Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery.

Autor:	McQuail J; Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK., Matera G; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany., Gräfenhan T; Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany., Bischler T; Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany., Haberkant P; Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany., Stein F; Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany., Vogel J; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.; Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany., Wigneshweraraj S; Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2024 Mar 21; Vol. 52 (5), pp. 2323-2339.
DOI:	10.1093/nar/gkad1211
Abstrakt:	The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process. (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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