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EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli.

Abstract：

:Developing computational tools for a chassis-centered biosynthetic pathway design is very important for a productive heterologous biosynthesis system by considering enormous foreign biosynthetic reactions. For many cases, a pathway to produce a target molecule consists of both native and heterologous reactions when utilizing a microbial organism as the host organism. Due to tens of thousands of biosynthetic reactions existing in nature, it is not trivial to identify which could be served as heterologous ones to produce the target molecule in a specific organism. In the present work, we integrate more than 10,000 E. coli non-native reactions and utilize a probability-based algorithm to search pathways. Moreover, we built a user-friendly Web server named EcoSynther. It is able to explore the precursors and heterologous reactions needed to produce a target molecule in Escherichia coli K12 MG1655 and then applies flux balance analysis to calculate theoretical yields of each candidate pathway. Compared with other chassis-centered biosynthetic pathway design tools, EcoSynther has two unique features: (1) allow for automatic search without knowing a precursor in E. coli and (2) evaluate the candidate pathways under constraints from E. coli physiological states and growth conditions. EcoSynther is available at http://www.rxnfinder.org/ecosynther/ .

journal_name

ACS Chem Biol

journal_title

ACS chemical biology

authors

Ding S,Liao X,Tu W,Wu L,Tian Y,Sun Q,Chen J,Hu QN

doi

10.1021/acschembio.7b00605

subject

Has Abstract

pub_date

2017-11-17 00:00:00

pages

2823-2829

issue

11

eissn

1554-8929

issn

1554-8937

journal_volume

12

pub_type

杂志文章

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