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Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex
Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895269/ https://www.ncbi.nlm.nih.gov/pubmed/24310371 http://dx.doi.org/10.1261/rna.041285.113 |
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author | Fu, Yang Deiorio-Haggar, Kaila Soo, Mark W. Meyer, Michelle M. |
author_facet | Fu, Yang Deiorio-Haggar, Kaila Soo, Mark W. Meyer, Michelle M. |
author_sort | Fu, Yang |
collection | PubMed |
description | Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not widely distributed across bacterial phyla. It is increasingly common for RNA motifs associated with ribosomal protein genes to be identified using comparative genomic methods, yet these are rarely experimentally validated. In this work, we characterize one such motif that precedes operons containing rpsF and rpsR, which encode ribosomal proteins S6 and S18. This RNA structure is widely distributed across many phyla of bacteria despite differences within the downstream operon, and examples are present in both E. coli and Bacillus subtilis. We demonstrate a direct interaction between an example of the RNA from B. subtilis and an S6:S18 complex using in vitro binding assays, verify our predicted secondary structure, and identify a putative protein-binding site. The proposed binding site bears a strong resemblance to the S18 binding site within the 16S rRNA, suggesting molecular mimicry. This interaction is a valuable addition to the canon of ribosomal protein mRNA interactions. This work shows how experimental verification translates computational results into concrete knowledge of biological systems. |
format | Online Article Text |
id | pubmed-3895269 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-38952692015-02-01 Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex Fu, Yang Deiorio-Haggar, Kaila Soo, Mark W. Meyer, Michelle M. RNA Articles Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not widely distributed across bacterial phyla. It is increasingly common for RNA motifs associated with ribosomal protein genes to be identified using comparative genomic methods, yet these are rarely experimentally validated. In this work, we characterize one such motif that precedes operons containing rpsF and rpsR, which encode ribosomal proteins S6 and S18. This RNA structure is widely distributed across many phyla of bacteria despite differences within the downstream operon, and examples are present in both E. coli and Bacillus subtilis. We demonstrate a direct interaction between an example of the RNA from B. subtilis and an S6:S18 complex using in vitro binding assays, verify our predicted secondary structure, and identify a putative protein-binding site. The proposed binding site bears a strong resemblance to the S18 binding site within the 16S rRNA, suggesting molecular mimicry. This interaction is a valuable addition to the canon of ribosomal protein mRNA interactions. This work shows how experimental verification translates computational results into concrete knowledge of biological systems. Cold Spring Harbor Laboratory Press 2014-02 /pmc/articles/PMC3895269/ /pubmed/24310371 http://dx.doi.org/10.1261/rna.041285.113 Text en © 2014 Fu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/3.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/. |
spellingShingle | Articles Fu, Yang Deiorio-Haggar, Kaila Soo, Mark W. Meyer, Michelle M. Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex |
title | Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex |
title_full | Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex |
title_fullStr | Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex |
title_full_unstemmed | Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex |
title_short | Bacterial RNA motif in the 5′ UTR of rpsF interacts with an S6:S18 complex |
title_sort | bacterial rna motif in the 5′ utr of rpsf interacts with an s6:s18 complex |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3895269/ https://www.ncbi.nlm.nih.gov/pubmed/24310371 http://dx.doi.org/10.1261/rna.041285.113 |
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