Natural RNA polymerase aptamers regulate transcription in E. coli [SELEX]

In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP) we deep-sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches we characterized a subset of RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing growth conditions. The mechanism of iRAPs involves active uncoupling of transcription and translation, making the nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription. Examination of RNAP-binding aptamers in E. coli based on a single paired-end SELEX library sequenced on an Illumina GA Iix

本研究旨在探寻可通过与RNA聚合酶（RNA polymerase, RNAP）直接相互作用调控转录的RNA信号，为此我们对富集了可结合RNAP的RNA的大肠杆菌（E. coli）基因组文库开展了深度测序。诸多天然的RNAP结合适体（RNAP-binding aptamers，被命名为RAPs）被定位至大肠杆菌基因组中，其中超过60%的大肠杆菌基因的mRNA内均带有RAPs。结合体外与体内实验手段，我们对一类可促进依赖Rho的转录终止的RAPs亚群（iRAPs）进行了功能表征。位于必需基因nadD编码区的代表性iRAP，可在稳定期与氧化应激条件下大幅降低该基因的转录产出，证实iRAPs可响应生长条件变化调控基因表达。iRAPs的作用机制涉及主动解偶联转录与翻译过程，使新生RNA可被Rho因子结合。由反义链编码的iRAPs亦可通过降低转录干扰促进基因表达。本质而言，本研究揭示了一类广泛存在的顺式作用RNA信号，可全局性调控细菌转录过程。本研究依托在Illumina GA Iix测序平台上完成测序的单个双端SELEX文库，对大肠杆菌中的RNAP结合适体进行了检测分析。