Construction and analysis of an integrated biological network of Escherichia coli

Escherichia coli is a model organism with a clear genetic background that is widely used in metabolic engineering and synthetic biology research. To gain a complete picture of the complexly metabolic and regulatory interactions in E. coli, researchers often need to retrieve information from various databases which cover different types of interactions. A central one-stop service integrating various molecular interactions in E. coli would be helpful for the community. We constructed a database called E. coli integrated network (EcoIN) by integrating known molecular interaction information from databases and literature. EcoIN contains nearly 160,000 pairs of interactions and users can easily search the different types of interacting partners for a metabolite, gene or protein, and thus gain access to a more comprehensive interaction map of E. coli. To illustrate the application of EcoIN, we used the full path algorithm to identify metabolic feedback/feedforward regulatory loops having at least two different types of regulatory interactions. Applying this algorithm to analyze the regulatory loops for the amino acid biosynthetic pathways, we found some multi-step regulation loops which may affect the metabolic flux and are potential new engineering targets. The EcoIN database is freely accessible at http://ecoin.ibiodesign.net/ and analysis codes are available at GitHub: https://github.com/maozhitao/EcoIN .