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Viruses. 2017 Apr 26;9(5). pii: E93. doi: 10.3390/v9050093.

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

Author information

1
Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA. egamache@iu.edu.
2
Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA. junghdoh@gmail.com.
3
Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA. justin.ritz1@gmail.com.
4
Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA. alain@unc.edu.
5
Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA. stasuofr@gmail.com.
6
Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA. David_Mathews@URMC.Rochester.edu.
7
Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA. joan.curcio@health.ny.gov.
8
Department of Biomedical Sciences, University at Albany-SUNY, Albany, NY 12201, USA. joan.curcio@health.ny.gov.

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.

KEYWORDS:

RNA kissing complex; RNA packaging; RNA secondary structure; SHAPE analysis; Saccharomyces cerevisiae; Ty1; kissing loop; long terminal repeat-retrotransposon; pseudoknot

PMID:
28445416
PMCID:
PMC5454406
DOI:
10.3390/v9050093
[Indexed for MEDLINE]
Free PMC Article

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