A genome-scale metabolic model of Arabidopsis and some of its properties.
We describe the construction and analysis of a genome-scale metabolic model of Arabidopsis (Arabidopsis thaliana) primarily derived from the annotations in the Aracyc database. We used techniques based on linear programming to demonstrate the following: (1) that the model is capable of producing biomass components (amino acids, nucleotides, lipid, starch, and cellulose) in the proportions observed experimentally in a heterotrophic suspension culture; (2) that approximately only 15% of the available reactions are needed for this purpose and that the size of this network is comparable to estimates of minimal network size for other organisms; (3) that reactions may be grouped according to the changes in flux resulting from a hypothetical stimulus (in this case demand for ATP) and that this allows the identification of potential metabolic modules; and (4) that total ATP demand for growth and maintenance can be inferred and that this is consistent with previous estimates in prokaryotes and yeast.
Poolman
Mark G
MG
School of Life Science, Oxford Brookes University, Headington, Oxford OX3 OBP, United Kingdom. mgpoolman@brookes.ac.uk
Miguet
Laurent
L
Sweetlove
Lee J
LJ
Fell
David A
DA
D000255:Adenosine Triphosphate / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D018533:Biomass; D002478:Cells, Cultured; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways; D055442:Metabolome; D008954:Models, Biological
D000255:Adenosine Triphosphate