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Construction and analysis of an integrated biological network of Escherichia coli

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Abstract

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.

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Data availability

The datasets supporting the conclusions of this article are included at GitHub: https://github.com/maozhitao/EcoIN.

Code availability

All analysis codes supporting the conclusions of this article are included at GitHub: https://github.com/maozhitao/EcoIN.

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Acknowledgements

This work was supported by the National Key Research and Development Program of China (2018YFA0900300, 2018YFA0901400); the International Partnership Program of Chinese Academy of Sciences (153D31KYSB20170121); Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project (TSBICIP-PTJS-001, TSBICIP-KJGG-005).

Funding

Publication costs are funded by the National Key Research and Development Program of China (2018YFA0900300, 2018YFA0901400); the International Partnership Program of Chinese Academy of Sciences (153D31KYSB20170121); Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project (TSBICIP-PTJS-001, TSBICIP-KJGG-005).

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Authors and Affiliations

  1. Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China

    Zhitao Mao, Teng Huang, Qianqian Yuan & Hongwu Ma

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Zhitao Mao

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ZM and HM participated in the design of the study. ZM collected and analyzed the data. ZM and TH designed the online website. ZM, HM, TH and QY wrote and edited the manuscript. All authors revised and approved the final manuscript.

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Correspondence to Hongwu Ma.

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Mao, Z., Huang, T., Yuan, Q. et al. Construction and analysis of an integrated biological network of Escherichia coli. Syst Microbiol and Biomanuf 2, 165–176 (2022). https://doi.org/10.1007/s43393-021-00051-x

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