Wong Oi Kwan, Guthold Martin, Erie Dorothy A, Gelles Jeff
Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA.
PLoS Biol. 2008 Sep 30;6(9):e232. doi: 10.1371/journal.pbio.0060232.
At many promoters, transcription is regulated by simultaneous binding of a protein to multiple sites on DNA, but the structures and dynamics of such transcription factor-mediated DNA loops are poorly understood. We directly examined in vitro loop formation mediated by Escherichia coli lactose repressor using single-molecule structural and kinetics methods. Small ( approximately 150 bp) loops form quickly and stably, even with out-of-phase operator spacings. Unexpectedly, repeated spontaneous transitions between two distinct loop structures were observed in individual protein-DNA complexes. The results imply a dynamic equilibrium between a novel loop structure with the repressor in its crystallographic "V" conformation and a second structure with a more extended linear repressor conformation that substantially lessens the DNA bending strain. The ability to switch between different loop structures may help to explain how robust transcription regulation is maintained even though the mechanical work required to form a loop may change substantially with metabolic conditions.
在许多启动子处，转录是通过蛋白质同时结合到DNA上的多个位点来调控的，但是这种转录因子介导的DNA环的结构和动力学却知之甚少。我们使用单分子结构和动力学方法直接检测了由大肠杆菌乳糖阻遏物介导的体外环形成。即使操纵基因间距不同步，小（约150 bp）环也能快速稳定地形成。出乎意料的是，在单个蛋白质-DNA复合物中观察到了两种不同环结构之间的反复自发转变。结果表明，阻遏物处于其晶体学“V”构象的新型环结构与线性阻遏物构象更伸展从而显著降低DNA弯曲应变的第二种结构之间存在动态平衡。尽管形成环所需的机械功可能会随代谢条件而发生很大变化，但在不同环结构之间切换的能力可能有助于解释如何维持强大的转录调控。
