Examining the Tradeoffs Between Protein Quantity and Quality in Synthetic Biology

View all posters

Thomas Gorochowski, Johannes A. Roubos, Roel A.L. Bovenberg

DSM and EU ITN-NICHE program on understanding cellular stress, Netherlands

Synthetic biology makes extensive use of protein machinery to enable, regulate and extend cellular capabilities. Due to the difficulties in creating functional proteins de novo most systems to date have relied on natural diversity, combining genetic parts from multiple organisms into a common chassis. By expressing these genes and connecting them together in novel ways, larger systems can be built. While this approach has enabled the development of sensor systems able to signal the presence of chemicals and detect spatial boundaries, it relies on the ability of genes taken from one organism to be functionally expressed in another. Often this is not the case with extensive `tuning’ required to create a fully working part or device. Problems stem from differences in the native and required expression levels causing production of inactive aggregated forms or misfolded proteins, divergent codon usages across organisms affecting translational dynamics, and in some cases the protein being toxic to the host. To better understand the influence of these factors, we designed a set of expression constructs for multiple proteins known to be either easy or difficult to express in E. coli. Experiments will be performed to measure both the quantity (concentration) and quality (enzymatic activity) of these proteins produced in different ways. By varying the promoter strength (mRNA copy number), RBS strength (translational initiation rate), and codon usage (ribosomal movement speed), we will be able to examine how both the mode of expression and coding sequence play a role in the forms of protein product produced. This will provide insight into the inherent tradeoffs between protein quantity and quality. Result will become available first half 2013. As the ambitions of synthetic biology grow, studies like this will be essential for gaining sufficient foundational knowledge to ensure synthetic parts work as intended in differing contexts.