMITTER: Pedro Saa

PROVIDER: MODEL1603150000 | BioModels | 2016-07-17

REPOSITORIES: BioModels

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Publications

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.

Saa Pedro A PA Nielsen Lars K LK

Scientific reports 20160715

Kinetic models are essential to quantitatively understand and predict the behaviour of metabolic networks. Detailed and thermodynamically feasible kinetic models of metabolism are inherently difficult to formulate and fit. They have a large number of heterogeneous parameters, are non-linear and have complex interactions. Many powerful fitting strategies are ruled out by the intractability of the likelihood function. Here, we have developed a computational framework capable of fitting feasible an ...[more]

PMID: 27417285

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Project description:In this study, we combined metabolic reconstruction, growth assays, metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway and of thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, of at least one gene of the transsulfuration pathway (aecD) and of genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC9175 during sulfur starvation and in the presence of sulfate, cystine or methionine plus cystine. In sulfur starvation, 690 genes including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in presence of cysteine, while the expression of metX, metY, metE1, metE2 and BL613 encoding a probable cystathionine-γ-synthase decreased in the presence of methionine. We identified three ABC transporters: two stronger transcribed during cysteine limitation and one during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase, BL929, and a methionine transporter (metPS) was induced in the presence of methionine, in conjunction with a significant increase of volatile sulfur compounds production. Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE25418: BA-Methionine plus Cystine vs Cystine GSE25419: BA-Sulfate vs Cystine GSE25420: BA-Methionine plus Cystine vs Sulfate GSE25421: BA-Sulfate vs Sulfate starvation

Dataset Information

Saa2016 - Mammalian methionine cycle - approximate bayesian computation

Publications

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.

Similar Datasets

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