Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids.
Building a minimal and generalizable model of transcription factor-based biosensors: Showcasing flavonoids.
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构建基于转录因子的最小和可推广的生物传感器模型：展示类黄酮。
DOI：
10.1002/bit.26726
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发表时间：
2018-09
影响因子：
3.8
通讯作者：
Faulon JL
中科院分区：
文献类型：
--
作者：
Trabelsi H;Koch M;Faulon JL
合成生物学工具的进步已经改变了我们设计活细胞的方式。电路设计的应用已经达到了一个新的水平，为代谢工程的挑战提供了解决方案，包括开发途径变体库的筛选方法。利用基于转录因子的生物传感器进行筛选已显示出良好的结果，但传感器与被测分子之间的定量关系仍需要更合理的理解。在此，我们已经成功地开发了一种基于转录调节因子的新型生物传感器来检测匹诺匹纳松蛋白。已知对柚皮素有反应的FdeR转录因子（TF）与荧光报告蛋白结合。通过组合文库改变其质粒的拷贝数和生物传感器TF的浓度，记录和模拟了不同的反应。拟合的模型提供了一种工具，可以了解这些参数对生物传感器在剂量-反应和时间曲线方面的行为的影响，并为构建面向提高灵敏度和/或在更高滴度下线性检测能力的结构提供指导。我们的模型是第一个使用Hill - based形式主义明确考虑到质粒拷贝数对生物传感器灵敏度的影响的模型，能够在不了解TF特性的情况下解释未表征的系统。此外，它可以用来模拟生物传感器对不同化合物（这里是柚皮素和皮诺曹蛋白）的响应，只需最小的参数修改。
Progress in synthetic biology tools has transformed the way we engineer living cells. Applications of circuit design have reached a new level, offering solutions for metabolic engineering challenges that include developing screening approaches for libraries of pathway variants. The use of transcription‐factor‐based biosensors for screening has shown promising results, but the quantitative relationship between the sensors and the sensed molecules still needs more rational understanding. Herein, we have successfully developed a novel biosensor to detect pinocembrin based on a transcriptional regulator. The FdeR transcription factor (TF), known to respond to naringenin, was combined with a fluorescent reporter protein. By varying the copy number of its plasmid and the concentration of the biosensor TF through a combinatorial library, different responses have been recorded and modeled. The fitted model provides a tool to understand the impact of these parameters on the biosensor behavior in terms of dose–response and time curves and offers guidelines to build constructs oriented to increased sensitivity and or ability of linear detection at higher titers. Our model, the first to explicitly take into account the impact of plasmid copy number on biosensor sensitivity using Hill‐based formalism, is able to explain uncharacterized systems without extensive knowledge of the properties of the TF. Moreover, it can be used to model the response of the biosensor to different compounds (here naringenin and pinocembrin) with minimal parameter refitting.
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DOI：
10.1021/ci010132r
发表时间：
2002-11-01
期刊：
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
影响因子：
--
作者：
Durant, JL;Leland, BA;Nourse, JG
通讯作者：
Nourse, JG
DOI：
10.1073/pnas.1409523111
发表时间：
2014-12-16
影响因子：
11.1
作者：
Raman, Srivatsan;Rogers, Jameson K.;Church, George M.
通讯作者：
Church, George M.
影响因子：
14.9
作者：
Kim S;Thiessen PA;Bolton EE;Chen J;Fu G;Gindulyte A;Han L;He J;He S;Shoemaker BA;Wang J;Yu B;Zhang J;Bryant SH
通讯作者：
Bryant SH
影响因子：
64.8
作者：
Looger, LL;Dwyer, MA;Hellinga, HW
通讯作者：
Hellinga, HW
影响因子：
8.4
作者：
Pfleger, Brian F.;Pitera, Douglas J.;Keasling, Jay D.
通讯作者：
Keasling, Jay D.