Retropath: Automated Pipeline for Embedded Metabolic Circuits

被引:61
作者
Carbonell, Pablo [1 ]
Parutto, Pierre [1 ]
Baudier, Claire [1 ]
Junot, Christophe [2 ]
Faulon, Jean-Loup [1 ]
机构
[1] Univ Evry, CNRS, iSSB, F-91000 Evry, France
[2] CEA, Ctr Etud Saclay, F-91190 Gif Sur Yvette, France
来源
ACS SYNTHETIC BIOLOGY | 2014年 / 3卷 / 08期
关键词
synthetic biology; circuits; metabolic network; biosynthesis; biosensor; regulation; ELEMENTARY FLUX MODES; ESCHERICHIA-COLI; SYSTEMS BIOLOGY; CEREBROSPINAL-FLUID; DESIGN; MICROORGANISMS; BIOSYNTHESIS; HOMEOSTASIS; EVOLUTION; PATHWAYS;
D O I
10.1021/sb4001273
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Metabolic circuits are a promising alternative to other conventional genetic circuits as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent applications such as smart therapeutics, however, require circuits that enable sensing and regulation. Here, we present RetroPath, an automated pipeline for embedded metabolic circuits that explores the circuit design space from a given set of specifications and selects the best circuits to implement based on desired constraints. Synthetic biology circuits embedded in a chassis organism that are capable of controlling the production, processing, sensing, and the release of specific molecules were enumerated in the metabolic space through a standard procedure. In that way, design and implementation of applications such as therapeutic circuits that autonomously diagnose and treat disease, are enabled, and their optimization is streamlined.
引用
收藏
页码:565 / 577
页数:13
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