3′ processing of eukaryotic precursor tRNAs

Abstract

Biogenesis of eukaryotic tRNAs requires transcription by RNA polymerase III and subsequent processing. 5′ processing of precursor tRNA occurs by a single mechanism, cleavage by RNase P, and usually occurs before 3′ processing although some conditions allow observation of the 3′-first pathway. 3′ processing is relatively complex and is the focus of this review. Precursor RNA 3′ end formation begins with pol III termination generating a variable length 3′ oligo(U) tract that represents an underappreciated and previously unreviewed determinant of processing. Evidence that the pol III-intrinsic 3′ exonuclease activity mediated by Rpc11p affects 3′ oligo(U) length is reviewed. In addition to multiple 3′ nucleases, pre-tRNA processing involves La and Lsm, distinct oligo(U)-binding proteins with proposed chaperone activities. 3′ processing is performed by the endonuclease RNase Z or the exonuclease Rex1p (possibly others) along alternate pathways conditional on La. We review a S. pombe tRNA reporter system that has been used to distinguish two chaperone activities of La protein to its two conserved RNA binding motifs. Pre-tRNAs with structural impairments are degraded by a nuclear surveillance system that mediates polyadenylation by the TRAMP complex followed by 3′ digestion by the nuclear exosome which appears to compete with 3′ processing. We also try to reconcile limited data on pre-tRNA processing and Lsm proteins which largely affects precursors but not mature tRNAs. A pathway is proposed in which 3′ oligo(U) length is a primary determinant of La binding with subsequent steps distinguished by 3′ endo-vs. exo-nucleases, chaperone activities and nuclear surveillance.

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

“…Although this review focuses on the studies from yeast, for perspective and where information is available, similarities and differences of the processes in budding yeast to those in other organisms are described. Many of the subjects considered here have been the subjects of other recent reviews (Hopper and Shaheen 2008;Hopper et al 2010;Phizicky and Alfonzo 2010;Phizicky and Hopper 2010;Rubio and Hopper 2011;Maraia and Lamichhane 2011;Parker 2012). Therefore, this article emphasizes the use of genetic and genomic analyses in yeast that led to the discoveries and provides information on new discoveries not previously reviewed.…”

“…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 exo-and endonucleases have been proposed to have differential access to particular pre-tRNAs dependent upon tRNA binding by the La protein (Lhp1), such that La binding to tRNA 39 ends inhibits access to Rex1 and 39 maturation occurs via Trz1-mediated endonucleolytic cleavage (Yoo and Wolin 1997).…”

“…So it is surprising that two separate pathways for tRNA turnover have been discovered (reviewed in Phizicky and Hopper 2010;Maraia and Lamichhane 2011;Parker 2012;Wolin et al 2012). Both tRNA turnover pathways appear to function in tRNA quality control, eliminating tRNAs that are inappropriately processed, modified, or folded ( Figure 5).…”

tsRNA signatures in cancer

“…Recently, a class of small ncRNAs was reported to derive from tRNA precursor or mature sequences, and their connection with cancer is currently under investigation (4). In eukaryotic cells, tRNAs are transcribed by RNA polymerase III, with transcription terminating after a stretch of four or more Ts located 10-60 nt downstream of the 3′ end of the tRNA mature sequence (5,6). Pre-tRNAs and mature tRNAs undergo extensive modifications before and after exportation to the cytoplasm (7) resulting in the production of three types of tRNA-derived ncRNAs: tRNA-derived small RNAs (tsRNAs) (4), tRNA halves (tiRNAs) (8), and tRNA-derived fragments (tRFs or tDRs) (9,10).…”

“…Pre-tRNAs and mature tRNAs undergo extensive modifications before and after exportation to the cytoplasm (7) resulting in the production of three types of tRNA-derived ncRNAs: tRNA-derived small RNAs (tsRNAs) (4), tRNA halves (tiRNAs) (8), and tRNA-derived fragments (tRFs or tDRs) (9,10). tsRNAs are generated in the nucleus as a consequence of the pre-tRNA 3′ end cleavage (4), whereas tiRNAs are generated from mature tRNAs by cytoplasmic angiogenin activated in response to stress (6,11). The biogenesis of tRFs is currently under investigation, but a Dicer-dependent cleavage of mature tRNAs in the cytoplasm has been proposed as a possible mechanism of tRF production (12)(13)(14).…”