Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli

Cell burden impacts the performance of engineered genetic constructs with great interest towards the development of tools to track it and improve biotechnology applications. Fluorogenic RNA aptamers are excellent candidates for live monitoring of burden because their production is expected to impose negligible load on the host. Here, we characterised a library of aptamers when expressed from different promoters in two Escherichia coli strains. We found that aptamer performance is dependent on the context of expression, and that, contrary to expectation, aptamer production impacts host fitness. We then built a library of burden-responsive biosensors testing their response to heterologous expression. The tRNA-Broc biosensor was selected for its fluorescence response, minimal impact on growth and ability to differentiate the burden imposed by different expression levels and constructs. The biosensor developed here adds to the collection of tools available to characterise burden and support applications where improved host performance is sought.