Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation

Abstract

Although nascent noncoding RNAs can undergo maturation to functional RNAs or degradation by quality control pathways, the events that influence the choice of pathway are not understood. We report that the targeting of pre-tRNAs and certain other noncoding RNAs for decay by the TRAMP pathway is strongly influenced by competition between the La protein and the Rex1 exonuclease for access to their 39 ends. The La protein binds the 39 ends of many nascent noncoding RNAs, protecting them from exonucleases. We demonstrate that unspliced, end-matured, partially aminoacylated pre-tRNAs accumulate in yeast lacking the TRAMP subunit Trf4p, indicating that these pre-tRNAs normally undergo decay. By comparing RNA extracted from wild-type and mutant yeast strains, we show that Rex1p is the major exonuclease involved in pre-tRNA trailer trimming and may also function in nuclear CCA turnover. As the accumulation of end-matured pre-tRNAs in trf4D cells requires Rex1p, these pretRNAs are formed by exonucleolytic trimming. Accumulation of truncated forms of 5S rRNA and SRP RNA in trf4D cells also requires Rex1p. Overexpression of the La protein Lhp1p reduces both exonucleolytic pre-tRNA trimming in wild-type cells and the accumulation of defective RNAs in trf4D cells. Our experiments reveal that one consequence of Rex1p-dependent 39 trimming is the generation of aberrant RNAs that are targeted for decay by TRAMP.

An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors

“…For the pre-U4 snRNA and pre-U3 snoRNAs, we speculate that in addition to the role of Lhp1p in protecting newly synthesized 3′ ends from exonucleases (9,26), interactions with the C terminus could protect other vulnerable sites from endonucleases. For the mutant pre-tRNA Arg , where binding by Lhp1p to the pre-tRNA is required for production of aminoacylated mature tRNA (11), we favor a model in which contacts with the C terminus stabilize the correctly folded anticodon stem.…”

Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the YeastSaccharomyces cerevisiae

“…G 21 added to the 59 end of tRNA His is not shown. rRNA, and snRNAs (van Hoof et al 2000;Copela et al 2008;Ozanick et al 2009). RNase Z, Trz1, is the endonuclease that participates in 39 end processing for both mitochondrial and nuclear encoded tRNAs (Chen et al 2005;Daoud et al 2011;Maraia and Lamichhane 2011).…”

“…The activated substrate-containing TRAMP complex interacts with the nuclear exosome that contains two nucleases, Rrp6 and Rrp44, and numerous other proteins (Parker 2012). Interestingly, there appears to be competition between appropriate processing of pretRNA 39 trailer sequences by Rex1 and degradation by the TRAMP/nuclear exosome machinery (Copela et al 2008;Ozanick et al 2009). Thus, this 39 to 59 turnover machinery likely serves as a quality control pathway that monitors both appropriate tRNA nuclear modification as well as 39 end maturation.…”

Healing for destruction: tRNA intron degradation in yeast is a two-step cytoplasmic process catalyzed by tRNA ligase Rlg1 and 5′-to-3′ exonuclease Xrn1

“…To date, two tRNA degradation pathways have been identified in yeast as tRNA quality control mechanisms. The nuclear surveillance pathway provides one mechanism; pre-tRNA Met i lacking m 1 A 58 and pre-tRNAs with aberrant 39 ends are polyadenylated by the TRAMP complex and further degraded by the nuclear exosome (Kabada et al 2004;Copela et al 2008;Ozanick et al 2009). The other pathway, the rapid tRNA decay (RTD) pathway, destroys mature tRNAs that lack certain combinations of modifications or tRNAs that bear unstable T or acceptor stems (Chernyakov et al 2008;Whipple et al 2011).…”