title: Elementary flux modes analysis of functional domain networks allows a better metabolic pathway interpretation.
abstract: Metabolic network analysis is an important step for the functional understanding of biological systems. In these networks, enzymes are made of one or more functional domains often involved in different catalytic activities. Elementary flux mode (EFM) analysis is a method of choice for the topological studies of these enzymatic networks. In this article, we propose to use an EFM approach on networks that encompass available knowledge on structure-function. We introduce a new method that allows to represent the metabolic networks as functional domain networks and provides an application of the algorithm for computing elementary flux modes to analyse them. Any EFM that can be represented using the classical representation can be represented using our functional domain network representation but the fine-grained feature of functional domain networks allows to highlight new connections in EFMs. This methodology is applied to the tricarboxylic acid cycle (TCA cycle) of Bacillus subtilis, and compared to the classical analyses. This new method of analysis of the functional domain network reveals that a specific inhibition on the second domain of the lipoamide dehydrogenase (pdhD) component of pyruvate dehydrogenase complex leads to the loss of all fluxes. Such conclusion was not predictable in the classical approach.
authors.affiliation: Laboratoire de Recherche en Informatique, Université Paris-Sud, CNRS UMR 8623 and INRIA Saclay, Orsay, France ; SysDiag UMR3145 CNRS/Bio-Rad Parc Euromédecine, Montpellier, France.
authors.forename: Sabine
authors.initials: S
authors.lastname: Pérès
authors.forename: Liza
authors.initials: L
authors.lastname: Felicori
authors.forename: Franck
authors.initials: F
authors.lastname: Molina
mesh_terms: D000255:Adenosine Triphosphate / Q000096:biosynthesis; D000465:Algorithms; D001412:Bacillus subtilis / Q000201:enzymology / Q000378:metabolism; D002384:Catalysis; D002952:Citric Acid Cycle; D003198:Computer Simulation; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D049490:Systems Biology
chemical_list: D000255:Adenosine Triphosphate