RNA binding by Hfq and ring-forming (L)Sm proteins

Weichenrieder, Oliver

doi:10.4161/rna.29144

Cited by 40 publications

(23 citation statements)

References 111 publications

(264 reference statements)

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“…The distal face of E. coli Hfq preferentially interacts with a repeated (AAN) triplet motif (9, 31), but this protein surface varies among Hfq homologs, resulting in altered binding specificities (32). For example, the Bacillus protein is reported to bind an AG dinucleotide (33).…”

Section: Rna Binding To the Distal Facementioning

confidence: 99%

Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria

Zheng

Panja

Woodson

2016

Journal of Molecular Biology

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The Sm-protein Hfq facilitates interactions between small non-coding RNA (sRNA) and target mRNAs. In enteric Gram negative bacteria, Hfq is required for sRNA regulation, and hfq deletion results in stress intolerance and reduced virulence. By contrast, the role of Hfq in Gram positive is less established and varies among species. The RNA binding and RNA annealing activity of Hfq from Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus subtilis and Staphylococcus aureus were compared using minimal RNAs fluorescence spectroscopy. The results show that RNA annealing activity increases with the number of arginines in a semi-conserved patch on the rim of the Hfq hexamer and correlates with the previously reported requirement for Hfq in sRNA regulation. Thus, the amino acid sequence of the arginine patch can predict the chaperone function of Hfq in sRNA regulation in different organisms.

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Section: Rna Binding To the Distal Facementioning

confidence: 99%

Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria

Zheng

Panja

Woodson

2016

Journal of Molecular Biology

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“…Hfq uses a mixture of RNA binding surfaces and disordered domains to recognize a broad family of RNA substrates (122), while ignoring other RNA in the cell. The “proximal” face of Hfq is conserved among Sm/Lsm proteins and interacts with single-stranded U’s at the 3′ ends of sRNAs (123–126).…”

Section: Introductionmentioning

confidence: 99%

Proteins That Chaperone RNA Regulation

Woodson¹,

Panja²,

Santiago-Frangos

2018

Microbiol Spectr

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RNA-binding proteins chaperone the biological functions of non-coding RNA by reducing RNA misfolding, improving matchmaking between regulatory RNA and targets, and exerting quality control over RNP biogenesis. Recent studies of E. coli CspA, HIV NCp and E. coli Hfq, are beginning to show how RNA-binding proteins remodel RNA structures. These different protein families use common strategies for disrupting or annealing RNA double helices, which can be used to understand the mechanisms by which proteins chaperone RNA-dependent regulation in bacteria.

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“…Transacting sRNAs activate or repress expression of certain genes by base pairing with the 5′-UTR of the target mRNAs 4 , either masking or exposing the Shine-Dalgarno ribosome binding site, or recruiting RNase E for mRNA turnover 5; 6 . In Gram-negative bacteria, sRNAs typically act together with the RNA chaperone protein Hfq 6; 7 , which accelerates annealing of complementary RNA strands and stabilizes sRNA-mRNA duplexes 8; 9; 10; 11 . The observed regulation depends on the specificity of these complexes, as different sRNAs must compete for binding to Hfq and their proper mRNA target.…”

Section: Introductionmentioning

confidence: 99%

Acidic Residues in the Hfq Chaperone Increase the Selectivity of sRNA Binding and Annealing

Panja

Santiago-Frangos

Schu

et al. 2015

Journal of Molecular Biology

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Hfq facilitates gene regulation by small non-coding RNAs (sRNAs), thereby affecting bacterial attributes such as biofilm formation and virulence. E. coli Hfq recognizes specific U-rich and AAN motifs in sRNAs and target mRNAs, after which an arginine patch on the rim promotes base pairing between their complementary sequences. In the cell, Hfq must discriminate between many similar RNAs. Here, we report that acidic amino acids lining the sRNA binding channel between the inner pore and rim of the Hfq hexamer contribute to the selectivity of Hfq’s chaperone activity. RNase footprinting, in vitro binding and stopped-flow fluorescence annealing assays showed that alanine substitution of D9, E18 or E37 strengthened RNA interactions with the rim of Hfq and increased annealing of non-specific or U-tailed RNA oligomers. Although the mutants were less able than WT Hfq to anneal sRNAs with wild type rpoS mRNA, the D9A mutation bypassed recruitment of Hfq to an (AAN)4 motif in rpoS, both in vitro and in vivo. These results suggest that acidic residues normally modulate access of RNAs to the arginine patch. We propose that this selectivity limits indiscriminate target selection by E. coli Hfq, and enforces binding modes that favor genuine sRNA and mRNA pairs.

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RNA binding by Hfq and ring-forming (L)Sm proteins

Cited by 40 publications

References 111 publications

Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria

Arginine Patch Predicts the RNA Annealing Activity of Hfq from Gram-Negative and Gram-Positive Bacteria

Proteins That Chaperone RNA Regulation

Acidic Residues in the Hfq Chaperone Increase the Selectivity of sRNA Binding and Annealing

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