Cell Factory Design

Microbial cell factories have a lot of important and promising applications in producing bulk chemicals, natural products, biofuels, and so on. The new bottleneck of microbial cell factory is how to design reaction, enzyme, and pathway, based on enormous biosynthesis data.Our team has been focused on the construction of data-driven biosynthesis design platform (www.rxnfinder.org), which is composed of the following sections: (1) Biochemical reaction database (RxnFinder): our team manually curated more than 300,000 biochemical reactions, which are 10 times larger than the KEGG reactions, from more than 550,000 biosynthesis references retrieved from PubMed using more than 40 biosynthesis related keywords. More than 10 third party databases are linked, and more than 10 informatics methods are provided. (2) Enzyme discovery (ECAssignment): a chemical transformation-based method (ECAssigner) is proposed for enzyme discovery using biochemical reaction difference fingerprints and reaction similarity.(3) Biosynthetic pathway design (BioSynther): BioSynther tool was developed to design biosynthesis pathways between starting molecules and target molecules, in which users can interactively re-design biosynthetic pathways. One of the most promising applications of biosynthetic methods is to produce chemical products of high value from the ready-made chemicals. BioSynther is also developed to explore the biosynthetic potentials of precursor chemicals using BKM-react, Rhea, and more than 300,000 in house RxnFinder reactions manually curated. (4) Cell -based pathway optimization platform (SynBioEcoli, EcoSynther, LifeSynther): Based on the comprehensive biosynthetic data curated above, whole-cell modelling methods are proposed to optimize heterogeneous biosynthetic pathways. The proposed data-driven one-stop informatics platform could be used as a useful tool in metabolic engineering, biosynthesis, and synthetic biology.