scholarly journals Acidic C-terminal domains autoregulate the RNA chaperone Hfq

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Andrew Santiago-Frangos ◽  
Jeliazko R Jeliazkov ◽  
Jeffrey J Gray ◽  
Sarah A Woodson
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
De Novo ◽  
Sm Proteins ◽  
Rna Chaperone ◽  
E Coli ◽  
Intrinsically Disordered ◽  
Chaperone Function ◽  
Acidic Peptide ◽  
Sm Protein

The RNA chaperone Hfq is an Sm protein that facilitates base pairing between bacterial small RNAs (sRNAs) and mRNAs involved in stress response and pathogenesis. Hfq possesses an intrinsically disordered C-terminal domain (CTD) that may tune the function of the Sm domain in different organisms. In Escherichia coli, the Hfq CTD increases kinetic competition between sRNAs and recycles Hfq from the sRNA-mRNA duplex. Here, de novo Rosetta modeling and competitive binding experiments show that the acidic tip of the E. coli Hfq CTD transiently binds the basic Sm core residues necessary for RNA annealing. The CTD tip competes against non-specific RNA binding, facilitates dsRNA release, and prevents indiscriminate DNA aggregation, suggesting that this acidic peptide mimics nucleic acid to auto-regulate RNA binding to the Sm ring. The mechanism of CTD auto-inhibition predicts the chaperone function of Hfq in bacterial genera and illuminates how Sm proteins may evolve new functions.

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

2016 ◽  
Vol 113 (41) ◽  
pp. E6089-E6096 ◽  
Author(s):  
Andrew Santiago-Frangos ◽  
Kumari Kavita ◽  
Daniel J. Schu ◽  
Susan Gottesman ◽  
Sarah A. Woodson
Keyword(s):  
Rna Chaperone ◽  
E Coli ◽  
Small Noncoding Rnas ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Mrna Targets ◽  
Sm Protein ◽  
Target Rna ◽  
Kinetics Of

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.

scholarly journals Structural basis of nucleic acid binding byNicotiana tabacumglycine-rich RNA-binding protein: implications for its RNA chaperone function

2014 ◽  
Vol 42 (13) ◽  
pp. 8705-8718 ◽  
Author(s):  
Fariha Khan ◽  
Mark A. Daniëls ◽  
Gert E. Folkers ◽  
Rolf Boelens ◽  
S. M. Saqlan Naqvi ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Structural Basis ◽  
Nucleic Acid Binding ◽  
Rna Chaperone ◽  
Chaperone Function

scholarly journals Structure of anEscherichia coliHfq:RNA complex at 0.97 Å resolution

2014 ◽  
Vol 70 (11) ◽  
pp. 1492-1497 ◽  
Author(s):  
Eike C. Schulz ◽  
Orsolya Barabas
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Binding Site ◽  
Small Rnas ◽  
Target Genes ◽  
Rna Binding ◽  
Base Pairing ◽  
Rna Chaperone ◽  
Target Mrnas ◽  
Rna Interaction

In bacteria, small RNAs (sRNAs) silence or activate target genes through base pairing with the mRNA, thereby modulating its translation. A central player in this process is the RNA chaperone Hfq, which facilitates the annealing of sRNAs with their target mRNAs. Hfq has two RNA-binding surfaces that recognize A-rich and U-rich sequences, and is believed to bind an sRNA–mRNA pair simultaneously. However, how Hfq promotes annealing remains unclear. Here, the crystal structure ofEscherichia coliHfq is presented in complex with U6-RNA bound to its proximal binding site at 0.97 Å resolution, revealing the Hfq–RNA interaction in exceptional detail.

scholarly journals Different csrA Expression Levels in C versus K-12 E. coli Strains Affect Biofilm Formation and Impact the Regulatory Mechanism Presided by the CsrB and CsrC Small RNAs

2021 ◽  
Vol 9 (5) ◽  
pp. 1010
Author(s):  
Thomas Carzaniga ◽  
Federica A. Falchi ◽  
Francesca Forti ◽  
Davide Antoniani ◽  
Paolo Landini ◽  
...  
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Extracellular Polysaccharide ◽  
Transcriptional Level ◽  
E Coli ◽  
Protein Levels ◽  
Two Factors ◽  
Negative Effect ◽  
Operon Expression ◽  
K 12

Escherichia coli C is a strong biofilm producer in comparison to E. coli K-12 laboratory strains due to higher expression of the pgaABCD operon encoding the enzymes for the biosynthesis of the extracellular polysaccharide poly-β-1,6-N-acetylglucosamine (PNAG). The pgaABCD operon is negatively regulated at the post-transcriptional level by two factors, namely CsrA, a conserved RNA-binding protein controlling multiple pathways, and the RNA exonuclease polynucleotide phosphorylase (PNPase). In this work, we investigated the molecular bases of different PNAG production in C-1a and MG1655 strains taken as representative of E. coli C and K-12 strains, respectively. We found that pgaABCD operon expression is significantly lower in MG1655 than in C-1a; consistently, CsrA protein levels were much higher in MG1655. In contrast, we show that the negative effect exerted by PNPase on pgaABCD expression is much stronger in C-1a than in MG1655. The amount of CsrA and of the small RNAs CsrB, CsrC, and McaS sRNAs regulating CsrA activity is dramatically different in the two strains, whereas PNPase level is similar. Finally, the compensatory regulation acting between CsrB and CsrC in MG1655 does not occur in E. coli C. Our results suggest that PNPase preserves CsrA-dependent regulation by indirectly modulating csrA expression.

