Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030.
Department of Chemistry and Biochemistry, University of St. Thomas, Houston, TX 77006.
Proc Natl Acad Sci U S A. 2021 Mar 9;118(10). doi: 10.1073/pnas.2020429118.
Eukaryotes share a conserved messenger RNA (mRNA) decay pathway in which bulk mRNA is degraded by exoribonucleases. In addition, it has become clear that more specialized mRNA decay pathways are initiated by endonucleolytic cleavage at particular sites. The transfer RNA (tRNA) splicing endonuclease (TSEN) has been studied for its ability to remove introns from pre-tRNAs. More recently it has been shown that single amino acid mutations in TSEN cause pontocerebellar hypoplasia. Other recent studies indicate that TSEN has other functions, but the nature of these functions has remained obscure. Here we show that yeast TSEN cleaves a specific subset of mRNAs that encode mitochondrial proteins, and that the cleavage sites are in part determined by their sequence. This provides an explanation for the counterintuitive mitochondrial localization of yeast TSEN. To identify these mRNA target sites, we developed a "comPARE" (comparative parallel analysis of RNA ends) bioinformatic approach that should be easily implemented and widely applicable to the study of endoribonucleases. The similarity of tRNA endonuclease-initiated decay to regulated IRE1-dependent decay of mRNA suggests that mRNA specificity by colocalization may be an important determinant for the degradation of localized mRNAs in a variety of eukaryotic cells.
真核生物共享一个保守的信使 RNA（mRNA）降解途径，其中大量的 mRNA 被核酸外切酶降解。此外，越来越明显的是，更多的专门的 mRNA 降解途径是由特定位点的内切核酸酶切割引发的。转移 RNA（tRNA）剪接内切酶（TSEN）因其能够从前 tRNA 中去除内含子而被研究。最近，已经表明 TSEN 中的单个氨基酸突变导致桥小脑发育不良。最近的其他研究表明，TSEN 具有其他功能，但这些功能的性质仍然不清楚。在这里，我们表明酵母 TSEN 切割编码线粒体蛋白的特定亚组的 mRNAs，并且切割位点部分由其序列决定。这为酵母 TSEN 的反直觉的线粒体定位提供了一个解释。为了识别这些 mRNA 靶标位点，我们开发了一种“comPARE”（RNA 末端的比较平行分析）生物信息学方法，该方法应该易于实现并且广泛适用于内切核酸酶的研究。tRNA 内切酶起始的降解与受调控的 IRE1 依赖性 mRNA 降解的相似性表明，通过共定位的 mRNA 特异性可能是各种真核细胞中局部化 mRNAs 降解的重要决定因素。
