Effects of RNase Y mutation on operon organization of Streptococcus pyogenes NZ131

Purpose: RNase Y is a major enzyme responsible for mRNA degradation in Streptococcus pyogenes. The goals of this study are to understand whether RNase Y plays a role in operon transcription of S. pyogenes NZ131 by using RNA-seq analysis. Methods: S. pyogenes mRNA profiles of wild type (WT) and RNase Y mutant (?rny) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. The sequence reads were aligned to the S. pyogenes genome using Bowtie2. The aligned files were sorted to BAM format and indexed using Samtools. The read depth of each base was derived from BAM files using BEDtools. Operon organization of S. pyogenes WT and ?rny strains were predicted based on base reads. Results: A total of 11 to 12 billion reads were obtained from each sample. More than 99% of these reads were mapped to the S. pyogenes genome. Predictions of operon organization using WT and ?rny samples showed little difference between the two strains. Conclusions: Our result shows that the mutation of RNase Y does not affect the operon organization of S. pyogenes NZ131. Overall design: Operon organization of S. pyogenes NZ131 wild type (WT) and RNase Y mutant (?rny) are compared by using RNA-seq analysis

研究目的：核糖核酸酶Y（RNase Y）是化脓性链球菌（Streptococcus pyogenes）中负责mRNA降解的核心酶。本研究旨在通过RNA测序（RNA-seq）分析，探究RNase Y是否参与化脓性链球菌NZ131的操纵子（operon）转录过程。
实验方法：采用Illumina HiSeq 2000测序平台，对野生型（WT）化脓性链球菌NZ131及其RNase Y缺失突变株（Δrny）的mRNA进行双重复深度测序。使用Bowtie2工具将测序读段比对至化脓性链球菌参考基因组；通过Samtools软件将比对结果排序并转换为BAM格式、构建索引；利用BEDtools工具从BAM文件中提取各碱基的测序深度信息。基于碱基读段数据，预测野生型与Δrny突变株的操纵子组织结构。
实验结果：每个样本共获得110~120亿条测序读段，其中超过99%的读段可比对至化脓性链球菌基因组。基于野生型与Δrny突变株样本的操纵子结构预测结果显示，两菌株间操纵子组织模式无显著差异。
研究结论：本研究结果表明，RNase Y的缺失突变不会影响化脓性链球菌NZ131的操纵子组织结构。
整体实验设计：通过RNA-seq分析，对比化脓性链球菌NZ131野生型（WT）与RNase Y缺失突变株（Δrny）的操纵子组织结构差异。