Mitigation of ribosome competition through distributed sRNA feedback (extended version)

Abstract

A current challenge in the robust engineering of synthetic gene networks is context dependence, the unintended interactions among genes and host factors. Ribosome competition is a specific form of context dependence, where all genes in the network compete for a limited pool of translational resources available for gene expression. Recently, theoretical and experimental studies have shown that ribosome competition creates a hidden layer of interactions among genes, which largely hinders our ability to predict design outcomes. In this work, we establish a control theoretic framework, where these hidden interactions become disturbance signals. We then propose a distributed feedback mechanism to achieve disturbance decoupling in the network. The feedback loop at each node consists of the protein product transcriptionally activating a small RNA (sRNA), which forms a translationally inactive complex with mRNA rapidly. We illustrate that with this feedback mechanism, protein production at each node is only dependent on its own transcription factor inputs, and almost independent of hidden interactions arising from ribosome competition.