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Papenfort K, Storz G. Insights into bacterial metabolism from small RNAs. Cell Chem Biol 2024:S2451-9456(24)00304-0. [PMID: 39094580 DOI: 10.1016/j.chembiol.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/08/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024]
Abstract
The study of small, regulatory RNAs (sRNA) that act by base-pairing with target RNAs in bacteria has been steadily advancing, particularly with the availability of more and more transcriptome and RNA-RNA interactome datasets. While the characterization of multiple sRNAs has helped to elucidate their mechanisms of action, these studies also are providing insights into protein function, control of metabolic flux, and connections between metabolic pathways as we will discuss here. In describing several examples of the metabolic insights gained, we will summarize the different types of base-pairing sRNAs including mRNA-derived sRNAs, sponge RNAs, RNA mimics, and dual-function RNAs as well as suggest how information about sRNAs could be exploited in the future.
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Affiliation(s)
- Kai Papenfort
- Friedrich Schiller University Jena, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-4417, USA.
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McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Res 2024; 52:2323-2339. [PMID: 38142457 PMCID: PMC10954441 DOI: 10.1093/nar/gkad1211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
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.
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Affiliation(s)
- Josh McQuail
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
| | - Gianluca Matera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Tom Gräfenhan
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Jörg Vogel
- 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
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
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Ruhland E, Siemers M, Gerst R, Späth F, Vogt LN, Figge MT, Papenfort K, Fröhlich KS. The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division. Proc Natl Acad Sci U S A 2024; 121:e2317322121. [PMID: 38377209 PMCID: PMC10907235 DOI: 10.1073/pnas.2317322121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen Klebsiella pneumoniae, deletion of the hfq gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions. In addition to dozens of RNA-RNA pairs, our study revealed an Hfq-dependent small regulatory RNA (sRNA), DinR, which is processed from the 3' terminal portion of dinI mRNA. Transcription of dinI is controlled by the master regulator of the SOS response, LexA. As DinR accumulates in K. pneumoniae in response to DNA damage, the sRNA represses translation of the ftsZ transcript by occupation of the ribosome binding site. Ectopic overexpression of DinR causes depletion of ftsZ mRNA and inhibition of cell division, while deletion of dinR antagonizes cell elongation in the presence of DNA damage. Collectively, our work highlights the important role of RNA-based gene regulation in K. pneumoniae and uncovers the central role of DinR in LexA-controlled division inhibition during the SOS response.
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Affiliation(s)
- Eric Ruhland
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Malte Siemers
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Ruman Gerst
- Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Felix Späth
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Laura Nicole Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
| | - Marc Thilo Figge
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena07745, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
| | - Kathrin Sophie Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena07743, Germany
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Miyakoshi M. Multilayered regulation of amino acid metabolism in Escherichia coli. Curr Opin Microbiol 2024; 77:102406. [PMID: 38061078 DOI: 10.1016/j.mib.2023.102406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024]
Abstract
Amino acid metabolism in Escherichia coli has long been studied and has established the basis for regulatory mechanisms at the transcriptional, posttranscriptional, and posttranslational levels. In addition to the classical signal transduction cascade involving posttranslational modifications (PTMs), novel PTMs in the two primary nitrogen assimilation pathways have recently been uncovered. The regulon of the master transcriptional regulator NtrC is further expanded by a small RNA derived from the 3´UTR of glutamine synthetase mRNA, which coordinates central carbon and nitrogen metabolism. Furthermore, recent advances in sequencing technologies have revealed the global regulatory networks of transcriptional and posttranscriptional regulators, Lrp and GcvB. This review provides an update of the multilayered and interconnected regulatory networks governing amino acid metabolism in E. coli.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Institute of Medicine, University of Tsukuba, 305-8575 Ibaraki, Japan.
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