biostudies-literatureMonti MUKRI | Innovate UK)Cancer Research UKMedical Research CouncilHerchel Smith Postoctoral FellowshipEuropean Union Horizon 2020 research and innovation programmeWellcome TrustUKRI | Medical Research CouncilBiotechnology and Biological Sciences Research CouncilHerchel Smith PhD Research Studenship573-589https://www.ebi.ac.uk/biostudies/studies/S-EPMC11066096biostudies-literatureUnknown20(5)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, tMolecular systems biologyInterrogation of RNA-protein interaction dynamics in bacterial growth.PMC11066096BB/N01040X/15TR00835300-RNPdynamics110071/Z/15/ZFC001110MC_PC_24008Monti MCapitanchik CVillanueva EThomas GHDavey KHerman RMancini LUle JLilley KSDawson CSWillis AEfalseInterrogation 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, t2024-01-01T00:00:00Z2024 May2026-07-15T04:50:27.847Z2025-08-27T03:11:11.129ZS-EPMC110660963853197110.1038/s44320-024-00031-y