EcoSynther—E.coli生物合成潜力挖掘能手
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- 英文论文题名：EcoSynther:biosynthetic potential explorer of E.coli
- 论文作者：丁邵珍 ; 廖小平 ; 涂伟忠 ; 吴玲 ; 胡黔楠
- 英文论文作者：Shaozhen Ding ; Xiaoping Liao ; Weizhong Tu ; Ling Wu ; Qian-Nan Hu ; Pharmaceutical Sciences ; University of Wuhan ; Key Laboratory of Systems Microbial Biotechnology ; Tianjin Institute of Industrial Biotechnology ; Chinese Academy of Sciences
- 年：2016
- 作者机构：武汉大学药学院组合生物合成与新药发现教育部重点实验室;中国科学院天津工业生物技术研究所;
- 论文关键词：生物合成 ; 途径设计 ; E.coli合成潜力挖掘 ; 途径评估
- 会议召开时间：2016-07-01
- 会议录名称：中国化学会第30届学术年会摘要集-第二十八分会：化学生物学
- 语种：中文
- 分类号：Q81
- 学会代码：ZGHY
- 会议名称：中国化学会第30届学术年会-第二十八分会 ; 化学生物学
- 会议地点：中国辽宁大连
- 主办单位：中国化学会
- 学会名称：中国化学会
- 页数：1
- 文件大小：180k
- 原文格式：D
- 会议级别：全国
摘要
生物合成在利用前体化合物高效合成大宗化学品,生物燃油以及天然产品等高附加值化合物的应用中发挥重要角色,对微生物生产目标化合物合成途径中涉及到的内源以及外源反应的探索是代谢工程的重难点。EcoSynther利用反应数据库Rhea中将近10,000条质量和电荷平衡的反应为外源反应数据源,并整合野生型E.coli K12 MG1655代谢网络模型中内源反应,利用途径搜索的概率分析算法计算在设置的外源反应步数内合成目标化合物所需要的外源反应,并利用平衡流量分析方法对每一条合成途径效率进行量化评估。EcoSynther利用计算机全面系统模拟生产目标化合物的E.coli菌株在选择生长条件下(底物供给,有氧情况)细胞整体代谢,目标化合物合成途径以及量化合成情况,能够为实验方案设计提供指导建议。我们拟汇报在构建微生物细胞工厂设计技术体系过程中,在目标化合物选择,生物合成途径设计以及途径评估等方面取得的进展[1-6]。
One of the most promising applications of biosynthetic methods is to produce chemical products of high value from the ready-made chemicals,It is significant for metabolic engineering to explore the native and heterologous reactions needed to synthesize valuable chemicals produced by a microorganism.EcoSynther utilizes the Rhea database as the heterologous reactions source which contains more than 10,000 reactions,and the metabolism network model of Ecoli K12 Mg1655 as the native reactions,an algorithm based probability was used to design pathway involved in finitely heterologous reactions and FBA algorithm was used to calculate the production rate of each candidate pathway.EcoSynther utilizes computer to simulate the metabolism physiological in E.coli on the selected growth condition,and give several candidate pathway and then assess their efficiency.Several aspects of progress will be displayed in the report.
One of the most promising applications of biosynthetic methods is to produce chemical products of high value from the ready-made chemicals,It is significant for metabolic engineering to explore the native and heterologous reactions needed to synthesize valuable chemicals produced by a microorganism.EcoSynther utilizes the Rhea database as the heterologous reactions source which contains more than 10,000 reactions,and the metabolism network model of Ecoli K12 Mg1655 as the native reactions,an algorithm based probability was used to design pathway involved in finitely heterologous reactions and FBA algorithm was used to calculate the production rate of each candidate pathway.EcoSynther utilizes computer to simulate the metabolism physiological in E.coli on the selected growth condition,and give several candidate pathway and then assess their efficiency.Several aspects of progress will be displayed in the report.
引文
[1]Weizhong Tu;Haoran Zhang;Liu J(*);Qian-Nan(*).Bioinformatics,2016 32(3):472
[2]Wang CH,Liu J(*),Luo F,Deng ZX,Hu,Qian-Nan(*).BMC Systems Biology,2015,9:S2.
[3]Hu,Qian-Nan(*),Z Deng.CPT Pharmacometrics Syst.Pharmacol,2014,3:el05.
[4]Cao,Dong-Sheng,Liang,Yi-Zeng(*),Deng,Zhe,Hu,Qian-Nan(*),He,Min,Xu,Qing-Song,Zhou,Guang-Hua,Zhang,Liu-Xia,Deng,Zi-xin,Liu,Shao.PLOS ONE,2013,8(4):e57680.
[5]Hu,Qian-Nan(*),Zhu,Hui,Li,Xiaobing,Zhang,Manman,Deng,Zhe,Yang,Xiaoyan,Deng,Zixin.PLos One,2012,7(12).
[6]Hu,Qian-Nan(*),Deng,Zhe,Hu,Huanan,Cao,Dong-Sheng,Liang,Yi-Zeng.Bioinformatics,2011,27(17):2465
[2]Wang CH,Liu J(*),Luo F,Deng ZX,Hu,Qian-Nan(*).BMC Systems Biology,2015,9:S2.
[3]Hu,Qian-Nan(*),Z Deng.CPT Pharmacometrics Syst.Pharmacol,2014,3:el05.
[4]Cao,Dong-Sheng,Liang,Yi-Zeng(*),Deng,Zhe,Hu,Qian-Nan(*),He,Min,Xu,Qing-Song,Zhou,Guang-Hua,Zhang,Liu-Xia,Deng,Zi-xin,Liu,Shao.PLOS ONE,2013,8(4):e57680.
[5]Hu,Qian-Nan(*),Zhu,Hui,Li,Xiaobing,Zhang,Manman,Deng,Zhe,Yang,Xiaoyan,Deng,Zixin.PLos One,2012,7(12).
[6]Hu,Qian-Nan(*),Deng,Zhe,Hu,Huanan,Cao,Dong-Sheng,Liang,Yi-Zeng.Bioinformatics,2011,27(17):2465