Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Fu, Yang, Deiorio-Haggar, Kaila, Soo, Mark W., Meyer, Michelle M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
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
_version_ 1782299950549303296
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
work_keys_str_mv AT fuyang bacterialrnamotifinthe5utrofrpsfinteractswithans6s18complex
AT deioriohaggarkaila bacterialrnamotifinthe5utrofrpsfinteractswithans6s18complex
AT soomarkw bacterialrnamotifinthe5utrofrpsfinteractswithans6s18complex
AT meyermichellem bacterialrnamotifinthe5utrofrpsfinteractswithans6s18complex