Interrogation of RNA-protein interaction dynamics in bacterial growth

RNA-protein interactions are fundamental for bacterial homeostasis. However, we lack a system-wide understanding of their dynamics upon environmental perturbation. In this study, we have characterised the dynamics of 91% of the Escherichia coli proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and reveal novel RBP functions for proteins like the chaperone HtpG, a new tRNA-binding protein. Moreover, we characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mainly present in Proteobacteria, two of them have human orthologs in the form of mitochondrial proteins associated with rare metabolic disorders. Altogether, we provide the first dynamic RBPome of a bacterium, showcasing how this approach can reveal the function of uncharacterised proteins, and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies. Individual-nucleotide resolution UV cross-linking and immunoprecipitation-sequencing (iCLIP-seq) for candidate RBPs HtpG and YfiF in E. coli. Proteins of interest were N-terminal his-tagged and transformed into WT E. colis trains. Untransformed WT strain was negative control as well as non-cross-linked samples.