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Exploring the energy landscape of a SAM-I riboswitch
SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg(2+) and SAM ligand...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Netherlands
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8603990/ https://www.ncbi.nlm.nih.gov/pubmed/34698957 http://dx.doi.org/10.1007/s10867-021-09584-7 |
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author | Manz, Christoph Kobitski, Andrei Yu Samanta, Ayan Nienhaus, Karin Jäschke, Andres Nienhaus, Gerd Ulrich |
author_facet | Manz, Christoph Kobitski, Andrei Yu Samanta, Ayan Nienhaus, Karin Jäschke, Andres Nienhaus, Gerd Ulrich |
author_sort | Manz, Christoph |
collection | PubMed |
description | SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg(2+) and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg(2+) concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription. |
format | Online Article Text |
id | pubmed-8603990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Springer Netherlands |
record_format | MEDLINE/PubMed |
spelling | pubmed-86039902021-11-24 Exploring the energy landscape of a SAM-I riboswitch Manz, Christoph Kobitski, Andrei Yu Samanta, Ayan Nienhaus, Karin Jäschke, Andres Nienhaus, Gerd Ulrich J Biol Phys Original Paper SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg(2+) and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg(2+) concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription. Springer Netherlands 2021-10-26 2021-12 /pmc/articles/PMC8603990/ /pubmed/34698957 http://dx.doi.org/10.1007/s10867-021-09584-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Original Paper Manz, Christoph Kobitski, Andrei Yu Samanta, Ayan Nienhaus, Karin Jäschke, Andres Nienhaus, Gerd Ulrich Exploring the energy landscape of a SAM-I riboswitch |
title | Exploring the energy landscape of a SAM-I riboswitch |
title_full | Exploring the energy landscape of a SAM-I riboswitch |
title_fullStr | Exploring the energy landscape of a SAM-I riboswitch |
title_full_unstemmed | Exploring the energy landscape of a SAM-I riboswitch |
title_short | Exploring the energy landscape of a SAM-I riboswitch |
title_sort | exploring the energy landscape of a sam-i riboswitch |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8603990/ https://www.ncbi.nlm.nih.gov/pubmed/34698957 http://dx.doi.org/10.1007/s10867-021-09584-7 |
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