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Core Metabolism Arabidopsis thaliana

ABSTRACT: Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.

SUBMITTER: Kira Trares  

PROVIDER: MODEL1801090001 | BioModels | 2020-04-09

REPOSITORIES: BioModels

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Publications

Modeling the Metabolism of <i>Arabidopsis thaliana</i>: Application of Network Decomposition and Network Reduction in the Context of Petri Nets.

Koch Ina I   Nöthen Joachim J   Schleiff Enrico E  

Frontiers in genetics 20170630

<b>Motivation:</b><i>Arabidopsis thaliana</i> is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inc  ...[more]

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