Control of Saccharomyces cerevisiae pre-tRNA processing by environmental conditions

Abstract

tRNA is essential for translation and decoding of the proteome. The yeast proteome responds to stress and tRNA biosynthesis contributes in this response by repression of tRNA transcription and alterations of tRNA modification. Here we report that the stress response also involves processing of pre-tRNA 3 ′ termini. By a combination of Northern analyses and RNA sequencing, we show that upon shift to elevated temperatures and/or to glycerol-containing medium, aberrant pre-tRNAs accumulate in yeast cells. For pre-tRNA UAU Ile and pre-tRNA UUU Lys these aberrant forms are unprocessed at the 5 ′ ends, but they possess extended 3 ′ termini. Sequencing analyses showed that partial 3 ′ processing precedes 5 ′ processing for pre-tRNA UAU Ile . An aberrant pre-tRNA Tyr that accumulates also possesses extended 3 ′ termini, but it is processed at the 5 ′ terminus. Similar forms of these aberrant pretRNAs are detected in the rex1Δ strain that is defective in 3 ′ exonucleolytic trimming of pre-tRNAs but are absent in the lhp1Δ mutant lacking 3 ′ end protection. We further show direct correlation between the inhibition of 3 ′ end processing rate and the stringency of growth conditions. Moreover, under stress conditions Rex1 nuclease seems to be limiting for 3 ′ end processing, by decreased availability linked to increased protection by Lhp1. Thus, our data document complex 3 ′ processing that is inhibited by stress in a tRNA-type and condition-specific manner. This stress-responsive tRNA 3 ′ end maturation process presumably contributes to fine-tune the levels of functional tRNA in budding yeast in response to environmental conditions.

Coupling of RNA polymerase III assembly to cell cycle progression in Saccharomyces cerevisiae

“…RNA isolation and northern hybridization was done as described previously [39], using 5 µg of RNA separated by electrophoresis on 10% polyacrylamide, 8 M urea gel. The following DIG-labeled oligonucleotides were used for RNA hybridization: tL(CAA) 5'-TATTCCCACAGTTAACTGCGGTC A-3'; tY(GUA) 5'-GAGAGTCGATTTCTTGC-3'; tF(GAA) 5'-GCGCTCTCCCAACTGAGCT-3'; and 5.8S rRNA, 5'-GCGTTGTTCATCGATGC-3'.…”

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

“…Here we extend this approach by applying it to tRNA-enriched size fragments with the aim to annotate and curate all tRNAs. Since tRNA processing, such as precursor trimming and intron removal, is a fast process (Foretek et al, 2016), we also aimed to enrich specifically for pre-tRNAs in order to identify and annotate the corresponding unique tRNA gene template. Thus, we performed PAR-CLIP on SSB, a conserved and ubiquitous protein involved in 3′ tRNA processing (Bayfield and Maraia, 2009; Bayfield et al, 2010; Stefano, 1984).…”

La Deletion from Mouse Brain Alters Pre-tRNA Metabolism and Accumulation of Pre-5.8S rRNA, with Neuron Death and Reactive Astrocytosis

“…Although we are unaware of other animal evidence that La functionally impacts pre-tRNA metabolism, it is accepted that 3= trailer-containing pre-tRNAs are destabilized in yeast with La deleted and stabilized by its overexpression (11,15,(135)(136)(137). Thus, by analogy, it might be expected that the observed decrease in 3= trailer-containing, spliced pre-tRNA Tyr in cKO cortex (46) was due to loss of La binding.…”