An altered basis of tRNA processing is linked to a distinct La protein in T. thermophila

La proteins bind the UUU-3’OH sequence found at the 3’-end of nascent RNA polymerase III transcripts, including pre-tRNAs, using a tandem arrangement of a winged-helix fold La motif (LaM) and an adjacent RNA recognition motif (RRM). La binding in diverse species results in protection of the 3’-end from exonucleases, stabilization of the pre-tRNA species and promotion of pre-tRNA folding until the UUU-3’OH containing trailer is endonucleolytically cleaved. Based on sequence conservation in the LaM, the Tetrahymena thermophila protein MLP1 (and related factors in other alveolates) has been hypothesized to function as a genuine La protein, despite the absence of the adjacent RRM found in La proteins of all prior investigated species. We show that MLP1 functions as a genuine La protein in that it binds and affects the processing of pre-tRNAs in T. thermophila and when expressed as a heterologous factor in fission yeast, however, unlike in other examined eukaryotes, depletion of MLP1 results in 3’-trailer stabilization. We also observed that 3’-trailers in T. thermophila are uniquely shortened relative to other examined eukaryotes, and that 5’-leaders in this species have evolved to disfavour pre-tRNA leader/trailer pairing. Our data suggest that the variant MLP1 architecture relative to other genuine La proteins is linked to an altered mechanism of tRNA processing in T. thermophila. Size-selected and fragmented TGIRT-Seq librairies were generated from RNA samples originating from wild type (WT), partial knockout of MLP1 (KO) and MLP1 immunoprecipitation (MLP1_IP) Tetrahymena thermophila samples with three biological replicates each.