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Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch

The widespread Mn(2+)-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn(2+) homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four...

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Autores principales: Suddala, Krishna C., Price, Ian R., Dandpat, Shiba S., Janeček, Michal, Kührová, Petra, Šponer, Jiří, Banáš, Pavel, Ke, Ailong, Walter, Nils G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754395/
https://www.ncbi.nlm.nih.gov/pubmed/31541094
http://dx.doi.org/10.1038/s41467-019-12230-5
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author Suddala, Krishna C.
Price, Ian R.
Dandpat, Shiba S.
Janeček, Michal
Kührová, Petra
Šponer, Jiří
Banáš, Pavel
Ke, Ailong
Walter, Nils G.
author_facet Suddala, Krishna C.
Price, Ian R.
Dandpat, Shiba S.
Janeček, Michal
Kührová, Petra
Šponer, Jiří
Banáš, Pavel
Ke, Ailong
Walter, Nils G.
author_sort Suddala, Krishna C.
collection PubMed
description The widespread Mn(2+)-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn(2+) homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg(2+). Only upon adding sub-millimolar Mn(2+), however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn(2+) in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.
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spelling pubmed-67543952019-09-23 Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch Suddala, Krishna C. Price, Ian R. Dandpat, Shiba S. Janeček, Michal Kührová, Petra Šponer, Jiří Banáš, Pavel Ke, Ailong Walter, Nils G. Nat Commun Article The widespread Mn(2+)-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn(2+) homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg(2+). Only upon adding sub-millimolar Mn(2+), however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn(2+) in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics. Nature Publishing Group UK 2019-09-20 /pmc/articles/PMC6754395/ /pubmed/31541094 http://dx.doi.org/10.1038/s41467-019-12230-5 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Suddala, Krishna C.
Price, Ian R.
Dandpat, Shiba S.
Janeček, Michal
Kührová, Petra
Šponer, Jiří
Banáš, Pavel
Ke, Ailong
Walter, Nils G.
Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch
title Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch
title_full Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch
title_fullStr Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch
title_full_unstemmed Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch
title_short Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch
title_sort local-to-global signal transduction at the core of a mn(2+) sensing riboswitch
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754395/
https://www.ncbi.nlm.nih.gov/pubmed/31541094
http://dx.doi.org/10.1038/s41467-019-12230-5
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