Modeling and analysis of gene expression mechanisms: a communication theory approach

The increase in the availability of genetic data in the last years is prompting the efforts to use tools from communications engineering for the understanding of genetic information. Processes in molecular biology can be modeled through the use of these tools. A communication theory based model for the process of translation in gene expression is proposed. The model is based on the assumption that the ribosome decodes the mRNA sequences using the 3´ end of the 16SrRNA molecule as a one dimensional codebook. The biological consistency of the model is proven in the detection of the Shine-Dalgarno signal and the initiation codon for translation initiation. Furthermore, implications on the role of the 16SrRNA 3´ end in the complete process of prokaryotic translation are presented and discussed. Interestingly, the obtained results lay out the possibility of an interaction of this part of the ribosome in the process of translation termination. Finally, results obtained via the proposed model are compared with published experimental results for different mutations of the rRNA molecule. Total agreement between both sets of results proves the validity of the proposed model. By means of simulated mutations in the last 13 bases of the 16SrRNA, a global analysis of this part of the ribosome in the process of translation is established. This work illustrates the relevance of communication theory based models for genetic regulatory systems.