Resource Allocation and Whole Cell Response in Heterologous Gene Expression

The expression of exogenous proteins triggers physiological changes in the host cell, usually leading to decreased growth due to consumption of cellular resources. This loading-effect results in undesired cross-interactions and can cause many of the unpredictable behaviours characteristic of the failures common to synthetic biology. Working in standard E. colistrains, we show here that the ‘load’ of exogenous expression mainly impacts on the cell’s translational resources and that this effect can be measured with a plate-based assay and predicted by a mathematical model of protein synthesis. We demonstrate that for the control of gene expression, riboswitches are less costly for the cell compared to equivalent transcription factor regulators, due to fewer resources being required for the production of RNA parts compared to proteins.

Extending from this we show preliminary RNAseq analysis of the E. coli transcriptome response to induced exogenous expression in the cell. Transcriptome profiling by this method provides a route to identify native genes whose expression changes in response to burden. We find that expression of many genes associated with general stress response, including ibpA, htpG, dnaK and lon, rapidly increase in the first 15 minutes of synthetic overexpression from an engineered plasmid. These native genes are thus useful biomarkers for host cell stress response to exogenous expression and their promoters can be exploited to engineer future burden-based feedback genetic devices.