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Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding

The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We...

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Autores principales: Cannon, John G. D., Sherman, Rachel M., Wang, Victoria M. Y., Newman, Grace A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674897/
https://www.ncbi.nlm.nih.gov/pubmed/26656258
http://dx.doi.org/10.1038/srep18054
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author Cannon, John G. D.
Sherman, Rachel M.
Wang, Victoria M. Y.
Newman, Grace A.
author_facet Cannon, John G. D.
Sherman, Rachel M.
Wang, Victoria M. Y.
Newman, Grace A.
author_sort Cannon, John G. D.
collection PubMed
description The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We observed significant matching between an amino acid’s nucleobase affinity and corresponding codon content in both the standard genetic code and mitochondrial variants. Furthermore, we showed that knowledge of nucleobase preferences allows statistically significant prediction of protein primary sequence from mRNA using purely physiochemical information. Interestingly, ribosomal primary sequences were more accurately predicted than non-ribosomal sequences, suggesting a potential role for direct amino acid-nucleobase interactions in the genesis of amino acid-based ribosomal components. Finally, we observed matching between amino acid-nucleobase affinities and corresponding mRNA sequences in 35 evolutionarily diverse proteomes. We believe these results have important implications for the study of the evolutionary origins of the genetic code and protein-mRNA cross-regulation.
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spelling pubmed-46748972015-12-16 Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding Cannon, John G. D. Sherman, Rachel M. Wang, Victoria M. Y. Newman, Grace A. Sci Rep Article The role of amino acid-RNA nucleobase interactions in the evolution of RNA translation and protein-mRNA autoregulation remains an open area of research. We describe the inference of pairwise amino acid-RNA nucleobase interaction preferences using structural data from known RNA-protein complexes. We observed significant matching between an amino acid’s nucleobase affinity and corresponding codon content in both the standard genetic code and mitochondrial variants. Furthermore, we showed that knowledge of nucleobase preferences allows statistically significant prediction of protein primary sequence from mRNA using purely physiochemical information. Interestingly, ribosomal primary sequences were more accurately predicted than non-ribosomal sequences, suggesting a potential role for direct amino acid-nucleobase interactions in the genesis of amino acid-based ribosomal components. Finally, we observed matching between amino acid-nucleobase affinities and corresponding mRNA sequences in 35 evolutionarily diverse proteomes. We believe these results have important implications for the study of the evolutionary origins of the genetic code and protein-mRNA cross-regulation. Nature Publishing Group 2015-12-10 /pmc/articles/PMC4674897/ /pubmed/26656258 http://dx.doi.org/10.1038/srep18054 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Cannon, John G. D.
Sherman, Rachel M.
Wang, Victoria M. Y.
Newman, Grace A.
Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
title Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
title_full Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
title_fullStr Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
title_full_unstemmed Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
title_short Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
title_sort cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674897/
https://www.ncbi.nlm.nih.gov/pubmed/26656258
http://dx.doi.org/10.1038/srep18054
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