Genome-wide profiling of RNA damage and repair in vivo

项目总结/摘要 生物体之间，特别是微生物之间，对有限营养资源的竞争是一种竞争。 基本的生物现象。为了确保营养的重要份额，生物体采用各种 来消除竞争对手目标生物反过来又采用了几种防御机制 为了活下去在各种毒素中，核糖毒素由于其有效性而构成最大的组之一 破坏了基本的和普遍保守的蛋白质翻译系统。RNA修复似乎 是某些生物体用作核糖毒素解毒剂的防御机制。但我们的 理解核糖毒素造成的RNA损伤和细胞修复系统的RNA修复， 有限公司因此，本申请的总体目标是鉴定体内RNA靶标，其具有显著的生物学活性。 一些新的核糖毒素以及几个RNA修复系统在全基因组范围内，并阐明 新的核糖毒素和新的RNA修复进行RNA损伤和修复的分子机制 系统. 以RNA-seq为主要工具，结合生物信息学、微生物学、 生物化学和结构生物学，我们的目标是追求以下调查路线：（1）我们将 进行生物信息学分析，以确定新的核糖毒素和RNA修复系统的候选者;（2）我们将 采用RNA-seq来精确定位新核糖毒素对RNA损伤的位点;（3）我们将采用RNA-seq来 询问每个修复系统修复由各种核糖毒素造成的各种受损RNA的能力; 和（4）我们将通过体外生物化学表征验证RNA-seq结果，并进行结构分析。 研究RNA损伤和修复的各种成分。 如果包括毒素-抗毒素（TA）系统，几乎可以肯定的是，几乎所有的细菌物种 拥有核糖毒素。如果所提出的RNA修复系统得到实验验证，我们估计， 大约40%的细菌物种具有RNA修复能力。最后，根据我们的生物信息学 根据本申请中存在的分析，RNA修复可能发生在真核生物中。

Project Summary/Abstract Competition between organisms, microbes in particular, for limited resources of nutrition is a fundamental biological phenomenon. To ensure a significant share of nutrition, organisms employ a variety of toxins to eliminate the competition. The targeted organisms in turn employ several defense mechanisms to stay alive. Among various toxins, ribotoxins constitute one of the biggest groups due to their effectiveness in disabling the essential and universally conserved protein translation system. And RNA repair appears to be the defense mechanism employed by certain organisms as antidotes of ribotoxins. However, our understanding of both RNA damage inflicted by ribotoxins and RNA repair by cellular repair systems is limited. Therefore, the overall goals of this application are to identify in vivo RNA targets of a significant number of new ribotoxins as well as several RNA repair systems on a genome-wide scale, and to elucidate molecular mechanisms of RNA damage and repair carried out by new ribotoxins and new RNA repair systems. Employing RNA-seq as our main tool, combined with approaches of bioinformatics, microbiology, biochemistry, and structural biology, we aim to pursue the following lines of investigation: (1) We will perform bioinformatic analyses to identify candidates of new ribotoxins and RNA repair systems; (2) We will employ RNA-seq to pinpoint sites of RNA damage by new ribotoxins; (3) We will employ RNA-seq to interrogate each repair system on its ability to repair diverse damaged RNAs inflicted by various ribotoxins; and (4) We will validate RNA-seq results with in vitro biochemical characterization and carry out structural studies of various components of RNA damage and repair. If toxin-antitoxin (TA) systems are included, it is almost certain that virtually all bacteria species possess ribotoxins. If the proposed RNA repair systems are experimentally verified, we estimate that approximately 40% of bacterial species possess RNA repair capability. Finally, based on our bioinformatic analysis present in this application, RNA repair is likely to occur in eukaryotic organisms.