Deep mutational scanning of RNA-binding protein ProQ suggests a mechanism of quality control by protease Lon

ProQ has become a paradigm for the emerging family of FinO domain-containing RNA binding proteins. ProQ in Salmonella enterica has been shown to act as a global RNA binding protein as it interacts with a plethora of sRNAs and mRNAs. However, little was known about processes ProQ regulates in Salmonella which have precluded to functionally characterize ProQ in vivo. In here, we show that ProQ represses the utilization of succinate as carbon source. The latter allowed applying deep mutational scanning to ProQ to identify residues within the protein important to its function in vivo. ProQ carries a FinO domain, responsible for RNA binding, as its N-terminal domain fused via a linker to a C-terminal domain with unknown function. Remarkably, residues within both the N-terminal domain and C-terminal domain of the protein are found to be essential for ProQ function. Mutations in the C-terminal lead to non-fuctional variants to regulate succinate utilization but capable to interact with RNA. On the contrary, mutations on the N-terminal domain leave ProQ functionally inactive to regulate ProQ function in vivo and to interact with RNA. Notably, the inability to interact with RNA render ProQ unstable. The latter leads to an active Lon protease mediated degradation suggesting that interaction with RNA represents a control mechanism to modulate ProQ turnover. Functional residues of ProQ were mapped via deep mutational scanning using the growth phenotype under succinate as a selection pressure for a non-functional protein. A resulting Mutant was used to perform a co-immunoprecipitation (CoIP) experiment to validate its inability to bind RNA.