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PreprintCited by 4Bacterial Genetics and BiotechnologyRNA and protein synthesis mechanismsRNA Research and Splicing

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Interrogation of RNA-protein interaction dynamics in bacterial growth

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Monti, Mie, Herman, Reyme, Davey, Karen, Dawson, Charlotte S., Ule, Jernej, Thomas, Gavin H., Willis, Anne E., Lilley, Kathryn S., Villanueva, Eneko·2023·bioRxiv (Cold Spring Harbor Laboratory)
DOI 10.1101/2023.07.03.547468

Preprint — published as 10.1038/s44320-024-00031-y · Paper page

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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 have human orthologs in the form of 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. 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.

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Metadata

Authors
Monti, M., Herman, R., Davey, K., Dawson, C. S., Ule, J., Thomas, G. H., Willis, A. E., Lilley, K. S., & Villanueva, E.
Affiliations
  • University of Cambridge (GB)
  • University of York (GB)
  • King's College London (GB)
Corresponding author
  • Willis, Anne E.
  • Lilley, Kathryn S.
  • Villanueva, Eneko
ORCID
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2023-07-03
DOI
10.1101/2023.07.03.547468
OpenAlex
W4383069540
Cited by
4
References
1
Citations by year
2025: 1 · 2024: 1 · 2023: 2
Type
posted content
Language
en
Open access
Licence
cc-by
Locations
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Figshare (submittedVersion, cc-by)
  • Apollo (cc-by)
  • The Francis Crick Institute (cc-by)
Funders
  • Wellcome Trust (5TR00, /Z/15/Z, FC001110, 110071/Z/15/Z)
  • Francis Crick Institute (FC001110)
  • Cancer Research UK (FC001110)
  • King's College London
  • European Commission (HORIZON2020)
  • Directorate for Biological Sciences
  • Medical Research Council (5TR00, FC001110, MC_UU_00025/7)
  • Biotechnology and Biological Sciences Research Council (5TR00, BB/X003035/1, BB/N01040X/1)
  • H2020 European Research Council (835300)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
RNA-protein interactions, RNA-binding proteins, Escherichia coli, bacterial growth phase, HtpG, molecular chaperones, unannotated proteins, Proteobacteria, mitochondrial proteins, antimicrobial drug targets

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