Sedlyarova Nadezda, Rescheneder Philipp, Magán Andrés, Popitsch Niko, Rziha Natascha, Bilusic Ivana, Epshtein Vitaly, Zimmermann Bob, Lybecker Meghan, Sedlyarov Vitaly, Schroeder Renée, Nudler Evgeny
Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria.
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, 1030 Vienna, Austria.
Mol Cell. 2017 Jul 6;67(1):30-43.e6. doi: 10.1016/j.molcel.2017.05.025. Epub 2017 Jun 22.
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 inhibitory 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 environment. The mechanism of iRAPs involves active uncoupling of transcription and translation, making 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.
为了寻找通过与RNA聚合酶（RNAP）直接相互作用来调节转录的RNA信号，我们对富含RNAP结合RNA的大肠杆菌基因组文库进行了深度测序。许多天然的RNAP结合适体，称为RAP，被定位到基因组上。超过60%的大肠杆菌基因在其mRNA中携带RAP。结合体外和体内方法，我们鉴定了一组抑制性RAP（iRAP），它们促进Rho依赖性转录终止。必需基因nadD编码区内的一个代表性iRAP在稳定期和氧化应激条件下极大地降低了其转录输出，表明iRAPs可根据环境变化控制基因表达。iRAPs的作用机制涉及转录和翻译的主动解偶联，使新生RNA可被Rho利用。反义链中编码的iRAPs也通过减少转录干扰来促进基因表达。本质上，我们的工作揭示了一类广泛的顺式作用RNA信号，它们全局控制细菌转录。
