Interrogation of RNA-protein interaction dynamics in bacterial growth

Mie Monti, Reyme Herman, Leonardo Mancini, Charlotte Capitanchik, Karen Davey, Charlotte S Dawson, Jernej Ule, Gavin H Thomas, Anne E Willis, Kathryn S Lilley, Eneko Villanueva

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)573-589
Number of pages17
JournalMolecular systems biology
Volume20
Issue number5
DOIs
Publication statusPublished - 26 Mar 2024

Bibliographical note

© 2024. The Author(s).

Keywords

  • RNA-Binding Proteins/metabolism
  • Escherichia coli/growth & development
  • Escherichia coli Proteins/metabolism
  • RNA, Bacterial/metabolism
  • Proteome/metabolism
  • Protein Binding
  • Gene Expression Regulation, Bacterial
  • Humans

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