CF-Targeter: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals
文献类型：期刊论文
| 作者 | Ding, Shaozhen1; Cai, Pengli1; Zhang, Dachuan1; Cheng, Xingxiang1; Sun, Dandan1; Hu, Qian-Nan1; Yuan, Le2; Tian, Yu2; Tu, Weizhong3; Chen, Junni3 |
| 刊名 | ACS SYNTHETIC BIOLOGY
 |
| 出版日期 | 2019 |
| 卷号 | 8期号:10页码:2280-2286 |
| 关键词 | chassis hosts selection genome-scale metabolic model theoretical yield heterologous pathway design |
| ISSN号 | 2161-5063 |
| DOI | 10.1021/acssynbio.9b00070 |
| 文献子类 | Article |
| 英文摘要 | Biosynthesis is a promising method for chemical synthesis. However, due to varieties between different microorganism hosts, yield and heterologous pathways needed for production of target chemical may also vary from different strains. One of the main challenges in metabolic engineering is to select an appropriate chassis host for specified target chemical production. However, with thousands of microorganisms existing in nature and extremely complicated metabolism within them, it is still time- consuming and error-prone work to achieve such a goal only through experimental methods, even with some existing computational methods. Hence, more efficient methods should be proposed to assist in selecting appropriate chassis hosts. In this article, based on symbolic reaction repositories and a pathway search algorithm which performed 1 400 000 searches for per target compound, we established a biological reasoning system for appropriate chassis host selection by coupling with various GEM-models. By using a supercomputer to calculate the biosynthetic pathways for more than 1 month, nearly 50 000 000 biosynthetic pathways are computed for production of 6026 compounds within 70 microorganisms. With retrieved organisms for specified target production, several heterologous biosynthetic pathways can be shown in length order, and then the maximum theoretical yields and thermodynamic feasibility can be calculated in real time under customized growth conditions and physiological states. From the computation results, the system not only identifies experimentally validated pathways but also outputs more efficient solutions with less heterologous steps or higher maximum possible theoretical yield by engineering other organism hosts. CF-targeter is available at http://www.rxnfinder.org/cf_targeter/ |
| 学科主题 | Cell Biology |
| WOS关键词 | SYNTHETIC BIOLOGY ; PATHWAYS ; ENZYMES ; DESIGN ; MODELS ; TOOL |
| 语种 | 英语 |
| CSCD记录号 | CSCD:31518497 |
| WOS记录号 | WOS:000492115800011 |
| 出版者 | AMER CHEMICAL SOC |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1218]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Univ Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai Inst Nutr & Hlth, CAS MPG Partner Inst Computat Biol,CAS Key Lab Co, Shanghai 200333, Peoples R China; 2.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China; 3.Wuhan LifeSynther Sci & Technol Co Ltd, Wuhan 430070, Hubei, Peoples R China, |
| 推荐引用方式 GB/T 7714 | Ding, Shaozhen,Cai, Pengli,Zhang, Dachuan,et al. CF-Targeter: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals[J]. ACS SYNTHETIC BIOLOGY,2019,8(10):2280-2286. |
| APA | Ding, Shaozhen.,Cai, Pengli.,Zhang, Dachuan.,Cheng, Xingxiang.,Sun, Dandan.,...&,.(2019).CF-Targeter: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals.ACS SYNTHETIC BIOLOGY,8(10),2280-2286. |
| MLA | Ding, Shaozhen,et al."CF-Targeter: A Rational Biological Cell Factory Targeting Platform for Biosynthetic Target Chemicals".ACS SYNTHETIC BIOLOGY 8.10(2019):2280-2286. |
入库方式： OAI收割
来源：上海营养与健康研究所
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