Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli

Lalaouna, David; Prévost, Karine; Park, Seong-Jin; Chénard, Thierry; Bouchard, Marie-Pier; Caron, Marie-Pier; Vanderpool, Carin K.; Fei, Jingyi; Massé, Éric

doi:10.3390/ncrna7040064

Cited by 4 publications

(4 citation statements)

References 79 publications

(134 reference statements)

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“…These data are consistent with earlier studies, which demonstrated that sRNA-induced efficient cleavage of target mRNAs by RNase E requires both Hfq and a functional RNA degradosome ( 21 , 25 ). Additionally, it was previously shown that target mRNA decay subsequently drives the sequential degradation of the paired sRNAs in certain cases ( 20 , 21 , 24 ). However, the mechanism by which the CTD recognizes Hfq in vivo to initiate RNase E–dependent degradation of the mRNA–sRNA hybrid remained elusive.…”

Section: Discussionmentioning

confidence: 99%

“…Despite the crucial role of the CTD in modulating Hfq-dependent sRNA regulation, the molecular mechanisms underlying the Hfq–sRNA–mRNA complex (Hfq–RNA complex) recognition by RNase E CTD in vivo remain unknown. Indeed, there has been an increasing body of evidence suggesting that association of Hfq with the CTD of RNase E likely occurs in the presence of RNA ( 15 , 22 – 24 ).…”

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confidence: 99%

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Target recognition by RNase E RNA-binding domain AR2 drives sRNA decay in the absence of PNPase

Sinha

Lay

2022

Proc. Natl. Acad. Sci. U.S.A.

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The C-terminal domain (CTD) of the major endoribonuclease RNase E not only serves as a scaffold for the central RNA decay machinery in gram-negative bacteria but also mediates coupled degradation of small regulatory RNAs (sRNAs) and their cognate target transcripts following RNA chaperone Hfq–facilitated sRNA–mRNA base pairing. Despite the crucial role of RNase E CTD in sRNA-dependent gene regulation, the contribution of particular residues within this domain in recruiting sRNAs and mRNAs upon base pairing remains unknown. We have previously shown that in Escherichia coli , the highly conserved 3′-5′-exoribonuclease polynucleotide phosphorylase (PNPase) paradoxically stabilizes sRNAs by limiting access of RNase E to Hfq-bound sRNAs and by degrading target mRNA fragments that would otherwise promote sRNA decay. Here, we report that in the absence of PNPase, the RNA-binding region AR2 in the CTD is required for RNase E to initiate degradation of the Hfq-dependent sRNAs CyaR and RyhB. Additionally, we show that introducing mutations in either hfq that disrupts target mRNA binding to Hfq or the AR2 coding region of rne impairs RNase E binding to sRNAs. Altogether, our data support a model where sRNAs are recruited via bound mRNA targets to RNase E by its AR2 domain after Hfq catalyzes sRNA–mRNA pairing. These results also support our conclusion that in a PNPase-deficient strain, more rapid decay of sRNAs occurs due to accelerated pairing with mRNA targets as a consequence of their accumulation. Our findings provide insights into the mechanisms by which sRNAs and mRNAs are regulated by RNase E.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Target recognition by RNase E RNA-binding domain AR2 drives sRNA decay in the absence of PNPase

Sinha

Lay

2022

Proc. Natl. Acad. Sci. U.S.A.

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“…Interestingly, all fifteen of the isrR* mutant strains, isolated during two separate screening events, contained the same mutation in the operator of isrR suggesting that there is something unique about this allele. In alternate organisms, small proteins, such as Hfq in E. coli , promote interaction between a sRNA and a target mRNA (49). The finding that suppressor mutations only mapped to the promoter of isrR , and not to alternate loci including hfq , suggest that S. aureus does not require a single protein to facilitate interaction between IsrR and target RNAs.…”

Section: Discussionmentioning

confidence: 99%

TheStaphylococcus aureussmall non-coding RNA IsrR regulates TCA cycle activity and virulence

Rios-Delgado,

McReynolds,

Pagella

et al. 2024

Preprint

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Staphylococcus aureushas evolved mechanisms to cope with low iron (Fe) availability in host tissues.S. aureususes the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that anS. aureusΔfurmutant has decreased expression ofacnA, which codes for the Fe-dependent enzyme aconitase. DecreasedacnAexpression prevented the Δfurmutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation inisrR, which produces a regulatory RNA, permitted growth by decreasingisrRtranscription. The decreased AcnA activity of the Δfurmutant was partially relieved by an ΔisrRmutation. Directed mutation of bases predicted to facilitate the interaction between theacnAtranscript and IsrR, decreased the ability of IsrR to controlacnAexpressionin vivoand IsrR bound to theacnAtranscriptin vitro. IsrR also bound to the transcripts coding the alternate TCA cycle proteinssdhC,mqo,citZ, andcitM. Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models.Graphical Abstract

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“…The Hfq protein of E. coli is a relatively small polypeptide composed of 102 amino acid residues (aa), which interacts with different transcripts, in particular small noncoding RNAs, and functions as an RNA chaperone [38,39]. This activity operates predominantly through facilitating RNA-RNA interactions, thus modulating the availability of mRNA molecules to the translation machinery [9].…”

Section: Discussionmentioning

confidence: 99%

Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies

Turbant,

Waeytens,

Blache

et al. 2023

IJMS

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The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host–bacteria interactions which may not be defined solely by protein–protein and protein–outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.

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Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli

Cited by 4 publications

References 79 publications

Target recognition by RNase E RNA-binding domain AR2 drives sRNA decay in the absence of PNPase

Target recognition by RNase E RNA-binding domain AR2 drives sRNA decay in the absence of PNPase

TheStaphylococcus aureussmall non-coding RNA IsrR regulates TCA cycle activity and virulence

Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies

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