Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.
Biophys J. 2014 Jan 7;106(1):55-64. doi: 10.1016/j.bpj.2013.11.4487.
Previous electron-microscopic imaging has shown high RNA polymerase occupation densities in the 16S and 23S encoding regions and low occupation densities in the noncoding leader, spacer, and trailer regions of the rRNA (rrn) operons in E. coli. This indicates slower transcript elongation within the coding regions and faster elongation within the noncoding regions of the operon. Inactivation of four of the seven rrn operons increases the transcript initiation frequency at the promoters of the three intact operons and reduces the time for RNA polymerase to traverse the operon. We have used the DNA sequence-dependent standard free energy variation of the transcription complex to model the experimentally observed changes in the elongation rate along the rrnB operon. We also model the stimulation of the average transcription rate over the whole operon by increasing rate of transcript initiation. Monte Carlo simulations, taking into account initiation of transcription, translocation, and backward and forward tracking of RNA polymerase, partially reproduce the observed transcript elongation rate variations along the rrn operon and fully account for the increased average rate in response to increased frequency of transcript initiation.
先前的电子显微镜成像研究表明，在大肠杆菌的 rRNA（rrn）操纵子中，16S 和 23S 编码区的 RNA 聚合酶占据密度较高，而非编码的启动子、间隔区和尾随区的占据密度较低。这表明在编码区的转录延伸速度较慢，而在操纵子的非编码区的延伸速度较快。七个 rrn 操纵子中的四个失活会增加三个完整操纵子启动子处的转录起始频率，并减少 RNA 聚合酶穿过操纵子的时间。我们使用依赖于 DNA 序列的转录复合物的标准自由能变化来模拟 rrnB 操纵子上观察到的延伸率的变化。我们还通过增加转录本起始的速率来模拟整个操纵子的平均转录速率的刺激。考虑到转录起始、易位以及 RNA 聚合酶的前后跟踪的蒙特卡罗模拟，部分再现了观察到的 rrn 操纵子上转录本延伸率的变化，并完全解释了由于转录本起始频率增加而导致的平均速率增加。
