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, precursor tRNA(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 Schizosaccharomyces 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 affect 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 versus exo nucleases,chaperone activities, and nuclear surveillance.

Keywords: La protein; Lhp1; Lsm8; RNase P; Rex1; Rpc11; Rrp6; Sla1; TRAMP complex; Trf4; tRNase Z.

Figure 1

Alternative pathways for pre-tRNA processing begin during transcription termination by RNA polymerase III. This figure incorporates protein nomenclature from multiple organisms (see text). A) Pol III pauses at the tRNA gene terminator. According to structure modeling the integral pol III subunit, Rpc11p, contains a N-terminal domain that resides on the surface of pol III and an acidic hairpin that enters through a pore to the catalytic center. The acidic tip of the Rpc11p hairpin (designated “- -”) mediates RNA 3′ cleavage of nascent pre-tRNA transcripts during pausing by pol III. B) Nascent pre-tRNA transcripts with different length 3′ oligo(U) termini are released from pol III and sorted into those that bind La and those that do not, depicted on the right and left sides of the vertical dashed arrow respectively. C) Lsm proteins (presumably Lsm2p-8p) can affect the degree to which nascent pre-tRNAs are associated with La and may function at this point (see text). Pre-tRNA transcripts with sufficient 3′ oligo(U) length maintain stable association with La protein. D) Pre-tRNAs move along alternative pathways, numbered 1-4, depicted for normal pre-tRNAs (pathways 1 & 2) and structurally-impaired pre-tRNAs (pathways 3 & 4), distinguished by 3′ endonucleolytic (pathways 1 & 3), or 3′ exonucleolytic (pathways 2 & 4), as well as nuclear surveillance involving TRAMP and Rrp6p (pathway 4). La protein gains early dominance over the pre-tRNAs with sufficient 3′ oligo(U) length (see text). The exact point in this scheme at which the RNA chaperone-like activity of La (La activity 2) appears to function is unclear from current data but occurs sometime before RNase Z separates the trailer from the tRNA body.