SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization

Abstract

Background: A comprehensive metabolism network of engineered E. coli is very important in systems biology and metabolomics studies. Many tools focus on two-dimensional space to display pathways in metabolic network. However, the usage of three-dimensional visualization may help to understand better the intricate topology of metabolic and regulatory networks.

Methods: We manually curated large amount of experimental data (including pathways, reactions and metabolites) from literature related with different types of engineered E. coli and then utilized a novel technology of three dimensional visualization to develop a comprehensive metabolic network named SynBioEcoli.

Results: SynBioEoli contains 740 biosynthetic pathways, 3,889 metabolic reactions, 2,255 chemical compoundsmanually curated from about 11,000 metabolism publications related with different types of engineered E. coli. Furthermore, SynBioEcoli integrates with various informatics techniques.

Conclusions: SynBioEcoli could be regarded as a comprehensive knowledgebase of engineered E. coli and represents the next generation cellular metabolism network visualization technology. It could be accessed via web browsers (such as Google Chrome) supporting WebGL, at http://www.rxnfinder.org/synbioecoli/.

Graphical abstract

Keywords

engineered E. coli / three dimensional metabolic network / biosynthetic ability

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ACKNOWLEDGEMENTS

This work was supported by the National Science Foundation of China (Nos. 31270101 and 31570092), the national high technology research and development program (No. 2012CB721000) and the Natural Science Foundation of Tianjin, China.

This article does not contain any studies with human or animal subjects performed by any of the authors.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Weizhong Tu, Shaozhen Ding, Ling Wu, Zhe Deng, Hui Zhu, Xiaotong Xu, Chen Lin, Chaonan Ye, Minlu Han, Mengna Zhao, Juan Liu, Zixin Deng, Junni Chen, Dong-Qing Wei and Qian-Nan Hu declare they have no conflict of interests.

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2017 Higher Education Press and Springer-Verlag Berlin Heidelberg