Beyond participating in splicing per se, some spliceosomal factors from higher eukaryotes play pivotal roles in coupling splicing to other RNA-processing events. The massive spliceosomal helicase Aquarius (172 kDa) binds at a specific location on the intron, where it acts as a key molecular linker between splicing, the deposition of the exon-junction complex and the formation of snoRNPs.
We determined two structures of the full-length human Aquarius in complex with an ATP analog and with a single-stranded RNA, providing snapshots of different steps of the catalytic pathway. The structures revealed the presence of specific accessory domains and evidence a novel mode of RNA binding by a helicase. Strikingly, we found that Aquarius exhibits opposite unwinding polarity in comparison to the structurally similar helicase Upf1, a key player in the non-sense mediated RNA decay. The Aquarius-RNA structure unraveled architectural adaptations that support the reversal of polarity and brought insightful implications into the structural and functional divergence of the two helicases.
Additionally, we identified an accessory domain from the armadillo-repeat (ARM) protein family. We evidenced that the ARM domain of Aquarius scaffolds a hetero-pentameric complex that acts as a vehicle for Aquarius recruitment to the spliceosome and guides its precise positioning on the intron by sensing the branch-site-associated U2 snRNP. Following these findings, we demonstrated that the
ATPase activity of Aquarius is important for splicing per se.