scholarly journals Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein

2020 ◽  
Author(s):  
Ewa M Stein ◽  
Joanna Kwiatkowska ◽  
Maciej M Basczok ◽  
Chandra M Gravel ◽  
Katherine E Berry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Rna Recognition ◽  
Rna Molecules ◽  
E Coli ◽  
Rna Ligands

Abstract The regulation of gene expression by small RNAs in Escherichia coli depends on RNA binding proteins Hfq and ProQ, which bind mostly distinct RNA pools. To understand how ProQ discriminates between RNA substrates, we compared its binding to six different RNA molecules. Full-length ProQ bound all six RNAs similarly, while the isolated N-terminal FinO domain (NTD) of ProQ specifically recognized RNAs with Rho-independent terminators. Analysis of malM 3′-UTR mutants showed that tight RNA binding by the ProQ NTD required a terminator hairpin of at least 2 bp preceding an 3′ oligoU tail of at least four uridine residues. Substitution of an A-rich sequence on the 5′ side of the terminator to uridines strengthened the binding of several ProQ-specific RNAs to the Hfq protein, but not to the ProQ NTD. Substitution of the motif in the malM-3′ and cspE-3′ RNAs also conferred the ability to bind Hfq in E. coli cells, as measured using a three-hybrid assay. In summary, these data suggest that the ProQ NTD specifically recognizes 3′ intrinsic terminators of RNA substrates, and that the discrimination between RNA ligands by E. coli ProQ and Hfq depends both on positive determinants for binding to ProQ and negative determinants against binding to Hfq.

scholarly journals Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein

2020 ◽  
Author(s):  
Ewa M. Stein ◽  
Joanna Kwiatkowska ◽  
Maciej M. Basczok ◽  
Chandra M. Gravel ◽  
Katherine E. Berry ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Rna Recognition ◽  
Base Pairs ◽  
Rna Molecules ◽  
E Coli ◽  
Rna Ligands

ABSTRACTThe regulation of gene expression by small RNAs in Escherichia coli depends on RNA binding proteins Hfq and ProQ, which bind mostly distinct RNA pools. To understand how ProQ discriminates between RNA substrates, we compared its binding to six different RNA molecules. Full-length ProQ bound all six RNAs similarly, while the isolated N-terminal FinO domain (NTD) of ProQ specifically recognized RNAs with Rho-independent terminators. Analysis of malM 3’-UTR mutants showed that tight RNA binding by the ProQ NTD required a terminator hairpin of at least two base pairs preceding an 3’ oligoU tail of at least four uridine residues. Substitution of an A-rich sequence on the 5’ side of the terminator to uridines strengthened the binding of several ProQ-specific RNAs to the Hfq protein, but not to the ProQ NTD. Substitution of the motif in the malM-3’ and cspE-3’ RNAs also conferred the ability to bind Hfq in E. coli cells, as measured using a three-hybrid assay. In summary, these data suggest that the ProQ NTD specifically recognizes 3’ intrinsic terminators of RNA substrates, and that the discrimination between RNA ligands by E. coli ProQ and Hfq depends both on positive determinants for binding to ProQ and negative determinants against binding to Hfq.

scholarly journals RNA chaperone activity and RNA-binding properties of the E. coli protein StpA

2007 ◽  
Vol 35 (4) ◽  
pp. 1257-1269 ◽  
Author(s):  
O. Mayer ◽  
L. Rajkowitsch ◽  
C. Lorenz ◽  
R. Konrat ◽  
R. Schroeder
Keyword(s):  
Rna Binding ◽  
Chaperone Activity ◽  
Binding Properties ◽  
Rna Chaperone ◽  
E Coli

Dri1 mediates heterochromatin assembly via RNAi and histone deacetylation

Genetics ◽  
2021 ◽  
Author(s):  
Hyoju Ban ◽  
Wenqi Sun ◽  
Yu-hang Chen ◽  
Yong Chen ◽  
Fei Li
Keyword(s):  
Histone Deacetylases ◽  
Genome Stability ◽  
Rna Binding ◽  
Histone Deacetylation ◽  
Rnai Pathway ◽  
Chromatin Domain ◽  
Heterochromatin Protein 1 ◽  
Intrinsically Disordered ◽  
C Terminus ◽  
Heterochromatin Assembly

Abstract Heterochromatin, a transcriptionally silenced chromatin domain, is important for genome stability and gene expression. Histone 3 lysine 9 methylation (H3K9me) and histone hypoacetylation are conserved epigenetic hallmarks of heterochromatin. In fission yeast, RNA interference (RNAi) plays a key role in H3K9 methylation and heterochromatin silencing. However, how RNAi machinery and histone deacetylases (HDACs) are coordinated to ensure proper heterochromatin assembly is still unclear. Previously, we showed that Dpb4, a conserved DNA polymerase epsilon subunit, plays a key role in the recruitment of HDACs to heterochromatin during S phase. Here, we identified a novel RNA-binding protein Dri1 that interacts with Dpb4. GFP-tagged Dri1 forms distinct foci mostly in the nucleus, showing a high degree of colocalization with Swi6/Heterochromatin Protein 1. Deletion of dri1+ leads to defects in silencing, H3K9me, and heterochromatic siRNA generation. We also showed that Dri1 physically associates with heterochromatic transcripts, and is required for the recruitment of the RNA-induced transcriptional silencing (RITS) complex via interacting with the complex. Furthermore, loss of Dri1 decreases the association of the Sir2 HDAC with heterochromatin. We further demonstrated that the C-terminus of Dri1 that includes an intrinsically disordered (IDR) region and three zinc fingers is crucial for its role in silencing. Together, our evidences suggest that Dri1 facilitates heterochromatin assembly via the RNAi pathway and HDAC.

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