Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.

Wenjun Deng,I Ramesh Babu,Thomas J Begley,Dan Su,Peter C Dedon,Shanye Yin,Alan G Hinnebusch

doi:10.1371/journal.pgen.1005706

Abstract

Post-transcriptional modifications of transfer RNAs (tRNAs) have long been recognized to play crucial roles in regulating the rate and fidelity of translation. However, the extent to which they determine global protein production remains poorly understood. Here we use quantitative proteomics to show a direct link between wobble uridine 5-methoxycarbonylmethyl (mcm5) and 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modifications catalyzed by tRNA methyltransferase 9 (Trm9) in tRNAArg(UCU) and tRNAGlu(UUC) and selective translation of proteins from genes enriched with their cognate codons. Controlling for bias in protein expression and alternations in mRNA expression, we find that loss of Trm9 selectively impairs expression of proteins from genes enriched with AGA and GAA codons under both normal and stress conditions. Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. Consistent with these results, proteins subject to enhanced ribosome pausing in yeast lacking mcm5U and mcm5s2U are more likely to be down-regulated and contain a larger number of AGA/GAA clusters. Together, these results suggest that Trm9-catalyzed tRNA modifications play a significant role in regulating protein expression within the cell.

Highlights

A striking feature of transfer RNAs (tRNAs) molecules is the large number of post-transcriptional modifications, representing up to 10% of the ribonucleoside content [1,2]
We present evidence for a more complicated role for transfer RNAs than as mere adapters that link the genetic code in messenger RNA to the amino acid sequence of a protein during translation. tRNAs have long been known to be modified with dozens of different chemical structures other than the 4 canonical ribonucleosides, PLOS Genetics | DOI:10.1371/journal.pgen
Modifications in or around the anticodon loop of tRNA affect translation rate and fidelity through stabilization of codon-anticodon pairing, while other modifications remote from the anticodon loop have specific roles in regulating tRNA stability and folding [1,3,4,6,7,8,9,10]. These observations fuel the hypothesis that tRNA modifications play a broader role in regulating global protein expression, with a focus here on wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) in budding yeast

Summary

Introduction

A striking feature of tRNA molecules is the large number of post-transcriptional modifications, representing up to 10% of the ribonucleoside content [1,2]. Modifications in or around the anticodon loop of tRNA affect translation rate and fidelity through stabilization of codon-anticodon pairing, while other modifications remote from the anticodon loop have specific roles in regulating tRNA stability and folding [1,3,4,6,7,8,9,10] These observations fuel the hypothesis that tRNA modifications play a broader role in regulating global protein expression, with a focus here on wobble uridine modifications catalyzed by tRNA methyltransferase 9 (Trm9) in budding yeast. Modification of the wobble uridine in tRNAArg(UCU), tRNAGly(UCC), tRNALys(UUU), tRNAGln(UUG) and tRNAGlu(UUC) requires a number of key activities (Fig 1). In association with Trm112, Trm will use cm5U as a substrate and catalyze the formation of 5-methoxycarbonyl-methyluridine (mcm5U) at the wobble position of tRNAArg(UCU), tRNAGly(UCC), tRNALys(UUU), tRNAGln(UUG) and tRNAGlu(UUC) (Fig 1) [11,12,13,14]. The wobble position of tRNALys(UUU), tRNAGln(UUG) and tRNAGlu(UUC) is further thiolated by an enzyme cascade involving Urm, Uba, Ctu, Ncs and Ncs to yield mcm5s2U (Fig 1) [11,12,14]

Results

Discussion

Conclusion