Cavanagh Amy T, Klocko Andrew D, Liu Xiaochun, Wassarman Karen M
Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
Mol Microbiol. 2008 Mar;67(6):1242-56. doi: 10.1111/j.1365-2958.2008.06117.x. Epub 2008 Jan 15.
6S RNA binds sigma70-RNA polymerase and downregulates transcription at many sigma70-dependent promoters, but others escape regulation even during stationary phase when the majority of the transcription machinery is bound by the RNA. We report that core promoter elements determine this promoter specificity; a weak -35 element allows a promoter to be 6S RNA sensitive, and an extended -10 element similarly determines 6S RNA inhibition except when a consensus -35 element is present. These two features together predicted that hundreds of mapped Escherichia coli promoters might be subject to 6S RNA dampening in stationary phase. Microarray analysis confirmed 6S RNA-dependent downregulation of expression from 68% of the predicted genes, which corresponds to 49% of the expressed genes containing mapped E. coli promoters and establishes 6S RNA as a global regulator in stationary phase. We also demonstrate a critical role for region 4.2 of sigma70 in RNA polymerase interactions with 6S RNA. Region 4.2 binds the -35 element during transcription initiation; therefore we propose one mechanism for 6S RNA regulation of transcription is through competition for binding region 4.2 of sigma70.
6S RNA与σ70-RNA聚合酶结合，并在许多依赖σ70的启动子处下调转录，但其他启动子即使在稳定期（此时大多数转录机制被RNA结合）也能逃避调控。我们报告核心启动子元件决定了这种启动子特异性；一个弱的-35元件使启动子对6S RNA敏感，而一个延伸的-10元件同样决定了6S RNA抑制作用，除非存在一致的-35元件。这两个特征共同预测，数百个已定位的大肠杆菌启动子在稳定期可能受到6S RNA的抑制。微阵列分析证实了6S RNA对68%的预测基因表达的依赖性下调，这相当于含有已定位大肠杆菌启动子的表达基因的49%，并确立了6S RNA作为稳定期的全局调节因子。我们还证明了σ70的4.2区域在RNA聚合酶与6S RNA相互作用中的关键作用。4.2区域在转录起始时与-35元件结合；因此我们提出6S RNA转录调控的一种机制是通过竞争结合σ70的4.2区域。
