Team:Tianjin/Modeling/Expression

Background

Within our chassis bacteria, the protein expression system is special because there are two channels to express the protein: the canonical channel exists within any wild type bacteria and the orthogonal channel created artificially with the help of orthogonal ribosomes and orthogonal mRNA whose protein expression is relatively independent of the canonical ones. There are two kinds of ribosome and mRNA: host ribosome (also known as normal ribosome, canonical ribosome or n-ribosome) orthogonal-ribosome (also known as o-ribosome), normal-mRNA with canonical RBS sequence (abbreviate as n-mRNA) and orthogonal mRNA with artificial RBS sequence which cannot complement with canonical 16S sequence) within the chassis bacteria. The canonical mRNA with normal RBS sequence, which is inborn within the bacteria, can express protein with the help of canonical ribosome. In particular, o-ribosomes can also translate genes with altered Shine-Dalgarno (SD) sequences not recognized by host ribosomes. </b>

In the case of o-ribosomes, mutations are introduced into the ASD region such that they can base pair with complementary, noncanonical SD sequences not recognized by host ribosomes. However, we are not familiar with the internal mechanism of how the two kinds of mRNA interact with the two kinds of ribosomes to express the two kinds of protein. In order to investigate the mechanism of how the four components interact with each other within our chassis bacteria, we simulate the whole process through mathematical modeling.

Modeling Necessity and Objective

As shown in Figure 1, there are two kinds of ribosome and two mRNA with two orthogonal RBS sequence. There can be four kinds of interactions between the four components. The combination of the canonical ribosome with the canonical RBS sequence, o-ribosome with o-RBS, the inter combination of the canonical ribosome with o-RBS and that of the canonical RBS with o-ribosome. However, there are many questions which are unclear to us and thus need answering: How can the orthogonal mRNA express their encoded protein? How can the two proteins expressed system interact with each other? Since there are too much known about the mechanism of the protein expressed with coexistence of two protein expression system. Thus, our goal of modeling is to describe the whole process with the help of mathematical tool and to predict the result of the wet lab. Specifically, there are two goals: the verification of orthogonality and the prediction of protein expressed after introducing the orthogonal system by two steps.