Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Cell Compartment-specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome

Małgorzata Zawadzka
ORCID logo ,
Angelika Andrzejewska-Romanowska
ORCID logo ,
Julita Gumna
,
David J. Garfinkel
ORCID logo ,
Katarzyna Pachulska-Wieczorek
* ORCID logo
Version 1 : Received: 21 July 2022 / Approved: 25 July 2022 / Online: 25 July 2022 (10:07:00 CEST)

A peer-reviewed article of this Preprint also exists.

Zawadzka, M.; Andrzejewska-Romanowska, A.; Gumna, J.; Garfinkel, D.J.; Pachulska-Wieczorek, K. Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome. Viruses 2022, 14, 2007. Zawadzka, M.; Andrzejewska-Romanowska, A.; Gumna, J.; Garfinkel, D.J.; Pachulska-Wieczorek, K. Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome. Viruses 2022, 14, 2007.

Abstract

The structural transitions RNAs undergo during trafficking are not well-understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon. Through a detailed comparison of nuclear Ty1 gRNA structure with those established in the cytoplasm, virus-like particles (VLPs), and synthesized in vitro, we detected Ty1 gRNA structural alternations that occur during retrotransposition. Full-length Ty1 gRNA serves as the mRNA for Gag and Gag-Pol proteins and as the genome that is reverse transcribed within VLPs. We show that about 60% of base pairs predicted for the nuclear Ty1 gRNA appear in the cytoplasm, and active translation does not account for such structural differences. Most of the shared base pairs are represented by short-range interactions, while the long-distance pairings seem unique for each compartment. Highly structured motifs tend to be preserved after nuclear export of Ty1 gRNA. In addition, our study highlights the important role of Ty1 Gag in mediating critical RNA:RNA interactions required for retrotransposition.

Keywords

RNA genome; RNA structure; Cell compartment-specific folding; LTR-retrotransposon; gRNA dimerization; gRNA cyclization; tRNA annealing; Ty1; Gag.

Subject

Biology and Life Sciences, Virology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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