Team:NCTU Formosa/modeling

Measurement

A new measurement method can calculate the protein expression rate in the different E. coli population density for the protein expression device

In previous studies, the transcriptional strengths of promoter and transcriptional strengths of RBSs was defined as a constant values. But in biological concepts, we know the expression rates of most proteins decreased dramatically while the bacteria at the stationary phase. To overcome this problem, our team developed a new measurement method can calculate the protein expression activity of promoter_RBS device changes with cell density in the culture tube directly. We provide a simple polynomial equation which can describe linear relationship between the protein expression activity p(s) of promoter_RBS device and cell desity s (OD600).

where p0 denotes zero-order coefficient, p1 denotes first-order coefficient. We found that using this linear function to describe the activity of a protein expression device during log phase and stationary phase improved simulation results significantly. That means that the simple model equation can character a protein expression device (a promoter combined with a RBS) during cell grow from log phase to stationary phase. The fitting results indicate this hypothesis is reasonable. Furthermore, this model enable us to rational connect a promote_RBS device with different strength to obtain a target protein expression level in a synthetic genetic circuit.

In previous studies to model a protein expression, the transcription rates of promoters and translation rates of ribosome binding sites (RBSs) are defined as a constant value. However, the values are not constant during cell growth. For example, the transcription rates of promoters and the translation rates of RBSs are lager in log phase than bacteria growth in stationary phase. To overcome this problem, we selected four promoters and three RBSs with different regulation strength and constructed 12 protein expression devices which combine promoter, RBS and green fluorescent protein (GFP) in Escherichia coli. The GFP expression levels with time were measured using a flow cytometry, and the experimental data can used to characterize a protein expression rate of a protein expression device which contains a promoters and a RBS. A dynamic model that captured the experimentally observed differences for each protein expression device was developed in this study. Using this method, we can measurement the protein expression rate in the different E. coli population density for the protein expression device.

We selected four promoters and three RBSs with different regulation strength and constructed 12 protein expression devices which combine promoter, RBS and green fluorescent protein (GFP) in E. coli (Fig.1 &table.1). The GFP expression level with time was measured using a flow cytometry (Fig.3 &Fig.4)