Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.
RNA. 2012 Oct;18(10):1934-45. doi: 10.1261/rna.033431.112. Epub 2012 Aug 24.
RNA surveillance systems function at critical steps during the formation and function of RNA molecules in all organisms. The RNA exosome plays a central role in RNA surveillance by processing and degrading RNA molecules in the nucleus and cytoplasm of eukaryotic cells. The exosome functions as a complex of proteins composed of a nine-member core and two ribonucleases. The identity of the molecular determinants of exosome RNA substrate specificity remains an important unsolved aspect of RNA surveillance. In the nucleus of Saccharomyces cerevisiae, TRAMP complexes recognize and polyadenylate RNAs, which enhances RNA degradation by the exosome and may contribute to its specificity. TRAMPs contain either of two putative RNA-binding factors called Air proteins. Previous studies suggested that these proteins function interchangeably in targeting the poly(A)-polymerase activity of TRAMPs to RNAs. Experiments reported here show that the Air proteins govern separable functions. Phenotypic analysis and RNA deep-sequencing results from air mutants reveal specific requirements for each Air protein in the regulation of the levels of noncoding and coding RNAs. Loss of these regulatory functions results in specific metabolic and plasmid inheritance defects. These findings reveal differential functions for Air proteins in RNA metabolism and indicate that they control the substrate specificity of the RNA exosome.
RNA 监测系统在所有生物体的 RNA 分子形成和功能的关键步骤中发挥作用。RNA 外切体通过在真核细胞的核和细胞质中加工和降解 RNA 分子，在 RNA 监测中发挥核心作用。外切体作为一个由九种核心蛋白和两种核糖核酸酶组成的复合物发挥作用。外切体 RNA 底物特异性的分子决定因素的鉴定仍然是 RNA 监测中一个重要的未解决的方面。在酿酒酵母的细胞核中，TRAMP 复合物识别并多聚腺苷酸化 RNA，这增强了外切体对 RNA 的降解作用，并可能有助于其特异性。TRAMP 包含两种假定的 RNA 结合因子之一，称为 Air 蛋白。先前的研究表明，这些蛋白在将 TRAMP 的多聚(A)聚合酶活性靶向 RNA 方面可互换发挥作用。这里报告的实验表明，Air 蛋白具有可分离的功能。空气突变体的表型分析和 RNA 深度测序结果显示，每个 Air 蛋白在调节非编码和编码 RNA 的水平方面都有特定的要求。失去这些调节功能会导致特定的代谢和质粒遗传缺陷。这些发现揭示了 Air 蛋白在 RNA 代谢中的不同功能，并表明它们控制 RNA 外切体的底物特异性。
