Transcriptome and translatome of Streptomyces avermitilis MA-4680

The gram-positive bacterium, Streptomyces avermitilis holds industrial importance, which produces widely used anthelmintic agent, avermectin. Furthermore, S. avermitilis is generally considered as a prominent heterologous gene expression host for diverse secondary metabolites biosynthesis. However, despite of its industrial importance, it largely remains unknown how its genome is organized and regulated for timely gene expression. Here, we determined 1,601 transcription units (TU) encoded in its genome using the integrated analysis of high-throughput sequencing data including dRNA-Seq, Term-Seq, RNA-Seq, and Ribo-Seq. In addition to TU cataloguing, these information-rich results also revealed the presence of diverse regulatory elements for the transcriptional and translational control of individual TU, such as promoters, 5¢-UTRs, terminators, 3¢-UTRs, and riboswitches. The conserved promoter sequences for transcription initiation were identified from 2,361 transcription start sites as 5¢-TANNNT and 5¢-TGAC for -10 and -35 elements, respectively. Interestingly, the -35 element and spacer length between them were critical for transcriptional regulation of functionally distinct genes. Total 2,017 transcription termination sites were detected from Term-Seq analysis, revealing that stem structure formation is a prerequisite for transcription termination and that Rho-independent termination prevails in S. avermitilis. Lastly, the TU architecture suggests the presence of novel small RNAs and cis-regulatory elements in the genome. Our findings will serve as invaluable resources for comprehensive understanding on regulatory features of S. avermitilis. Moreover, it is anticipated the elevation of its potential as the heterologous expression host for diverse secondary metabolite biosynthesis. Overall design: Profiles of 5' termini of primary transcripts, 3' termini of whole transcripts, whole transcripts and ribosome protected RNA fragements of Streptomyces avermitilis were generated by deep sequencing using Illumina Hi-Seq 2500

革兰氏阳性细菌阿维链霉菌（Streptomyces avermitilis）具有重要工业价值，其可合成广泛应用的驱虫剂阿维菌素。此外，阿维链霉菌通常被认为是用于合成多种次级代谢产物的优质异源基因表达宿主。然而，尽管其具有重要工业价值，人们对其基因组如何组织并调控以实现适时基因表达的机制仍知之甚少。本研究通过整合分析dRNA-Seq、Term-Seq、RNA-Seq及Ribo-Seq等高通量测序数据，解析了该菌基因组中编码的1601个转录单元（Transcription Unit, TU）。除构建转录单元目录外，这些富含信息的分析结果还揭示了多种可调控单个转录单元转录与翻译的调控元件，包括启动子、5'-非翻译区（5'-UTR）、终止子、3'-非翻译区（3'-UTR）以及核糖开关（riboswitch）。研究人员从2361个转录起始位点中鉴定出转录起始的保守启动子序列，其中-10区为5'-TANNNT，-35区为5'-TGAC。有趣的是，-35区及其与-10区间的间隔长度对功能不同基因的转录调控至关重要。通过Term-Seq分析共检测到2017个转录终止位点，结果表明茎环结构的形成是转录终止的必要条件，且Rho非依赖型转录终止在阿维链霉菌中占主导地位。最后，转录单元的结构暗示该基因组中存在新型小RNA（small RNA, sRNA）及顺式调控元件。本研究的发现将为全面解析阿维链霉菌的调控特征提供宝贵的资源。此外，该研究还有望提升其作为多种次级代谢产物合成异源表达宿主的应用潜力。总体实验设计：本研究利用Illumina HiSeq 2500平台进行深度测序，获取了阿维链霉菌的初级转录本5'端、完整转录本3'端、完整转录本及核糖体保护RNA片段的测序图谱。