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DNA错配导致构象改变从而利于蛋白质-DNA的识别
2020-10-24 21:53

美国杜克大学医学院Raluca Gordn和Hashim M. Al-Hashimi课题组合作在研究中取得进展。他们研究发现DNA错配导致构象改变从而利于蛋白质-DNA识别。该项研究成果在线发表在2020年10月21日出版的《自然》上。

在本研究中,研究人员研发了SaMBA(饱和错配结合测定)高通量测定法来探究DNA构象变化在转录因子-DNA识别中的作用。在SaMBA系统中,通过引入错配的碱基对预先导致DNA中的结构畸变,该畸变要比由Watson-Crick序列变化引起的畸变大得多。值得注意的是,大约10%的错配增加了转录因子的结合;在检测的22种转录因子中,每种转录因子都发现至少一种错配增加了结合亲和力。

错配还将非特异性位点转化为高亲和力位点,并将高亲和力位点转化为“超级位点”,与任何已知的典型结合位点相比,它们都具有更强的亲和力。高分辨率X衍射结构结合核磁共振测量和结构分析表明许多增加结合力的DNA错配会导致与蛋白质结合所引起的相似的畸变,从而降低了部分DNA畸变的能量成本。该工作表明构象转换是蛋白质-DNA识别的主要决定因素,并揭示了错配可以招募转录因子从而调节细胞中DNA的复制和修复。

据了解,转录因子通过识别特定的基因组序列来调节复杂的基因表达。尽管已经研究证明利用碱基读取结合结构域识别将转录因子结合到特定的DNA序列,但是关于蛋白质-DNA结合的一些基本知识仍然知之甚少。许多DNA结合蛋白会诱导固有B-DNA包膜之外的DNA结构发生变化。然而,关于扭曲DNA对转录因子识别的能量贡献知之甚少,因为扭曲DNA在未结合环境中的丰度很低。

附:英文原文

Title: DNA mismatches reveal conformational penalties in protein–DNA recognition

Author: Ariel Afek, Honglue Shi, Atul Rangadurai, Harshit Sahay, Alon Senitzki, Suela Xhani, Mimi Fang, Raul Salinas, Zachery Mielko, Miles A. Pufall, Gregory M. K. Poon, Tali E. Haran, Maria A. Schumacher, Hashim M. Al-Hashimi, Raluca Gordn

Issue&Volume: 2020-10-21

Abstract: Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein–DNA binding remain poorly understood1,2. Many DNA-binding proteins induce changes in the structure of the DNA outside the intrinsic B-DNA envelope. However, how the energetic cost that is associated with distorting the DNA contributes to recognition has proven difficult to study, because the distorted DNA exists in low abundance in the unbound ensemble3,4,5,6,7,8,9. Here we use a high-throughput assay that we term SaMBA (saturation mismatch-binding assay) to investigate the role of DNA conformational penalties in transcription factor–DNA recognition. In SaMBA, mismatched base pairs are introduced to pre-induce structural distortions in the DNA that are much larger than those induced by changes in the Watson–Crick sequence. Notably, approximately 10% of mismatches increased transcription factor binding, and for each of the 22 transcription factors that were examined, at least one mismatch was found that increased the binding affinity. Mismatches also converted non-specific sites into high-affinity sites, and high-affinity sites into ‘super sites’ that exhibit stronger affinity than any known canonical binding site. Determination of high-resolution X-ray structures, combined with nuclear magnetic resonance measurements and structural analyses, showed that many of the DNA mismatches that increase binding induce distortions that are similar to those induced by protein binding—thus prepaying some of the energetic cost incurred from deforming the DNA. Our work indicates that conformational penalties are a major determinant of protein–DNA recognition, and reveals mechanisms by which mismatches can recruit transcription factors and thus modulate replication and repair activities in the cell10,11.

DOI: 10.1038/s41586-020-2843-2

Source: https://www.nature.com/articles/s41586-020-2843-2

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:43.07
官方网址:http://www.nature.com/
投稿链接:http://www.nature.com/authors/submit_manuscript.html


本期文章:《自然》:Online/在线发表

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