Deng Wenjun, Babu I Ramesh, Su Dan, Yin Shanye, Begley Thomas J, Dedon Peter C
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.
Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America.
PLoS Genet. 2015 Dec 15;11(12):e1005706. doi: 10.1371/journal.pgen.1005706. eCollection 2015 Dec.
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.
长期以来，人们一直认为转运RNA（tRNA）的转录后修饰在调节翻译速率和保真度方面起着关键作用。然而，它们在多大程度上决定整体蛋白质产量仍知之甚少。在这里，我们使用定量蛋白质组学来表明，tRNA甲基转移酶9（Trm9）催化的tRNAArg(UCU)和tRNAGlu(UUC)中摆动尿苷5-甲氧基羰基甲基（mcm5）和5-甲氧基羰基甲基-2-硫代（mcm5s2）修饰与来自富含其同源密码子的基因的蛋白质的选择性翻译之间存在直接联系。在控制蛋白质表达偏差和mRNA表达变化后，我们发现Trm9的缺失在正常和应激条件下均选择性损害来自富含AGA和GAA密码子的基因的蛋白质表达。此外，我们表明AGA和GAA密码子在转录本上以簇的形式高频出现，这可能在调节翻译中起作用。与这些结果一致，在缺乏mcm5U和mcm5s2U的酵母中核糖体暂停增强的蛋白质更有可能被下调，并且包含更多的AGA/GAA簇。总之，这些结果表明Trm9催化的tRNA修饰在调节细胞内蛋白质表达中起重要作用。
