Marcano-Velázquez Joan G, Batey Robert T
From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0596.
From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0596
J Biol Chem. 2015 Feb 13;290(7):4464-75. doi: 10.1074/jbc.M114.613497. Epub 2014 Dec 30.
Riboswitches are a broadly distributed form of RNA-based gene regulation in Bacteria and, more rarely, Archaea and Eukarya. Most often found in the 5'-leader sequence of bacterial mRNAs, they are generally composed of two functional domains: a receptor (aptamer) domain that binds an effector molecule and a regulatory domain (or expression platform) that instructs the expression machinery. One of the most studied riboswitches is the Bacillus subtilis adenine-responsive pbuE riboswitch, which regulates gene expression at the transcriptional level, up-regulating expression in response to increased intracellular effector concentrations. In this work, we analyzed sequence and structural elements that contribute to efficient ligand-dependent regulatory activity in a co-transcriptional and cellular context. Unexpectedly, we found that the P1 helix, which acts as the antitermination element of the switch in this RNA, supported ligand-dependent activation of a reporter gene over a broad spectrum of lengths from 3 to 10 bp. This same trend was also observed using a minimal in vitro single-turnover transcription assay, revealing that this behavior is intrinsic to the RNA sequence. We also found that the sequences at the distal tip of the terminator not directly involved in alternative secondary structure formation are highly important for efficient regulation. These data strongly support a model in which the switch is highly localized to the P1 helix adjacent to the ligand-binding pocket that likely presents a local kinetic block to invasion of the aptamer by the terminator.
核糖开关是细菌中一种广泛分布的基于RNA的基因调控形式,在古细菌和真核生物中较少见。它们最常出现在细菌mRNA的5'前导序列中,通常由两个功能域组成:一个结合效应分子的受体(适体)域和一个指导表达机制的调节域(或表达平台)。研究最多的核糖开关之一是枯草芽孢杆菌腺嘌呤响应性pbuE核糖开关,它在转录水平上调节基因表达,随着细胞内效应物浓度的增加而上调表达。在这项工作中,我们分析了在共转录和细胞环境中有助于有效依赖配体的调节活性的序列和结构元件。出乎意料的是,我们发现作为该RNA中开关的抗终止元件的P1螺旋,在3到10个碱基对的广泛长度范围内支持报告基因的依赖配体的激活。使用最小的体外单轮转录测定也观察到了相同的趋势,表明这种行为是RNA序列固有的。我们还发现,终止子远端末端不直接参与形成替代二级结构的序列对于有效调节非常重要。这些数据有力地支持了一个模型,即开关高度定位于与配体结合口袋相邻的P1螺旋,这可能对终止子侵入适体形成局部动力学障碍。