Rational design of modular circuits for gene transcription: A test of the bottom-up approach

We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure.This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.Synthetic biology has evolved to the point where the design of gene circuits with complex functionalities has become a real option [1]. Inside living cells, complex behaviors arise from molecular interplays in complicated regulatory networks. In the first instance, the ability to isolate single elements from these regulatory networks - and to use them as independent modules - makes synthetic biology possible [2]. Synthetic gene circuits are thus created by assembling elementary modules together. The increasing complexity of these synthetic gene networks asks for a rational approach to design gene circuits [3]. A possible strategy to tackle this complexity is the bottom-up approach [4-7]. In bottom-up design, the behavior of a complicated system is predicted from the characteristics of its elementary parts. Such a prediction requires well-characterized mathematical models of these elementary parts, and of how they behave when assembled together. In the presen