A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases
A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases
复制标题
多亚基 RNA 聚合酶进行转录延伸和回溯长暂停的动态模型
DOI：
10.1002/prot.24090
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发表时间：
2012-08-01
影响因子：
2.9
通讯作者：
Xie, Ping
中科院分区：
文献类型：
--
作者：
Xie, Ping
RNA聚合酶是将基因从DNA转录到RNA链上的酶。多亚基RNA聚合酶的转录延伸是进行性的，但不均匀：一种酶可以沿着DNA模板移位沿着数千个核苷酸添加步骤，但有时，它可以进入回溯长的停顿。在这里，我们提出了一个布朗棘轮模型的进行性转录延长和回溯长停顿，这是发展的基础上，现有的结构和生化研究。使用该模型，我们分析研究了转录延伸的动力学，如外力和NTP浓度对无停顿的转录速度的影响，以及回溯长停顿的动力学，如进入和返回回溯停顿的概率，分析结果与现有的单分子实验数据吻合得很好。大肠杆菌和酿酒酵母RNA聚合酶的几个参数的值，如它们的DNA/RNA底物在转录延伸的亲和力进行了测定。此外，一些可检验的预测。Proteins 2012; © 2012 Wiley Periodicals，Inc.
RNA polymerases are enzymes that transcribe genes from DNA onto strands of RNA. The transcription elongation by multisubunit RNA polymerases is processive but nonuniform: one enzyme can translocate along the DNA template for thousands of nucleotide addition steps but, sometimes, it can enter backtracking long pauses. Here, we present a Brownian ratchet model for the processive transcription elongation and the backtracking long pauses, which is developed based on the available structural and biochemical studies. Using the model, we analytically study the dynamics of the transcription elongation, such as the effects of external force and NTP concentration on the transcription velocity free of pauses, and the dynamics of backtracking long pauses, such as the probabilities of entering and returning from the backtracking pauses, with the analytical results in good agreement with the available single molecule experimental data. Values of several parameters for both Escherichia coli and Saccharomyces cerevisiae RNA polymerases such as their affinities for the DNA/RNA substrate during transcription elongation are determined. Moreover, some testable predictions are presented. Proteins 2012; © 2012 Wiley Periodicals, Inc.