Lal Avantika, Krishna Sandeep, Seshasayee Aswin Sai Narain
National Centre for Biological Sciences, and
Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, Karnataka, India.
G3 (Bethesda). 2018 May 31;8(6):2079-2089. doi: 10.1534/g3.118.200265.
In , the sigma factor σ directs RNA polymerase to transcribe growth-related genes, while σ directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ, and the non-coding 6S RNA which binds to the RNA polymerase-σ holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show that Rsd and 6S RNA facilitate σ activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.
在[具体情况未提及]中，σ因子σ指导RNA聚合酶转录与生长相关的基因，而在稳定期，σ指导应激反应基因的转录。两种被假设调节RNA聚合酶的分子是与σ结合的蛋白质Rsd和与RNA聚合酶-σ全酶结合的非编码6S RNA。尽管有多项研究，但Rsd和6S RNA的功能仍存在争议。在这里，我们在五个生长阶段使用RNA测序来在全基因组范围内阐明它们的功能。我们表明，Rsd和6S RNA在整个细菌生长过程中促进σ的活性，而6S RNA还根据生长阶段调节广泛不同的基因。我们发现了6S RNA与Rsd之间的新相互作用，并展示了在缺乏这两种调节因子的菌株中广泛的表达变化。最后，我们提出了一个转录数学模型，该模型强调Rsd和6S RNA之间的相互作用是控制σ因子竞争和全局基因表达的关键因素。
