Ashwin and FAM98 paralogs define nuclear and cytoplasmic RNA ligase complexes for tRNA biogenesis and the unfolded protein response

Abstract

The tRNA ligase complex (tRNA-LC) seals tRNA exon halves in the nucleus after the removal of a single intron, and joins XBP1-mRNA exons in the cytoplasm as part of the unfolded protein response (UPR). This dual function requires simultaneous nuclear and cytoplasmic localization. Here, we reveal that Ashwin (ASW), the vertebrate-specific subunit of the tRNA-LC, serves as its nuclear import factor. ASW displays a dual nuclear localisation signal (NLS) which, upon disruption, leads to the retention of the tRNA-LC in the cytoplasm with a consequent impairment of pre-tRNA splicing and accumulation of 5 tRNA fragments. We also show that the tRNA-LC exists in three forms depending on which FAM98 paralog is chosen, either FAM98A, FAM98B or FAM98C. We find that ASW interacts exclusively with the FAM98B-containing complex, allowing its nuclear localization for tRNA biogenesis. Attaching an NLS to RTCB, the catalytic and indispensable subunit, rescues pre-tRNA splicing in cells depleted of ASW. We envision 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 for XBP1-mRNA splicing during UPR.