EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli,ACS Chemical Biology

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EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli
ACS Chemical Biology ( IF 3.5 ) Pub Date : 2017-10-12 00:00:00 , DOI: 10.1021/acschembio.7b00605
Shaozhen Ding _{1,

2} , Xiaoping Liao ₂ , Weizhong Tu ₃ , Ling Wu ₂ , Yu Tian _{2,

4} , Qiuping Sun ₂ , Junni Chen ₃ , Qian-Nan Hu _{1,

2}

Affiliation

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/.

中文翻译：

EcoSynther：一个定制的平台，以探索大肠杆菌的生物合成潜能

通过考虑大量的国外生物合成反应，开发以底盘为中心的生物合成途径设计的计算工具对于生产性异源生物合成系统非常重要。在许多情况下，当利用微生物作为宿主生物时，产生靶分子的途径既包括天然反应，也包括异源反应。由于自然界存在成千上万的生物合成反应，因此确定哪些可以用作异源反应在特定生物体中产生目标分子并非易事。在目前的工作中，我们整合了超过10,000个大肠杆菌非本地反应，并利用基于概率的算法来搜索路径。此外，我们构建了一个名为EcoSynther的用户友好型Web服务器。它能够探索在大肠杆菌K12 MG1655中产生靶分子所需的前体和异源反应，然后应用通量平衡分析来计算每个候选途径的理论产率。与其他以底盘为中心的生物合成途径设计工具相比，EcoSynther具有两个独特功能：（1）无需知道大肠杆菌中的前体即可进行自动搜索；（2）在受到大肠杆菌生理状态和生长限制的情况下评估候选途径条件。可从http://www.rxnfinder.org/ecosynther/获得EcoSynther。

更新日期：2017-10-12

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