Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-0647, USA.
Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
Nat Commun. 2022 Jun 20;13(1):3526. doi: 10.1038/s41467-022-31214-6.
Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.
细菌 RNA 聚合酶（RNAP）中的启动子识别受 sigma 亚基控制。sigma 识别的关键序列基序，即 -10 启动子元件，位于转录起始位点上游约 10 个核苷酸的双链 DNA 分子的非模板链上。在这里，我们解释了噬菌体 AR9 非病毒 RNA 聚合酶（nvRNAP），一种细菌 RNAP 同源物，如何识别其含有脱氧尿苷的启动子的模板链上的 -10 元件。AR9 类似 sigma 的亚基、nvRNAP 酶核心以及模板链共同形成两个核苷酸碱基接受口袋，其形状决定了保守的脱氧尿苷的要求。AR9 类似 sigma 的亚基中的单个氨基酸取代允许其中一个口袋接受胸腺嘧啶，从而扩展了启动子的共识。我们的工作表明，病毒在多大程度上可以进化出源自宿主的多亚基酶，使其自身基因的转录独立于宿主。
