Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing

In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computati...

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Main Authors:	Pancsa, Rita, Macossay-Castillo, Mauricio, Kosol, Simone, Tompa, Peter
Format:	Online
Language:	English
Published:	Nature Publishing Group 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999894/

id	pubmed-4999894
recordtype	oai_dc
spelling	pubmed-49998942016-09-07 Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing Pancsa, Rita Macossay-Castillo, Mauricio Kosol, Simone Tompa, Peter Article In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computational methods, we describe the structural and functional properties of previously proposed D. melanogaster and S. cerevisiae TR proteins and extensions. We found that in D. melanogaster TR affects long proteins in mainly regulatory roles. Their TR-extensions are structurally disordered and rich in binding motifs, which, together with their cell-type- and developmental stage-dependent inclusion, suggest that similarly to alternatively spliced exons they rewire cellular interaction networks in a temporally and spatially controlled manner. In contrast, yeast TR proteins are rather short and fulfil mainly housekeeping functions, like translation. Yeast extensions usually lack disorder and linear motifs, which precludes elucidating their functional relevance with sufficient confidence. Therefore we propose that by being much more restricted and by lacking clear functional hallmarks in yeast as opposed to fruit fly, TR shows remarkable parallels with alternative splicing. Additionally, the lack of conservation of TR extensions among orthologous TR proteins suggests that TR-mediated functions may be generally specific to lower taxonomic levels. Nature Publishing Group 2016-08-26 /pmc/articles/PMC4999894/ /pubmed/27561673 http://dx.doi.org/10.1038/srep32142 Text en Copyright © 2016, The Author(s) 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/
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Pancsa, Rita Macossay-Castillo, Mauricio Kosol, Simone Tompa, Peter
spellingShingle	Pancsa, Rita Macossay-Castillo, Mauricio Kosol, Simone Tompa, Peter Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing
author_facet	Pancsa, Rita Macossay-Castillo, Mauricio Kosol, Simone Tompa, Peter
author_sort	Pancsa, Rita
title	Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing
title_short	Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing
title_full	Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing
title_fullStr	Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing
title_full_unstemmed	Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing
title_sort	computational analysis of translational readthrough proteins in drosophila and yeast reveals parallels to alternative splicing
description	In translational readthrough (TR) the ribosome continues extending the nascent protein beyond the first in-frame termination codon. Due to the lack of dedicated analyses of eukaryotic TR cases, the associated functional-evolutionary advantages are still unclear. Here, based on a variety of computational methods, we describe the structural and functional properties of previously proposed D. melanogaster and S. cerevisiae TR proteins and extensions. We found that in D. melanogaster TR affects long proteins in mainly regulatory roles. Their TR-extensions are structurally disordered and rich in binding motifs, which, together with their cell-type- and developmental stage-dependent inclusion, suggest that similarly to alternatively spliced exons they rewire cellular interaction networks in a temporally and spatially controlled manner. In contrast, yeast TR proteins are rather short and fulfil mainly housekeeping functions, like translation. Yeast extensions usually lack disorder and linear motifs, which precludes elucidating their functional relevance with sufficient confidence. Therefore we propose that by being much more restricted and by lacking clear functional hallmarks in yeast as opposed to fruit fly, TR shows remarkable parallels with alternative splicing. Additionally, the lack of conservation of TR extensions among orthologous TR proteins suggests that TR-mediated functions may be generally specific to lower taxonomic levels.
publisher	Nature Publishing Group
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4999894/
_version_	1613636310089596928

Computational analysis of translational readthrough proteins in Drosophila and yeast reveals parallels to alternative splicing

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