Hfq variant with altered RNA binding functions

Ziółkowska, Katarzyna; Derreumaux, Philippe; Folichon, Marc; Pellegrini, Olivier; Régnier, Philippe; Boni, Irina V.; Hajnsdorf, Eliane

doi:10.1093/nar/gkj464

Cited by 34 publications

(46 citation statements)

References 58 publications

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“…This sequence is still present in the chromosomal hfq deletion and also in the hfq-lacZ chromosomal fusion in strain IBhfq95 Δhfq (Fig. 2A, lane p; Ziolkowska et al 2006). The reverse transcript measured in the strain carrying the vector plasmid corresponds to these two transcripts ( Fig.…”

Section: Resultsmentioning

confidence: 91%

“…Hfq autoregulates its own expression fourfold by binding to its own mRNA, although the mechanism has not been completely elucidated (Vecerek et al 2005;Ziolkowska et al 2006). Table 1 shows that Ec-Hfq and Cd-Hfq exhibit the same repression factor (4.0) but that the plasmids expressing just the N-terminal cores of Ec-Hfq and Cd-Hfq were inactive in repression.…”

Section: Cd-hfq Is Functional For Hfq Autoregulation In E Colimentioning

confidence: 99%

“…Quantification of the radioactivity (arbitrary units) was indicated below the gel. The transcript detected in the plasmid vector containing strain (IBhfq95 Δhfq/p) corresponds to the 5 ′ end of mRNA covering the hfq deletion on the chromosome and the 5 ′ end of the hfq-lacZ fusion present at lacZ (Ziolkowska et al 2006); both should respond to Hfq autoregulation. Fainter bands detected on the same gel due to unspecific hybridization of the primer do not vary between samples, revealing that equivalent loading has been applied on the gel.…”

Section: Cd-hfq Is Functional For Hfq Autoregulation In E Colimentioning

confidence: 99%

“…A 56-kDa protein identified as OppA, a periplasmic component of the oligopeptide transport system, was detected only in the hfq mutant (Ziolkowska et al 2006). We took advantage of this easy assay to examine the effect of the various Hfq derivatives on oppA expression.…”

Section: Negative Regulation Of Oppa Expression By Cd-hfqmentioning

confidence: 99%

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Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function

Caillet

Gracia

Fontaine

et al. 2014

RNA

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A gene for the Hfq protein is present in the majority of sequenced bacterial genomes. Its characteristic hexameric ring-like core structure is formed by the highly conserved N-terminal regions. In contrast, the C-terminal forms an extension, which varies in length, lacks homology, and is predicted to be unstructured. In Gram-negative bacteria, Hfq facilitates the pairing of sRNAs with their mRNA target and thus affects gene expression, either positively or negatively, and modulates sRNA degradation. In Gram-positive bacteria, its role is still poorly characterized. Numerous sRNAs have been detected in many Gram-positive bacteria, but it is not yet known whether these sRNAs act in association with Hfq. Compared with all other Hfqs, the C. difficile Hfq exhibits an unusual C-terminal sequence with 75% asparagine and glutamine residues, while the N-terminal core part is more conserved. To gain insight into the functionality of the C. difficile Hfq (Cd-Hfq) protein in processes regulated by sRNAs, we have tested the ability of Cd-Hfq to fulfill the functions of the E. coli Hfq (Ec-Hfq) by examining various functions associated with Hfq in both positive and negative controls of gene expression. We found that Cd-Hfq substitutes for most but not all of the tested functions of the Ec-Hfq protein. We also investigated the role of the C-terminal part of the Hfq proteins. We found that the C-terminal part of both Ec-Hfq and Cd-Hfq is not essential but contributes to some functions of both the E. coli and C. difficile chaperons.

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Section: Resultsmentioning

confidence: 91%

Section: Cd-hfq Is Functional For Hfq Autoregulation In E Colimentioning

confidence: 99%

Section: Cd-hfq Is Functional For Hfq Autoregulation In E Colimentioning

confidence: 99%

Section: Negative Regulation Of Oppa Expression By Cd-hfqmentioning

confidence: 99%

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Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function

Caillet

Gracia

Fontaine

et al. 2014

RNA

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“…S1). Since repression of the predicted GcvB target, oppA, is abrogated in hfq mutants of both E. coli and Salmonella (Ziolkowska et al 2006;Sittka et al 2007), we compared OppA protein levels in Salmonella strains deleted for gcvB, hfq, or both (Fig. 1C).…”

Section: Characterization Of Gcvb Srna In Salmonellamentioning

confidence: 99%

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

Sharma¹,

Darfeuille²,

Plantinga³

et al. 2007

Genes Dev.

340

479

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The interactions of numerous regulatory small RNAs (sRNAs) with target mRNAs have been characterized, but how sRNAs can regulate multiple, structurally unrelated mRNAs is less understood. Here we show that Salmonella GcvB sRNA directly acts on seven target mRNAs that commonly encode periplasmic substrate-binding proteins of ABC uptake systems for amino acids and peptides. Alignment of GcvB homologs of distantly related bacteria revealed a conserved G/U-rich element that is strictly required for GcvB target recognition. Analysis of target gene fusion regulation in vivo, and in vitro structure probing and translation assays showed that GcvB represses its target mRNAs by binding to extended C/A-rich regions, which may also serve as translational enhancer elements. In some cases (oppA, dppA), GcvB repression can be explained by masking the ribosome-binding site (RBS) to prevent 30S subunit binding. However, GcvB can also effectively repress translation by binding to target mRNAs at upstream sites, outside the RBS. Specifically, GcvB represses gltI mRNA translation at the C/A-rich target site located at positions −57 to −45 relative to the start codon. Taken together, our study suggests highly conserved regions in sRNAs and mRNA regions distant from Shine-Dalgarno sequences as important elements for the identification of sRNA targets.[Keywords: Small RNA; riboregulator; post-transcriptional control; translation inhibition; ABC transporter; GcvB] Supplemental material is available at http://www.genesdev.org.

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Molecular dynamics simulations of RNA: An in silico single molecule approach

et al. 2006

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RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA-small molecule and RNA-protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules.

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Hfq variant with altered RNA binding functions

Cited by 34 publications

References 58 publications

Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function

Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

Molecular dynamics simulations of RNA: An in silico single molecule approach

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