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Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA

The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT). To identify RNA motifs involved in dimerization and pa...

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Autores principales: Gamache, Eric R., Doh, Jung H., Ritz, Justin, Laederach, Alain, Bellaousov, Stanislav, Mathews, David H., Curcio, M. Joan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454406/
https://www.ncbi.nlm.nih.gov/pubmed/28445416
http://dx.doi.org/10.3390/v9050093
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author Gamache, Eric R.
Doh, Jung H.
Ritz, Justin
Laederach, Alain
Bellaousov, Stanislav
Mathews, David H.
Curcio, M. Joan
author_facet Gamache, Eric R.
Doh, Jung H.
Ritz, Justin
Laederach, Alain
Bellaousov, Stanislav
Mathews, David H.
Curcio, M. Joan
author_sort Gamache, Eric R.
collection PubMed
description The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT). To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1), a 1-nucleotide interhelical loop and an 8-bp stem (S2) that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging.
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spelling pubmed-54544062017-06-08 Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA Gamache, Eric R. Doh, Jung H. Ritz, Justin Laederach, Alain Bellaousov, Stanislav Mathews, David H. Curcio, M. Joan Viruses Article The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5′ terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT). To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1), a 1-nucleotide interhelical loop and an 8-bp stem (S2) that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging. MDPI 2017-04-26 /pmc/articles/PMC5454406/ /pubmed/28445416 http://dx.doi.org/10.3390/v9050093 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gamache, Eric R.
Doh, Jung H.
Ritz, Justin
Laederach, Alain
Bellaousov, Stanislav
Mathews, David H.
Curcio, M. Joan
Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA
title Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA
title_full Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA
title_fullStr Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA
title_full_unstemmed Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA
title_short Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA
title_sort structure-function model for kissing loop interactions that initiate dimerization of ty1 rna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454406/
https://www.ncbi.nlm.nih.gov/pubmed/28445416
http://dx.doi.org/10.3390/v9050093
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