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RNA-binding proteins in bacteria

Nature Reviews Microbiologyvolume 16pages601615 (2018) | Download Citation


RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA–protein interactions. Work over the years has identified major RBPs that act on cellular transcripts at the various stages of bacterial gene expression and that enable their integration into post-transcriptional networks that also comprise small non-coding RNAs. Bacterial RBP research has now entered a new era in which RNA sequencing-based methods permit mapping of RBP activity in a truly global manner in vivo. Moreover, the soaring interest in understudied members of host-associated microbiota and environmental communities is likely to unveil new RBPs and to greatly expand our knowledge of RNA–protein interactions in bacteria.

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The authors thank C. Beisel, Y. Chao, K. Papenfort and G. Wagner for comments on the manuscript. J.V. is supported by a DFG Gottfried Wilhelm Leibniz Award (Vo875/20). E.H. is supported by the Wenner-Gren Foundations, the Swedish Research Council (2016–03656) and the Swedish Foundation for Strategic Research (ICA 16–0021).

Reviewer information

Nature Reviews Microbiology thanks M. Hentze, B. Luisi and E. Nudler for their contribution to the peer review of this work.

Author information


  1. Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden

    • Erik Holmqvist
  2. Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany

    • Jörg Vogel
  3. Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany

    • Jörg Vogel


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E.H. and J.V. researched data for the article, made substantial contributions to discussions of the content, wrote the article and reviewed and/or edited the manuscript before submission.

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The authors declare no competing interests.

Corresponding author

Correspondence to Jörg Vogel.

Supplementary information


Ribosomal proteins

(r-proteins). All proteins that, together with the ribosomal RNA, form the two subunits of the ribosome, the molecular machine that synthesizes polypeptides from an mRNA template.

Small non-coding RNAs

(sRNAs). Bacterial, in most cases non-coding, RNAs in the size range of 50–300 nucleotides that carry out regulatory functions, either by base pairing to complementary sequences in other RNAs or by functioning as binding partners for proteins.

RNA sequencing

(RNA-seq). A method for the parallel determination of sequence and abundance of RNA molecules in a biological sample.

CRISPR–Cas systems

Bacterial adaptive immune systems consisting of short RNAs that guide Cas proteins to target invading nucleic acids for destruction.

Ribonucleoprotein particles

(RNPs). Macromolecular complexes that consist of RNA and RNA-binding proteins.


Enzymes that catalyse the cleavage of RNA. Endoribonucleases cleave RNA internally, whereas exoribonucleases degrade RNA from either the 5′ end or the 3′ end.

RNA-modification proteins

Proteins that introduce chemical modifications in RNA.

Intrinsic termination

A mechanism used by bacteria to stop transcription elongation and release the newly synthesized RNA. RNA polymerase is released from the nascent transcript as it encounters a palindromic GC-rich DNA sequence followed by a stretch of T residues. Also called Rho-independent termination.

Rho-dependent termination

A bacterial transcription termination mechanism whereby the release of the transcribing RNA polymerase from the DNA template is mediated by the Rho protein.


A homohexameric protein that promotes termination of transcription elongation by means of ATP hydrolysis. Rho is the target of the antibiotic bicyclomycin.

Ribosome binding site

(RBS). An mRNA sequence that recruits the 30 S ribosomal subunit to initiate translation. The Shine–Dalgarno sequence of the RBS is complementary to the 16 S ribosomal RNA (rRNA) and enables 30S–mRNA interaction.


A concept to describe the relation between two genetic elements. A small non-coding RNA (sRNA) is trans-encoded with respect to its mRNA target if the two are encoded by different genetic loci. By contrast, a cis-encoded sRNA is encoded by the same locus as its mRNA target, for instance, when the respective genes overlap.


Multi-protein complexes that carry out RNA degradation in bacteria.

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