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The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By usin...

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Detalles Bibliográficos
Autores principales: Li, Sanshu, Hwang, Xue Ying, Stav, Shira, Breaker, Ronald R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793209/
https://www.ncbi.nlm.nih.gov/pubmed/26843526
http://dx.doi.org/10.1261/rna.054890.115
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author Li, Sanshu
Hwang, Xue Ying
Stav, Shira
Breaker, Ronald R.
author_facet Li, Sanshu
Hwang, Xue Ying
Stav, Shira
Breaker, Ronald R.
author_sort Li, Sanshu
collection PubMed
description The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or “azaaromatics,” trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.
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spelling pubmed-47932092016-04-01 The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds Li, Sanshu Hwang, Xue Ying Stav, Shira Breaker, Ronald R. RNA Article The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or “azaaromatics,” trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics. Cold Spring Harbor Laboratory Press 2016-04 /pmc/articles/PMC4793209/ /pubmed/26843526 http://dx.doi.org/10.1261/rna.054890.115 Text en © 2016 Li et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by/4.0/ This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Li, Sanshu
Hwang, Xue Ying
Stav, Shira
Breaker, Ronald R.
The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
title The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
title_full The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
title_fullStr The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
title_full_unstemmed The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
title_short The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
title_sort yjdf riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793209/
https://www.ncbi.nlm.nih.gov/pubmed/26843526
http://dx.doi.org/10.1261/rna.054890.115
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