Optimization of Cellular Resource Allocation Using Global mRNA Decay

The behavior of synthetic circuits is shaped by the availability of cellular resources and the context of the host cell as the heterologous pathway relies on host transcription-translation machinery. Global control mechanisms for host gene expression could be used to optimize cellular resource allocation by decoupling the synthetic pathway and the host cell. Inspired by viral strategies that hijack cellular resources using global mRNA decay, we developed a control system to modulate resource allocation between the host and a synthetic pathway. This mechanism exhibits a fast response and can re-distribute ribosomes. A sequence-specific RNA degrading toxin from E. coli was used to trigger global mRNA decay while protecting the target gene(s) of interest. Our approach demonstrates a significant enhancement of protected gene expression and relies on the presence of negative feedback loop and specific induction timing. To optimize and understand the system, genome-wide measurements of RNA and protein levels were used to identify critical target genes for protection and provide key insights into the cellular response to the toxin. These measurements revealed a two-phase dynamic behavior in which transcript abundance is significantly reduced followed by a delayed activation in a set of target genes.