Korn, R. J.; Meyer, M. M.

RNA-based control of gene expression is common across all domains of life, yet shows extraordinary variety in terms of environmental cues recognized, mechanisms of action, and magnitude of gene expression changes. Furthermore, the fitness benefit conferred to an organism by RNA-induced regulation is often subtle and challenging to measure. In this work we measure the relative fitness conferred by all single mutants of an FMN riboswitch to the opportunistic pathogen Streptococcus pneumoniae under five distinct conditions. We find that in standard culture conditions the RNA sequence is not under strong selection, however the dynamic conditions encountered during mouse lung infection reveal an element that is mutationally robust, but also under weak purifying selection. Furthermore, fitness landscapes measured in the presence of two different targeting antibiotics reveal suites of mutations that confer constitutive activation or repression, which in turn provide insights into the mechanism of action for this RNA with lessons broadly applicable to interpretation of bacterial transcriptomics.