Three tRNA nuclear exporters in S. cerevisiae: parallel pathways, preferences, and precision

Abstract

tRNAs that are transcribed in the nucleus are exported to the cytoplasm to perform their iterative essential function in translation. However, the complex set of tRNA post-transcriptional processing and subcellular trafficking steps are not completely understood. In particular, proteins involved in tRNA nuclear export remain unknown since the canonical tRNA nuclear exportin, Los1/Exportin-t, is unessential in all tested organisms. We previously reported that budding yeast Mex67-Mtr2, a mRNA nuclear exporter, co-functions with Los1 in tRNA nuclear export. Here we employed in vivo co-purification of tRNAs with endogenously expressed nuclear exporters to document that Crm1 also is a bona fide tRNA nuclear exporter. We document that Los1, Mex67-Mtr2 and Crm1 possess individual tRNA preferences for forming nuclear export complexes with members of the 10 families of intron-containing pre-tRNAs. Remarkably, Mex67-Mtr2, but not Los1 or Crm1, is error-prone, delivering tRNAs to the cytoplasm prior to 5′ leader removal. tRNA retrograde nuclear import functions to monitor the aberrant leader-containing spliced tRNAs, returning them to the nucleus where they are degraded by 3′ to 5′ exonucleases. Overall, our work identifies a new tRNA nuclear exporter, uncovers exporter preferences for specific tRNA families, and documents contribution of tRNA nuclear import to tRNA quality control.

The life and times of a tRNA

“…The Los1/Exportin-t-independent tRNA nuclear exporters Mex67-Mtr2/NXF1-NXT1 and Crm1, which bind numerous RNAs and protein adapters (Reviews: (Kelly and Corbett 2009;Chatterjee et al 2018), would not necessarily have been expected to recognize all tRNA families equally well. As predicted, Mex67-Mtr2 and Crm1 have been documented to possess tRNA family preferences and these preferences differ from each other and from Los1 (Chatterjee et al 2022).…”

“…For budding yeast there are at least three additional tRNA nuclear exporters that function in parallel to Los1: (1) the −importin family member Msn5 which, for intron-containing tRNAs, appears to function solely in the tRNA nuclear re-export step (Murthi et al 2010;Huang and Hopper 2015); (2) the mRNA nuclear exporter Mex67-Mtr2 heterodimer, which functions in both the tRNA primary and nuclear re-export steps (Wu et al 2015;Chatterjee et al 2017); and (3) the −importin protein nuclear exporter, Crm1, which also functions in primary nuclear export (Wu et al 2015;Chatterjee et al 2022) (Fig. 8) .The RNA helicase, Dbp5, also functions in tRNA nuclear export (Lari et al 2019), but it likely serves as an adapter/scaffold for Mex67-Mtr2 and/or Crm1.…”

“…More recently, in vivo co-purification of nuclear exporters in complex with pre-tRNA cargo has served to assess tRNA nuclear export complexes (Huang and Hopper 2015). Both of these methodologies have documented that yeast Los1, Mex67-Mtr2, and Crm1 possess different preferences for each of the ten different tRNA families encoded by intron-containing genes (Chatterjee et al 2017;Chatterjee et al 2022). Moreover, vertebrate Exportin-t also has been reported to bind various tRNAs with different affinities (Li and Sprinzl 2006).…”

“…The tRNA retrograde pathway also serves an important role in tRNA quality control as demonstrated by studies in budding yeast (Kramer and Hopper 2013;Chatterjee et al 2022). Errors sometimes occur such that aberrant tRNAs that are unprocessed at the 5' and 3' termini or that are hypomodified are prematurely exported to the cytoplasm.…”

“…The levels of these inappropriate tRNAs increase upon deletion of the putative tRNA nuclear importer, Mtr10 (Kramer, 2013 #4276). Thus, tRNA retrograde nuclear import appears to remove aberrant tRNAs from the cytoplasm, returning them to the nucleus where they may be repaired and/or destroyed by the 5' to 3' nuclease Rat1 of the RTD pathway, or by the 3' to 5' nuclear surveillance pathway (Kramer and Hopper 2013;Chatterjee et al 2022). As described above, the retrograde pathway is also in apparent competition with the cytoplasmic RTD quality control pathway that destroys hypomodified tRNAs or tRNAs with destabilizing mutations (Whipple et al 2011;Kramer and Hopper 2013;Guy et al 2014).…”