Retrotransposition and Crystal Structure of an Alu RNP in the Ribosome-Stalling Conformation

The Alu element is the most successful human genomic parasite affecting development and causing disease. It originated as a retrotransposon during early primate evolution of the gene encoding the signal recognition particle (SRP) RNA. We defined a minimal Alu RNA sufficient for effective retrotransposition and determined a high-resolution structure of its complex with the SRP9/14 proteins. The RNA adopts a compact, closed conformation that matches the envelope of the SRP Alu domain in the ribosomal translation elongation factor-binding site. Conserved structural elements in SRP RNAs support an ancient function of the closed conformation that predates SRP9/14. Structure-based mutagenesis shows that retrotransposition requires the closed conformation of the Alu ribonucleoprotein particle and is consistent with the recognition of stalled ribosomes. We propose that ribosome stalling is a common cause for the cis-preference of the mammalian L1 retrotransposon and for the efficiency of the Alu RNA in hijacking nascent L1 reverse transcriptase. [Display omitted] •Identification of a minimal Alu RNA sufficient for retrotransposition•High-resolution crystal structure of a human Alu RNP in the closed conformation•An ancient Alu RNA structural core in SRP RNAs interfaces the ribosome•Targeting stalled ribosomes could overcome L1 cis-preference Ahl et al. determined the crystal structure of a conformationally closed Alu ribonucleoprotein particle that matters for the signal recognition particle and the retrotransposition of the human Alu element. A single Alu folding unit is sufficient for retrotransposition activity. It likely targets stalling ribosomes to recruit nascent L1 reverse transcriptase.