Influence of RNA structural elements on Ty1 retrotransposition

Abstract

The long-terminal repeat (LTR)-retrotransposon Ty1 is a mobile genetic element that replicates through an RNA intermediate. Retroelement genomic transcripts contain internal structures fundamental to gene expression and propagation. In addition, long non-coding antisense RNAs overlap the 5'-terminal region of the genomic RNA and confer post-translational copy number control. Although LTR- retrotransposons are functionally related to retroviruses, little is known about the structural determinants required for genomic RNA packaging or reverse transcription. This commentary summarizes two recent papers that provide the first snapshot of genomic RNA structures from the retrotransposon Ty1 involved in transposition. We combined structural approaches with functional and genetic assays to determine if antisense RNAs anneal with the genomic RNA. Analysis of various steps in the Ty1 life cycle showed that a novel RNA pseudoknot contributes to retrotransposon function. Comparing different RNA states provides additional information about regions potentially involved in Ty1 RNA dimerization or packaging.

Keywords: RNA packaging; RNA structure; Ty1 retrotransposon; pseudoknot; reverse transcription.

Figure 1. RNA secondary structure of nt 1–437 of Ty1 gRNA in the monomer state. tRNA-Met_i is shown in gray, cyclization motif in violet, PAL motifs in green.

Figure 2. Reciprocal interstrand interactions of the PAL motifs. This model is based on SHAPE constraints derived from the in vitro and in virio states of Ty1 RNA.

Figure 3. 3D structure model of Ty1 RNA. Proposed protein binding sites are depicted in blue.