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Viruses 2017, 9(5), 93; doi:10.3390/v9050093

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

1
Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
2
Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
3
Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
4
Department of Biomedical Sciences, University at Albany-SUNY, Albany, NY 12201, USA
*
Author to whom correspondence should be addressed.
Academic Editors: David J. Garfinkel and Katarzyna J. Purzycka
Received: 31 January 2017 / Revised: 20 April 2017 / Accepted: 21 April 2017 / Published: 26 April 2017
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Abstract

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. View Full-Text
Keywords: long terminal repeat-retrotransposon; Ty1; Saccharomyces cerevisiae; RNA secondary structure; RNA packaging; RNA kissing complex; pseudoknot; kissing loop; SHAPE analysis long terminal repeat-retrotransposon; Ty1; Saccharomyces cerevisiae; RNA secondary structure; RNA packaging; RNA kissing complex; pseudoknot; kissing loop; SHAPE analysis
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MDPI and ACS Style

Gamache, E.R.; Doh, J.H.; Ritz, J.; Laederach, A.; Bellaousov, S.; Mathews, D.H.; Curcio, M.J. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses 2017, 9, 93.

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