Abraha Biruck Woldai, Marchisio Mario Andrea
School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
Front Bioeng Biotechnol. 2022 Mar 11;10:845240. doi: 10.3389/fbioe.2022.845240. eCollection 2022.
In 2008, we were among the first to propose a method for the visual design and modular modeling of synthetic gene circuits, mimicking the way electronic circuits are realized . Basic components were DNA sequences that could be composed, first, into transcription units (TUs) and, then, circuits by exchanging fluxes of molecules, such as PoPS (polymerase per second) and RiPS (ribosomes per seconds) as suggested by Drew Endy. However, it became clear soon that such fluxes were not measurable, which highlighted the limit of using some concepts from electronics to represent biological systems. SBML Level 3 with the package permitted us to revise circuit modularity, especially for the modeling of eukaryotic networks. By using the libSBML Python API, TUs-rather than single parts-are encoded in SBML Level 3 files that contain species, reactions, and , i.e., the interfaces that permit to wire TUs into circuits. A circuit model consists of a collection of SBML Level 3 files associated with the different TUs plus a "main" file that delineates the circuit structure. Within this framework, there is no more need for any flux of molecules. Here, we present the SBML Level 3-based models and the wet-lab implementations of Boolean NOT gates that make use, in the yeast , of the bacterial ClpX-ClpP system for protein degradation. This work is the starting point towards a new piece of software for the modular design of eukaryotic gene circuits and shows an alternative way to build genetic Boolean gates.
2008年，我们率先提出了一种用于合成基因电路视觉设计和模块化建模的方法，模仿电子电路的实现方式。基本组件是DNA序列，首先可以将其组合成转录单元（TU），然后按照德鲁·恩迪（Drew Endy）的建议，通过交换分子通量（如每秒聚合酶数（PoPS）和每秒核糖体数（RiPS））来构建电路。然而，很快就清楚地发现，这种通量是无法测量的，这凸显了使用电子学中的一些概念来表示生物系统的局限性。带有该软件包的SBML Level 3使我们能够修正电路模块化，特别是对于真核网络的建模。通过使用libSBML Python应用程序编程接口（API），转录单元（而非单个部件）被编码在包含物种、反应和接口（即允许将转录单元连接成电路的接口）的SBML Level 3文件中。一个电路模型由与不同转录单元相关联的一组SBML Level 3文件以及一个描绘电路结构的“主”文件组成。在这个框架内，不再需要任何分子通量。在这里，我们展示了基于SBML Level 3的模型以及在酵母中利用细菌ClpX-ClpP系统进行蛋白质降解的布尔非门的湿实验室实现。这项工作是开发用于真核基因电路模块化设计的新软件的起点，并展示了构建遗传布尔门的另一种方法。
