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Hfq proximity and orientation controls RNA annealing
Regulation of bacterial gene networks by small non-coding RNAs (sRNAs) requires base pairing with messenger RNA (mRNA) targets, which is facilitated by Hfq protein. Hfq is recruited to sRNAs and mRNAs through U-rich- and A-rich-binding sites, respectively, but their distance from the sRNA–mRNA compl...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458560/ https://www.ncbi.nlm.nih.gov/pubmed/22761405 http://dx.doi.org/10.1093/nar/gks618 |
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author | Panja, Subrata Woodson, Sarah A. |
author_facet | Panja, Subrata Woodson, Sarah A. |
author_sort | Panja, Subrata |
collection | PubMed |
description | Regulation of bacterial gene networks by small non-coding RNAs (sRNAs) requires base pairing with messenger RNA (mRNA) targets, which is facilitated by Hfq protein. Hfq is recruited to sRNAs and mRNAs through U-rich- and A-rich-binding sites, respectively, but their distance from the sRNA–mRNA complementary region varies widely among different genes. To determine whether distance and binding orientation affect Hfq’s chaperone function, we engineered ‘toy’ RNAs containing strong Hfq-binding sites at defined distances from the complementary target site. We show that RNA annealing is fastest when the distal face of Hfq binds an A-rich sequence immediately 3′ of the target. This recruitment advantage is lost when Hfq binds >20 nt away from the target, but is partially restored by secondary structure that shortens this distance. Although recruitment through Hfq’s distal face accelerates RNA annealing, tight binding of six Us to Hfq’s proximal face inhibits annealing. Finally, we show that ectopic A-rich motifs dramatically accelerate base pairing between DsrA sRNA and a minimal rpoS mRNA in the presence of Hfq, demonstrating that proximity and orientation predict the activity of Hfq on long RNAs. |
format | Online Article Text |
id | pubmed-3458560 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-34585602012-09-27 Hfq proximity and orientation controls RNA annealing Panja, Subrata Woodson, Sarah A. Nucleic Acids Res RNA Regulation of bacterial gene networks by small non-coding RNAs (sRNAs) requires base pairing with messenger RNA (mRNA) targets, which is facilitated by Hfq protein. Hfq is recruited to sRNAs and mRNAs through U-rich- and A-rich-binding sites, respectively, but their distance from the sRNA–mRNA complementary region varies widely among different genes. To determine whether distance and binding orientation affect Hfq’s chaperone function, we engineered ‘toy’ RNAs containing strong Hfq-binding sites at defined distances from the complementary target site. We show that RNA annealing is fastest when the distal face of Hfq binds an A-rich sequence immediately 3′ of the target. This recruitment advantage is lost when Hfq binds >20 nt away from the target, but is partially restored by secondary structure that shortens this distance. Although recruitment through Hfq’s distal face accelerates RNA annealing, tight binding of six Us to Hfq’s proximal face inhibits annealing. Finally, we show that ectopic A-rich motifs dramatically accelerate base pairing between DsrA sRNA and a minimal rpoS mRNA in the presence of Hfq, demonstrating that proximity and orientation predict the activity of Hfq on long RNAs. Oxford University Press 2012-09 2012-07-02 /pmc/articles/PMC3458560/ /pubmed/22761405 http://dx.doi.org/10.1093/nar/gks618 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | RNA Panja, Subrata Woodson, Sarah A. Hfq proximity and orientation controls RNA annealing |
title | Hfq proximity and orientation controls RNA annealing |
title_full | Hfq proximity and orientation controls RNA annealing |
title_fullStr | Hfq proximity and orientation controls RNA annealing |
title_full_unstemmed | Hfq proximity and orientation controls RNA annealing |
title_short | Hfq proximity and orientation controls RNA annealing |
title_sort | hfq proximity and orientation controls rna annealing |
topic | RNA |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458560/ https://www.ncbi.nlm.nih.gov/pubmed/22761405 http://dx.doi.org/10.1093/nar/gks618 |
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