Sudzinová Petra, Kambová Milada, Ramaniuk Olga, Benda Martin, Šanderová Hana, Krásný Libor
Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czech Republic.
Microorganisms. 2021 Jan 1;9(1):87. doi: 10.3390/microorganisms9010087.
The expression of rRNA is one of the most energetically demanding cellular processes and, as such, it must be stringently controlled. Here, we report that DNA topology, i.e., the level of DNA supercoiling, plays a role in the regulation of σ-dependent rRNA promoters in a growth phase-dependent manner. The more negative DNA supercoiling in exponential phase stimulates transcription from rRNA promoters, and DNA relaxation in stationary phase contributes to cessation of their activity. Novobiocin treatment of cells relaxes DNA and decreases rRNA promoter activity despite an increase in the GTP level, a known positive regulator of rRNA promoters. Comparative analyses of steps during transcription initiation then reveal differences between rRNA promoters and a control promoter, P, whose activity is less affected by changes in supercoiling. Additional data then show that DNA relaxation decreases transcription also from promoters dependent on alternative sigma factors σ, σ, σ, σ, and σ with the exception of σ where the trend is the opposite. To summarize, this study identifies DNA topology as a factor important (i) for the expression of rRNA in in response to nutrient availability in the environment, and (ii) for transcription activities of RNAP holoenzymes containing alternative sigma factors.
rRNA的表达是细胞中能量需求最大的过程之一，因此必须受到严格控制。在此，我们报道DNA拓扑结构，即DNA超螺旋水平，以生长阶段依赖的方式在σ依赖性rRNA启动子的调控中发挥作用。指数生长期中更负的DNA超螺旋刺激rRNA启动子的转录，而稳定期的DNA松弛则导致其活性的停止。新生霉素处理细胞会使DNA松弛并降低rRNA启动子活性，尽管GTP水平升高，而GTP是已知的rRNA启动子的正调控因子。对转录起始过程中各步骤的比较分析揭示了rRNA启动子与对照启动子P之间的差异，P的活性受超螺旋变化的影响较小。其他数据表明，DNA松弛也会降低依赖于替代σ因子σ、σ、σ、σ和σ的启动子的转录，但σ除外，其趋势相反。总之，本研究确定DNA拓扑结构是一个重要因素：（i）对于在环境中营养物质可用性响应下的rRNA表达，以及（ii）对于含有替代σ因子的RNA聚合酶全酶的转录活性。
