Interrogation of RNA-protein interaction dynamics in bacterial growth.

Characterising RNA–protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of the Escherichia coli expressed 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 characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them are orthologs of human mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. For the first time, the dynamics of the bacterial RBPome have been interrogated, 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. Synopsis: A dynamic analysis of RNA-protein interaction rewiring across growth phases detects extensive reorganisation of the RBPome and reveals the RNA binding properties for 17 unannotated E. coli proteins and their differential impact on cell growth and evolutionary conservation. Mass spectrometry characterisation of the dynamics of 91% of the expressed E. coli proteome highlights extensive variation during cell growth. Determining RNA-protein interaction dynamics reveals that 68% of the RBPome differentially binds RNA according to the bacterial growth stage. iCLIP analysis of YfiF and HtpG unveils novel roles for these two proteins as ncRNA binders. A dynamic analysis of RNA-protein interaction rewiring across growth phases detects extensive reorganisation of the RBPome and reveals the RNA binding properties for 17 unannotated E. coli proteins and their differential impact on cell growth and evolutionary conservation. [ABSTRACT FROM AUTHOR]