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S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In...

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Autores principales: Matelska, Dorota, Purta, Elzbieta, Panek, Sylwia, Boniecki, Michal J., Bujnicki, Janusz M., Dunin-Horkawicz, Stanislaw
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854524/
https://www.ncbi.nlm.nih.gov/pubmed/23980204
http://dx.doi.org/10.1261/rna.038794.113
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author Matelska, Dorota
Purta, Elzbieta
Panek, Sylwia
Boniecki, Michal J.
Bujnicki, Janusz M.
Dunin-Horkawicz, Stanislaw
author_facet Matelska, Dorota
Purta, Elzbieta
Panek, Sylwia
Boniecki, Michal J.
Bujnicki, Janusz M.
Dunin-Horkawicz, Stanislaw
author_sort Matelska, Dorota
collection PubMed
description Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5′ untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.
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spelling pubmed-38545242014-10-01 S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA Matelska, Dorota Purta, Elzbieta Panek, Sylwia Boniecki, Michal J. Bujnicki, Janusz M. Dunin-Horkawicz, Stanislaw RNA Bioinformatics Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5′ untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism. Cold Spring Harbor Laboratory Press 2013-10 /pmc/articles/PMC3854524/ /pubmed/23980204 http://dx.doi.org/10.1261/rna.038794.113 Text en © 2013; 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 Bioinformatics
Matelska, Dorota
Purta, Elzbieta
Panek, Sylwia
Boniecki, Michal J.
Bujnicki, Janusz M.
Dunin-Horkawicz, Stanislaw
S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
title S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
title_full S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
title_fullStr S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
title_full_unstemmed S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
title_short S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA
title_sort s6:s18 ribosomal protein complex interacts with a structural motif present in its own mrna
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854524/
https://www.ncbi.nlm.nih.gov/pubmed/23980204
http://dx.doi.org/10.1261/rna.038794.113
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