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Cited by 47Bacterial Genetics and BiotechnologyRNA Research and SplicingRNA and protein synthesis mechanisms

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Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Open access
Gerovac, Milan, El Mouali, Youssef, Kuper, Jochen, Kisker, Caroline, Barquist, Lars, Vogel, Jörg·2020·RNA
DOI 10.1261/rna.076992.120

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Abstract

RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica , GradR confirms many known RBPs such as CsrA, Hfq, and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalog of microbial RBPs.

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Metadata

Authors
Gerovac, M., El Mouali, Y., Kuper, J., Kisker, C., Barquist, L., & Vogel, J.
Affiliations
  • University of Würzburg (DE)
  • Helmholtz Institute for RNA-based Infection Research (DE)
Corresponding author
Vogel, Jörg
ORCID
Venue
RNA
Publisher
Cold Spring Harbor Laboratory
Published
2020-07-09
Volume
26
Issue
10
Pages
1448-1463
ISSN
  • 1355-8382 (ISSN-L)
  • 1469-9001
DOI
10.1261/rna.076992.120
OpenAlex
W3041183625
Cited by
47
References
4
Citations by year
2026: 4 · 2025: 6 · 2024: 5 · 2023: 6 · 2022: 8 · 2021: 13 · 2020: 5
FWCI
4.69
Type
journal article
Language
en
Open access
Locations
  • RNA (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • HighWire Press Open Archive (submittedVersion)
  • HZI (Helmholtz Centre for Infection Research) (submittedVersion, cc-by-nc-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
ProQ, small RNA, plasmid replication, RNA recognition, Salmonella enterica, CsrA, Hfq
MeSH terms
Protein Domains, Bacterial Proteins, Poly A, Repressor Proteins, Ribonucleases, RNA, Bacterial, RNA-Binding Proteins, Salmonella enterica

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