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The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Klebsiella pneumoniae subsp. pneumoniae

PROVIDER: GSE244640 | GEO | 2024/02/05

REPOSITORIES: GEO

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The global RNA-RNA interactome of <i>Klebsiella pneumoniae</i> unveils a small RNA regulator of cell division.

Project description: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.

| S-EPMC10907235 | biostudies-literature

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIP-Seq)

Project description: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 previously unknown RNA-RNA pairs, our study revealed an Hfq-dependent 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 cell cycle inhibition during the SOS response.

2024-02-05 | GSE244639 | GEO

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIL-Seq)

Project description: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 previously unknown RNA-RNA pairs, our study revealed an Hfq-dependent 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 cell cycle inhibition during the SOS response.

2024-02-05 | GSE244638 | GEO

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (dRNA-Seq)

Project description: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 previously unknown RNA-RNA pairs, our study revealed an Hfq-dependent 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 cell cycle inhibition during the SOS response.

2024-02-05 | GSE244635 | GEO

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division

| PRJNA1023936 | ENA

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (dRNA-Seq)

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (dRNA-Seq)

| PRJNA1023941 | ENA

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIL-Seq)

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIL-Seq)

| PRJNA1023942 | ENA

The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIP-Seq)

Project description:The global RNA-RNA interactome of Klebsiella pneumoniae unveils a small RNA regulator of cell division (RIP-Seq)

| PRJNA1023944 | ENA

RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence.

Project description:Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging bacterial pathogen causing invasive infection in immune-competent humans. The hypervirulence is strongly linked to the overproduction of hypermucoviscous capsule, but the underlying regulatory mechanisms of hypermucoviscosity (HMV) have been elusive, especially at the post-transcriptional level mediated by small noncoding RNAs (sRNAs). Using a recently developed RNA interactome profiling approach iRIL-seq, we interrogate the Hfq-associated sRNA regulatory network and establish an intracellular RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNAs that repress or promote HMV. One of the strongest HMV repressors is ArcZ, which is activated by the catabolite regulator CRP and targets many HMV-related genes including mlaA and fbp. We discover that MlaA and its function in phospholipid transport is crucial for capsule retention and HMV, inactivation of which abolishes Klebsiella virulence in mice. ArcZ overexpression drastically reduces bacterial burden in mice and reduces HMV in multiple hypervirulent and carbapenem-resistant clinical isolates, indicating ArcZ is a potent RNA inhibitor of bacterial pneumonia with therapeutic potential. Our work unravels a novel CRP-ArcZ-MlaA regulatory circuit of HMV and provides mechanistic insights into the posttranscriptional virulence control in a superbug of global concern.

| S-EPMC11322559 | biostudies-literature

RNA interactome profiling in hypervirulent Klebsiella pneumoniae

Project description:To map the Hfq-mediated RNA regulatory network in HvKP, we harnessed the LiRIP-seq approach recently established in our lab, which enabled global profiling of RNA-RNA interactomes in live bacteria. Transformation of the pBAD-t4rnl1 plasmid into Klebsiella allowed us to express T4 RNA ligase 1 for proximity-ligation of RNAs in vivo, followed by co-immunoprecipitation (coIP) to enrich the Hfq-bound RNA transcripts (singleton reads) and ligated RNA fragments (chimeras: sRNA-mRNA, sRNA-sRNA, etc).

2024-07-17 | GSE243246 | GEO

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