Ashwin and FAM98 paralogs define nuclear and cytoplasmic RNA ligase complexes for tRNA biogenesis.

The tRNA ligase complex (tRNA-LC) seals tRNA exon halves in the nucleus during pre-tRNA splicing and XBP1-mRNA exons in the cytoplasm as part of the unfolded protein response (UPR). This dual function requires the tRNA-LC to be either nuclear or cytoplasmic. Here, we reveal that Ashwin (ASW), the vertebrate-specific subunit of the tRNA-LC, serves as its nuclear import factor. ASW contains a dual nuclear localisation signal (NLS) which, upon disruption, leads to the retention of the tRNA-LC in the cytoplasm, impairing pre-tRNA splicing with the consequent accumulation of 5' tRNA fragments. We also show that the tRNA-LC exists in three forms, depending on which FAM98 paralog is bound, either FAM98A, FAM98B or FAM98C. ASW interacts exclusively with the FAM98B-containing complex, ensuring its nuclear localization for tRNA biogenesis. Attaching an NLS to RTCB, the catalytic and indispensable tRNA-LC subunit, rescues pre-tRNA splicing in cells depleted of ASW. We hypothesize that vertebrates evolved ASW to localize a sub-population of tRNA-LC to the nucleus, while using FAM98 paralogs to retain a fraction of RTCB in the cytoplasm to splice XBP1-mRNA during UPR.