Evolutionary evidence for alternative structure in RNA sequence co-variation.

Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the functi...

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Autores principales:	Justin Ritz, Joshua S Martin, Alain Laederach
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/eb75c4770e06436ba6fef1d2f36ce839
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spelling	oai:doaj.org-article:eb75c4770e06436ba6fef1d2f36ce8392021-11-18T05:53:42ZEvolutionary evidence for alternative structure in RNA sequence co-variation.1553-734X1553-735810.1371/journal.pcbi.1003152https://doaj.org/article/eb75c4770e06436ba6fef1d2f36ce8392013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23935473/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. We set out to characterize the evolutionary co-variation supporting alternative conformations in riboswitches to determine the extent to which alternative secondary structures are conserved. We found strong co-variation support for the terminator, P1, and anti-terminator stems in the purine riboswitch by extending alignments to include terminator sequences. When we performed Boltzmann suboptimal sampling on purine riboswitch sequences with terminators we found that these sequences appear to have evolved to favor specific alternative conformations. We extended our analysis of co-variation to classic alignments of group I/II introns, tRNA, and other classes of riboswitches. In a majority of these RNAs, we found evolutionary evidence for alternative conformations that are compatible with the Boltzmann suboptimal ensemble. Our analyses suggest that alternative conformations are selected for and thus likely play functional roles in even the most structured of RNAs.Justin RitzJoshua S MartinAlain LaederachPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 7, p e1003152 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Justin Ritz Joshua S Martin Alain Laederach Evolutionary evidence for alternative structure in RNA sequence co-variation.
description	Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches), a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. We set out to characterize the evolutionary co-variation supporting alternative conformations in riboswitches to determine the extent to which alternative secondary structures are conserved. We found strong co-variation support for the terminator, P1, and anti-terminator stems in the purine riboswitch by extending alignments to include terminator sequences. When we performed Boltzmann suboptimal sampling on purine riboswitch sequences with terminators we found that these sequences appear to have evolved to favor specific alternative conformations. We extended our analysis of co-variation to classic alignments of group I/II introns, tRNA, and other classes of riboswitches. In a majority of these RNAs, we found evolutionary evidence for alternative conformations that are compatible with the Boltzmann suboptimal ensemble. Our analyses suggest that alternative conformations are selected for and thus likely play functional roles in even the most structured of RNAs.
format	article
author	Justin Ritz Joshua S Martin Alain Laederach
author_facet	Justin Ritz Joshua S Martin Alain Laederach
author_sort	Justin Ritz
title	Evolutionary evidence for alternative structure in RNA sequence co-variation.
title_short	Evolutionary evidence for alternative structure in RNA sequence co-variation.
title_full	Evolutionary evidence for alternative structure in RNA sequence co-variation.
title_fullStr	Evolutionary evidence for alternative structure in RNA sequence co-variation.
title_full_unstemmed	Evolutionary evidence for alternative structure in RNA sequence co-variation.
title_sort	evolutionary evidence for alternative structure in rna sequence co-variation.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/eb75c4770e06436ba6fef1d2f36ce839
work_keys_str_mv	AT justinritz evolutionaryevidenceforalternativestructureinrnasequencecovariation AT joshuasmartin evolutionaryevidenceforalternativestructureinrnasequencecovariation AT alainlaederach evolutionaryevidenceforalternativestructureinrnasequencecovariation
_version_	1718424701204692992

Evolutionary evidence for alternative structure in RNA sequence co-variation.

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