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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MDPI AG
2017-04-01
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| Series: | Viruses |
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| Online Access: | http://www.mdpi.com/1999-4915/9/5/93 |
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| author | Eric R. Gamache Jung H. Doh Justin Ritz Alain Laederach Stanislav Bellaousov David H. Mathews M. Joan Curcio |
| author_facet | Eric R. Gamache Jung H. Doh Justin Ritz Alain Laederach Stanislav Bellaousov David H. Mathews M. Joan Curcio |
| author_sort | Eric R. Gamache |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-22T19:06:51Z |
| format | Article |
| id | doaj.art-092065ad1c194d3f9c8436d34faf8610 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-22T19:06:51Z |
| publishDate | 2017-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-092065ad1c194d3f9c8436d34faf86102022-12-21T18:15:47ZengMDPI AGViruses1999-49152017-04-01959310.3390/v9050093v9050093Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNAEric R. Gamache0Jung H. Doh1Justin Ritz2Alain Laederach3Stanislav Bellaousov4David H. Mathews5M. Joan Curcio6Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USALaboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USADepartment of Biology, University of North Carolina, Chapel Hill, NC 27599, USADepartment of Biology, University of North Carolina, Chapel Hill, NC 27599, USADepartment of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USADepartment of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USALaboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USAThe 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.http://www.mdpi.com/1999-4915/9/5/93long terminal repeat-retrotransposonTy1Saccharomyces cerevisiaeRNA secondary structureRNA packagingRNA kissing complexpseudoknotkissing loopSHAPE analysis |
| spellingShingle | Eric R. Gamache Jung H. Doh Justin Ritz Alain Laederach Stanislav Bellaousov David H. Mathews M. Joan Curcio Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA Viruses long terminal repeat-retrotransposon Ty1 Saccharomyces cerevisiae RNA secondary structure RNA packaging RNA kissing complex pseudoknot kissing loop SHAPE analysis |
| 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 | long terminal repeat-retrotransposon Ty1 Saccharomyces cerevisiae RNA secondary structure RNA packaging RNA kissing complex pseudoknot kissing loop SHAPE analysis |
| url | http://www.mdpi.com/1999-4915/9/5/93 |
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