EctoGEM is a genome-scale metabolic network of Ectocarpus siliculosus.
This atlas of metabolic pathways consists of 1,866 reactions and 2,020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling, and manual refinement.
- Seed metabolites
- Target metabolites
- MetaCyc 17.0
A feedback questionnaire is available to propose changes to EctoGEM. Your modifications will be reviewed by our team and included in the next releases of EctoGEM.
Automatic reconstruction of EctoGEM, a functional metabolic network
The automatic reconstruction of the metabolic network of Ectocarpus siliculosus consists in the following steps:
- A first reconstruction was carried out with Pathway tools, based on available genome annotations and the metabolic reaction database MetaCyc. This draft metabolic network EctoGEM-annot contained 1,677 reactions and 1,889 metabolites.
- A second reconstruction was carried out based on protein orthology between E. siliculosus and A. thaliana. The list of A. thaliana enzymes was extracted from the AraGEM genome-scale metabolic network, and orthologous protein pairs between algal and plant sequences were detected by the InParanoid and the OrthoMCL tools. Results of these analyses were combined by the Pantograph tool in a draft metabolic network called EctoGEM-ortho that contained 786 reactions and 1,767 metabolites.
- To benefit from both approaches, EctoGEM-annot and EctoGEM-ortho were merged into a third metabolic network, called EctoGEM-combined. This required unifying identifiers of reactions and metabolites extracted from both the MetaCyc and the KEGG databases. It added 108 reactions and 92 metabolites to the annotation-based draft network EctoGEM-annot. EctoGEM-combined thus contained 1,785 reactions and 1,981 metabolites, illustrating the complementarity between the annotation- and the orthology-based approaches.
- To analyze the previous networks, we developed meneco, a method that uses qualitative constraints to test the producibility of a set of metabolites experimentally measured in E. siliculosus. This method is purely qualitative since it studies the topology of a network and the combinatorial interplays between pathways. Based on previous targeted metabolite profiling, 50 compounds (amino acids, sugars, polyols, fatty acids) were selected as biomass components. The analysis of the previous metabolic networks shows that, among the 50 target metabolites, EctoGEM-annot is able to produce 25 and EctoGEM-ortho is not able to produce any metabolites.
- To incorporate putative subcellular localization for the reactions, a similar approach was applied on chloroplast and mitochondrion genomes, leading to two metabolic network called ChloroGEM-combined and MitoGEM-combined respectively. ChloroGEM-combined contains 66 reactions and 136 metabolites, while MitoGEM-combined contains 22 reactions and 33 metabolites.
- Following a parsimony approach, the minimal number of reactions that must be taken from the MetaCyc 17.0 database - enriched with the two KEGG reactions producing eicosadienoic and docosanoic acid - to produce the 25 remaining targeted metabolites was computed. This assessment was performed with a constraint-based study using the meneco method. This added 55 reactions to EctoGEM-combined and produced a functional metabolic network called EctoGEM-functional. This metabolic network is able to produce the 50 target metabolites. Moreover, reactions and metabolites from ChloroGEM-combined and MitoGEM-combined were added to EctoGEM-functional. After this addition, EctoGEM-functional contains 1,851 reactions and 2,010 metabolites.
- To validate the automatic reconstruction process, and to investigate its reliability and completeness, we performed manual network curation based on expert review of both literature and HMM profiles to assess the existence of gene candidates in the algal genome. Special attention was paid to the reactions supported neither by annotation nor by orthology searches in order to use the metabolic network reconstruction as a way to discover new reactions for the sake of functional validation. The final metabolic network EctoGEM-1.0 contains 1,866 reactions and 2,020 metabolites.