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

Abstract

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.

Control of box C/D snoRNP assembly by N 6 ‐methylation of adenine

“…The nucleotide immediately 3′ of the GA sequence of SRP on the unbulged strand (C108 on the lower strand as drawn in Fig 7) is strongly conserved as cytosine, so creating a potential GAC methylation target. Examination of a recent crystal structure of SRP 58 (Appendix Fig S4B) shows that while this sequence did not adopt k‐turn conformation, consecutive trans sugar‐Hoogsteen G·A and A·G base pairs were formed that directed the adenine nucleobases into the minor groove of the juxtaposed helix 1 to make an A‐minor interaction to stabilize the tertiary structure. A107 N3 accepts an H‐bond from the O2′ of U24, and its O2′ donates an H‐bond to O2 of U24 (Fig 7B).…”

“…Below is shown methylated sequence, and its equivalent in the Alu element BC200. Both have been shown to be N 6 ‐methylated at the adenine boxed in red.The tertiary contact between helices 31 (green, containing the A·G pairs) and helix 1 (yellow) in the Alu domain of SRP, PDB 5AOX 58. The A·G pairs both form trans Hoogsteen‐sugar base pairs with the adenine bases directed into the minor groove of the H1 helix.…”

“…The tertiary contact between helices 31 (green, containing the A·G pairs) and helix 1 (yellow) in the Alu domain of SRP, PDB 5AOX 58. The A·G pairs both form trans Hoogsteen‐sugar base pairs with the adenine bases directed into the minor groove of the H1 helix.…”

Two modes of targeting transposable elements by piRNA pathway in human testis

“…One of the possible explanations could be the fact that Alu elements, which are the most abundant type of SINE class, hijack L1 reverse transcriptase for their retrotransposition (Dewannieux et al 2003). Furthermore, less than half of the length of an Alu element is required for an actual retrotransposition (Ahl et al 2015). Therefore, even an evolutionarily ancient and truncated insertion might still be capable of serving as substrate for a new retrotransposition event.…”

RNA Polymerase III Advances: Structural and tRNA Functional Views

“…Alu and related SINEs derived from RNAP III transcrips are not autonomous retroposons but are effective at commandeering the retrotransposition machinery of another type of mobile genetic element, the long interspersed element (LINE) which encode reverse transcriptase and integrase to propogate themselves [73]. Thus, there is an intimate relationship between class III genes and long retrotransposons.…”