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Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo
Histone mRNA degradation is controlled by the unique 3’ stem-loop of histone mRNA and the stem-loop binding protein (SLBP). As part of this process, the 3’ stem-loop is trimmed by the histone-specific 3’ exonuclease (3’hExo) and uridylated by the terminal uridylyl transferase 7 (TUT7), creating part...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Taylor & Francis
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388802/ https://www.ncbi.nlm.nih.gov/pubmed/37516934 http://dx.doi.org/10.1080/15476286.2023.2171760 |
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author | Shine, Morgan Harris, Sarah E. Pellegrene, Kendy A. Kensinger, Adam H. Mihailescu, Mihaela Rita Evanseck, Jeffrey D. Lackey, Patrick E. |
author_facet | Shine, Morgan Harris, Sarah E. Pellegrene, Kendy A. Kensinger, Adam H. Mihailescu, Mihaela Rita Evanseck, Jeffrey D. Lackey, Patrick E. |
author_sort | Shine, Morgan |
collection | PubMed |
description | Histone mRNA degradation is controlled by the unique 3’ stem-loop of histone mRNA and the stem-loop binding protein (SLBP). As part of this process, the 3’ stem-loop is trimmed by the histone-specific 3’ exonuclease (3’hExo) and uridylated by the terminal uridylyl transferase 7 (TUT7), creating partially degraded intermediates with short uridylations. The role of these uridylations in degradation is not fully understood. Our work examines changes in the stability of the ternary complex created by trimming and uridylation of the stem-loop to better understand the role of this process in the histone mRNA life cycle. In this study, we used fluorescence polarization and electrophoretic mobility shift assays to demonstrate that both SLBP and 3’hExo can bind to uridylated and partially degraded stem-loop intermediates, although with lower affinity. We further characterized this complex by performing 1-µs molecular dynamics simulations using the AMBER force field and Nanoscale Molecular Dynamics (NAMD). These simulations show that while uridylation helps maintain the overall shape of the stem-loop, the combination of uridylation and dephosphorylation of the TPNK motif in SLBP disrupts key RNA–protein interactions. They also demonstrate that uridylation allows 3’hExo to maintain contact with the stem-loop after partial degradation and plays a role in disrupting key base pairs in partially degraded histone mRNA intermediates. Together, these experiments and simulations suggest that trimming by 3’hExo, uridylation, and SLBP dephosphorylation weakens both RNA–protein interactions and the stem-loop itself. Our results further elucidate the role of uridylation and SLBP dephosphorylation in the early stages of histone mRNA degradation. |
format | Online Article Text |
id | pubmed-10388802 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Taylor & Francis |
record_format | MEDLINE/PubMed |
spelling | pubmed-103888022023-08-01 Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo Shine, Morgan Harris, Sarah E. Pellegrene, Kendy A. Kensinger, Adam H. Mihailescu, Mihaela Rita Evanseck, Jeffrey D. Lackey, Patrick E. RNA Biol Research Paper Histone mRNA degradation is controlled by the unique 3’ stem-loop of histone mRNA and the stem-loop binding protein (SLBP). As part of this process, the 3’ stem-loop is trimmed by the histone-specific 3’ exonuclease (3’hExo) and uridylated by the terminal uridylyl transferase 7 (TUT7), creating partially degraded intermediates with short uridylations. The role of these uridylations in degradation is not fully understood. Our work examines changes in the stability of the ternary complex created by trimming and uridylation of the stem-loop to better understand the role of this process in the histone mRNA life cycle. In this study, we used fluorescence polarization and electrophoretic mobility shift assays to demonstrate that both SLBP and 3’hExo can bind to uridylated and partially degraded stem-loop intermediates, although with lower affinity. We further characterized this complex by performing 1-µs molecular dynamics simulations using the AMBER force field and Nanoscale Molecular Dynamics (NAMD). These simulations show that while uridylation helps maintain the overall shape of the stem-loop, the combination of uridylation and dephosphorylation of the TPNK motif in SLBP disrupts key RNA–protein interactions. They also demonstrate that uridylation allows 3’hExo to maintain contact with the stem-loop after partial degradation and plays a role in disrupting key base pairs in partially degraded histone mRNA intermediates. Together, these experiments and simulations suggest that trimming by 3’hExo, uridylation, and SLBP dephosphorylation weakens both RNA–protein interactions and the stem-loop itself. Our results further elucidate the role of uridylation and SLBP dephosphorylation in the early stages of histone mRNA degradation. Taylor & Francis 2023-07-30 /pmc/articles/PMC10388802/ /pubmed/37516934 http://dx.doi.org/10.1080/15476286.2023.2171760 Text en © 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent. |
spellingShingle | Research Paper Shine, Morgan Harris, Sarah E. Pellegrene, Kendy A. Kensinger, Adam H. Mihailescu, Mihaela Rita Evanseck, Jeffrey D. Lackey, Patrick E. Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo |
title | Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo |
title_full | Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo |
title_fullStr | Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo |
title_full_unstemmed | Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo |
title_short | Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3’hExo |
title_sort | uridylation of the histone mrna stem-loop weakens binding interactions with slbp while maintaining interactions with 3’hexo |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388802/ https://www.ncbi.nlm.nih.gov/pubmed/37516934 http://dx.doi.org/10.1080/15476286.2023.2171760 |
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