Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.
Department of Chemistry, Rice University, Houston, Texas 77005, United States.
J Phys Chem Lett. 2023 Apr 13;14(14):3422-3429. doi: 10.1021/acs.jpclett.3c00345. Epub 2023 Apr 3.
Cleavage of dinucleotides after the misincorporational pauses serves as a proofreading mechanism that increases transcriptional elongation accuracy. The accuracy is further improved by accessory proteins such as GreA and TFIIS. However, it is not clear why RNAP pauses and why cleavage-factor-assisted proofreading is necessary despite transcriptional errors being of the same order as those in downstream translation. Here, we developed a chemical-kinetic model that incorporates most relevant features of transcriptional proofreading and uncovers how the balance between speed and accuracy is achieved. We found that long pauses are essential for high accuracy, whereas cleavage-factor-stimulated proofreading optimizes speed. Moreover, in comparison to the cleavage of a single nucleotide or three nucleotides, RNAP backtracking and dinucleotide cleavage improve both speed and accuracy. Our results thereby show how the molecular mechanism and the kinetic parameters of the transcriptional process were evolutionarily optimized to achieve maximal speed and tolerable accuracy.
核苷酸二聚体在错配暂停后的切割可作为一种校对机制，提高转录延伸的准确性。辅助蛋白，如 GreA 和 TFIIS，进一步提高了准确性。然而，尚不清楚为什么 RNA 聚合酶会暂停，以及为什么尽管转录错误与下游翻译中的错误处于同一数量级，但需要切割因子辅助校对。在这里，我们开发了一个化学动力学模型，该模型整合了转录校对的大多数相关特征，并揭示了如何在速度和准确性之间取得平衡。我们发现，长暂停对于高准确性是必不可少的，而切割因子刺激的校对则优化了速度。此外，与单个核苷酸或三个核苷酸的切割相比，RNA 聚合酶回溯和二核苷酸切割提高了速度和准确性。因此，我们的研究结果表明，转录过程的分子机制和动力学参数是如何被进化优化的，以达到最大的速度和可容忍的准确性。
