<i>Clostridium difficile</i> Hfq can replace <i>Escherichia coli</i> Hfq for most of its function

Caillet, J.; Gracia, Céline; Fontaine, Fanette; Hajnsdorf, Eliane

doi:10.1261/rna.043372.113

Cited by 23 publications

(29 citation statements)

References 88 publications

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“…We may hypothesize that a high level of hfq expression and some structural particularities of the Hfq protein, including the presence of a unique C-terminal domain (104), may explain these unique features. Hfq could control target gene expression either directly or indirectly.…”

Section: Discussionmentioning

confidence: 99%

“…The CD1974 protein has an unusual C-terminal region. In E. coli, the full-length CD1974 protein is functional in sRNA-mediated regulation (55,104) and substitutes for most, but not all, of the traits of E. coli Hfq in phenotypic assays while the C-terminal domain contributes to RNA-binding efficiency of this RNA chaperone (104). The C. difficile hfq gene is flanked by the miaA gene (CD1975) encoding a tRNA ⌬ 2 -isopentenylpyrophosphate transferase and CD1973 encoding a putative pyridoxal phosphate-dependent transferase.…”

Section: Construction Of a Strain Depleted For Hfq And Analysis Of Itmentioning

confidence: 99%

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Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium difficile

et al. 2014

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cClostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. Our recent data strongly suggest the importance of RNA-based mechanisms for the control of gene expression in C. difficile. In an effort to understand the function of the RNA chaperone protein Hfq, we constructed and characterized an Hfq-depleted strain in C. difficile. Hfq depletion led to a growth defect, morphological changes, an increased sensitivity to stresses, and a better ability to sporulate and to form biofilms. The transcriptome analysis revealed pleiotropic effects of Hfq depletion on gene expression in C. difficile, including genes encoding proteins involved in sporulation, stress response, metabolic pathways, cell wall-associated proteins, transporters, and transcriptional regulators and genes of unknown function. Remarkably, a great number of genes of the regulon dependent on sporulation-specific sigma factor, SigK, were upregulated in the Hfq-depleted strain. The altered accumulation of several sRNAs and interaction of Hfq with selected sRNAs suggest potential involvement of Hfq in these regulatory RNA functions. Altogether, these results suggest the pleiotropic role of Hfq protein in C. difficile physiology, including processes important for the C. difficile infection cycle, and expand our knowledge of Hfq-dependent regulation in Gram-positive bacteria.

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Section: Discussionmentioning

confidence: 99%

Section: Construction Of a Strain Depleted For Hfq And Analysis Of Itmentioning

confidence: 99%

Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium difficile

et al. 2014

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“…Deletion of the C-terminal tail in E. coli Hfq also reduced in vitro binding affinity to the V. cholera Qrr sRNAs [35], and tryptophan quenching experiments showed the C-terminus can bind the hfq mRNA [18]. Interestingly, Hfq from Clostridium difficile , which has an extremely asparagine and glutamine-rich tail, can complement many of the functions of E. coli Hfq [36]. In this heterologous context, deletion of the tail impacted some of the regulation by C. difficile Hfq.…”

Section: Binding Of Srnas and Mrnasmentioning

confidence: 99%

Hfq: the flexible RNA matchmaker

Updegrove

Zhang

Storz

2016

Current Opinion in Microbiology

282

242

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The RNA chaperone protein Hfq is critical to the function of small, base pairing RNAs in many bacteria. In the past few years, structures and modeling of wild type Hfq and assays of various mutants have documented that the homohexameric Hfq ring can contact RNA at four sites (proximal face, distal face, rim and C-terminal tail) and that different RNAs bind to these sites in various configurations. These studies together with novel in vitro and in vivo experimental approaches are beginning to give mechanistic insights into how Hfq acts to promote small RNA-mRNA pairing and indicate that flexibility is integral to the Hfq role in RNA matchmaking.

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“…By contrast, later studies found that the CTD was required for in vitro annealing and proper regulation by sRNAs and normal binding to long RNAs, such as the rpoS mRNA (19,26,27). Moreover, Hfq from Pseudomonas aeruginosa and Clostridium difficile, which have much shorter CTDs than E. coli Hfq, functionally replace E. coli Hfq for certain sRNA·mRNA pairs but not others (28,29).…”

mentioning

confidence: 95%

C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA

Santiago-Frangos

Kumari

Schu

et al. 2016

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

149

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The bacterial Sm protein and RNA chaperone Hfq stabilizes small noncoding RNAs (sRNAs) and facilitates their annealing to mRNA targets involved in stress tolerance and virulence. Although an arginine patch on the Sm core is needed for Hfq's RNA chaperone activity, the function of Hfq's intrinsically disordered C-terminal domain (CTD) has remained unclear. Here, we use stopped flow spectroscopy to show that the CTD of Escherichia coli Hfq is not needed to accelerate RNA base pairing but is required for the release of dsRNA. The Hfq CTD also mediates competition between sRNAs, offering a kinetic advantage to sRNAs that contact both the proximal and distal faces of the Hfq hexamer. The change in sRNA hierarchy caused by deletion of the Hfq CTD in E. coli alters the sRNA accumulation and the kinetics of sRNA regulation in vivo. We propose that the Hfq CTD displaces sRNAs and annealed sRNA·mRNA complexes from the Sm core, enabling Hfq to chaperone sRNA-mRNA interactions and rapidly cycle between competing targets in the cell.A member of the Sm protein family, Hfq was first identified as a host factor for phage Q beta. Hfq is found in at least 50% of sequenced bacterial genomes (1) and, in many bacteria, contributes to posttranscriptional regulation by small noncoding RNAs (sRNAs). Deletion of Hfq leads to pleiotropic effects, such as altered cellular morphology, slow growth, maladaptation to stress, and avirulence (2-5).Escherichia coli Hfq comprises an Sm domain (amino acids 7-66) that assembles into a stable hexameric ring and an intrinsically disordered C-terminal domain (CTD) that projects from the rim of the hexamer (6-10). The Sm ring binds to both sRNAs and target mRNAs, stabilizing the sRNAs against turnover (11-13) and facilitating base pairing with complementary sequences in the mRNA (7,14,15). The conserved "proximal" face of the Hfq hexamer interacts with uridines at the sRNA 3′ end (9, 16, 17), whereas the "distal" face of Hfq binds AAN triplet repeats (9, 16, 17) often found in the 5′ UTRs of target mRNAs. These sequence-specific interactions recruit sRNAs and mRNAs to Hfq, allowing arginine-rich patches along the rim of Hfq to catalyze base pairing between complementary strands (18).Although the functional importance of the Sm domain is established, the function of the disordered CTD has been unclear. The Hfq CTD varies greatly in length and sequence composition between bacterial families (1, 19), ranging from 7-residue stubs in Bacillaceae (20) to 100-residue tails in Moraxellaceae (21, 22) (Fig. S1). Previous studies reached conflicting conclusions about the importance of the Hfq CTD for sRNA regulation. In early studies, C-terminal deletions of hfq had no obvious phenotype in E. coli (23, 24) and little effect on sRNA binding (23,25). By contrast, later studies found that the CTD was required for in vitro annealing and proper regulation by sRNAs and normal binding to long RNAs, such as the rpoS mRNA (19,26,27). Moreover, Hfq from Pseudomonas aeruginosa and Clostridium difficile, which have much shor...

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

Cited by 23 publications

References 88 publications

Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium difficile

Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium difficile

Hfq: the flexible RNA matchmaker

C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA

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