title: The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.
abstract: Brown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post-genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome-scale metabolic network for E. siliculosus, EctoGEM (http://ectogem.irisa.fr). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co-factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models.
authors: Université de Rennes 1, IRISA UMR 6074, Campus de Beaulieu, 35042, Rennes, France; CNRS, IRISA UMR 6074, Campus de Beaulieu, 35042, Rennes, France; Centre Rennes-Bretagne-Atlantique, Projet Dyliss, INRIA, Campus de Beaulieu, 35042, Rennes Cedex, France.
authors: Sylvain
authors: S
authors: Prigent
authors: Guillaume
authors: G
authors: Collet
authors: Simon M
authors: SM
authors: Dittami
authors: Ludovic
authors: L
authors: Delage
authors: Floriane
authors: F
authors: Ethis de Corny
authors: Olivier
authors: O
authors: Dameron
authors: Damien
authors: D
authors: Eveillard
authors: Sven
authors: S
authors: Thiele
authors: Jeanne
authors: J
authors: Cambefort
authors: Catherine
authors: C
authors: Boyen
authors: Anne
authors: A
authors: Siegel
authors: Thierry
authors: T
authors: Tonon
mesh_terms: D018745:Genome, Plant; D008969:Molecular Sequence Data; D000459:Phaeophyceae / Q000235:genetics / Q000378:metabolism / Q000502:physiology*
keywords: Ectocarpus siliculosus; brown algae; gap filling; metabolic network; molybdenum co-factor biosynthesis; synthesis of aromatic amino acids; systems biology