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Cited by 16Bacterial 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, Mancini, Leonardo, Capitanchik, Charlotte, Davey, Karen, Dawson, Charlotte S, Ule, Jernej, Thomas, Gavin H, Willis, Anne E, Lilley, Kathryn S, Villanueva, Eneko·2024·Molecular Systems Biology
DOI 10.1038/s44320-024-00031-yPMC PMC11066096

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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 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.

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Metadata

Authors
Monti, M., Herman, R., Mancini, L., Capitanchik, C., 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
Molecular Systems Biology
Publisher
Springer Science and Business Media LLC
Published
2024-03-26
Volume
20
Issue
5
Pages
573-589
ISSN
1744-4292 (ISSN-L)
DOI
10.1038/s44320-024-00031-y
PMC
PMC11066096
OpenAlex
W4393192761
Cited by
16
References
1
Citations by year
2026: 4 · 2025: 5 · 2024: 4
FWCI
3.44
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Systems Biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research Portal (King's College London) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • UKRI | Medical Research Council (5TR00, FC001110)
  • Wellcome Trust (110071/Z/15/Z, FC001110)
  • Herchel Smith Postoctoral Fellowship
  • Herchel Smith PhD Research Studenship
  • European Union Horizon 2020 research and innovation programme (835300-RNPdynamics)
  • UKRI | Innovate UK) (BB/N01040X/1)
  • Cancer Research UK (FC001110)
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, Proteobacteria, antimicrobial drug targets, unannotated proteins
MeSH terms
Escherichia coli, Humans, Protein Binding, RNA, Bacterial, Gene Expression Regulation, Bacterial, RNA-Binding Proteins, Proteome, Escherichia coli Proteins

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