Pang Yan Ling Joy, Abo Ryan, Levine Stuart S, Dedon Peter C
Department of Biological Engineering and Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research & Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Nucleic Acids Res. 2014 Dec 16;42(22):e170. doi: 10.1093/nar/gku945. Epub 2014 Oct 27.
Emerging evidence points to roles for tRNA modifications and tRNA abundance in cellular stress responses. While isolated instances of stress-induced tRNA degradation have been reported, we sought to assess the effects of stress on tRNA levels at a systems level. To this end, we developed a next-generation sequencing method that exploits the paucity of ribonucleoside modifications at the 3'-end of tRNAs to quantify changes in all cellular tRNA molecules. Application of this tRNA-seq method to Saccharomyces cerevisiae identified all 76 expressed unique tRNA species out of 295 coded in the yeast genome, including all isoacceptor variants, with highly precise relative (fold-change) quantification of tRNAs. In studies of stress-induced changes in tRNA levels, we found that oxidation (H2O2) and alkylation (methylmethane sulfonate, MMS) stresses induced nearly identical patterns of up- and down-regulation for 58 tRNAs. However, 18 tRNAs showed opposing changes for the stresses, which parallels our observation of signature reprogramming of tRNA modifications caused by H2O2 and MMS. Further, stress-induced degradation was limited to only a small proportion of a few tRNA species. With tRNA-seq applicable to any organism, these results suggest that translational control of stress response involves a contribution from tRNA abundance.
新出现的证据表明，tRNA修饰和tRNA丰度在细胞应激反应中发挥作用。虽然已有应激诱导tRNA降解的个别报道，但我们试图从系统层面评估应激对tRNA水平的影响。为此，我们开发了一种新一代测序方法，该方法利用tRNA 3'端核糖核苷修饰的匮乏来量化所有细胞tRNA分子的变化。将这种tRNA测序方法应用于酿酒酵母，鉴定出酵母基因组编码的295种tRNA中的所有76种表达的独特tRNA种类，包括所有同功受体变体，并对tRNA进行了高精度的相对（倍数变化）定量。在应激诱导的tRNA水平变化研究中，我们发现氧化（H2O2）和烷基化（甲磺酸甲酯，MMS）应激诱导58种tRNA出现几乎相同的上调和下调模式。然而，18种tRNA在这两种应激下表现出相反的变化，这与我们观察到的由H2O2和MMS引起的tRNA修饰特征性重编程情况相似。此外，应激诱导的降解仅限于少数几种tRNA中的一小部分。由于tRNA测序适用于任何生物体，这些结果表明应激反应的翻译控制涉及tRNA丰度的作用。
