Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity.
Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity.
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相互作用的转录因子和 DNA 反应元件的相关进化压力可以指导 DNA 结合特异性的合理设计。
DOI：
10.1016/j.jmb.2005.04.054
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发表时间：
2005
期刊：
影响因子：
--
通讯作者：
Lichtarge,Olivier
中科院分区：
文献类型：
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作者：
Raviscioni,Michele;Gu,Peili;Sattar,Minawar;Cooney,AustinJ;Lichtarge,Olivier
了解转录因子蛋白和 DNA 之间特定相互作用的分子机制是理解基因表达调控和开发转录因子工程技术的关键。迄今为止，尽管已经多次尝试通过氨基酸碱基识别码、基于序列的图谱或相互作用的物理模型来阐明蛋白质-DNA 相互作用，但在设计 DNA 结合特异性方面取得的最大成功仍然处于实验阶段。在这里，我们提出了转录因子中氨基酸残基和 DNA 碱基对相互作用的相关进化压力的第一个系统证据，并表明它可以用于合理地设计 DNA 结合特异性。这种相关性存在于蛋白质残基和 DNA 碱基的相对进化重要性之间，分别用进化痕迹 (ET) 等级和信息熵来衡量。进化上最重要的残基与响应元件内最保守的碱基对相互作用，而最不重要的残基与最可变的碱基对相互作用。 12 个不相关的转录调节因子家族（包括核激素受体、基本螺旋-环-螺旋、ETS 和同源结构域家族）的相关性平均为 0.74。为了测试这种相关性的预测能力，我们针对转录因子 LRH-1 中排名最高的 ET 残基的突变交换。这按照预测重新定向了 LRH-1 结合，并表明，在这种情况下，进化重要性和结合特异性足够强地耦合，以便进化轨迹指导 DNA 结合特异性的计算设计。这证实了蛋白质-DNA 界面上进化重要性相关性的存在，并证明它是合理设计结合特异性的有用原理。
Understanding the molecular mechanisms of the specific interaction between transcription factor proteins and DNA is key to comprehend the regulation of gene expression and to develop technologies to engineer transcription factors. Thus far, although there have been several attempts to elucidate protein–DNA interaction through amino acid–base recognition codes, sequence based profiles, or physical models of interaction, the greatest successes in engineering DNA binding specificity remain experimental. Here we present the first systematic evidence of correlated evolutionary pressure at interacting amino acid residues and DNA base-pairs in transcription factors, and show that it can be used to rationally engineer DNA binding specificity. The correlation is between the relative evolutionary importance of protein residues and DNA bases, measured, respectively, in terms of the Evolutionary Trace (ET) rank and information entropy. The evolutionarily most important residues interact with the most conserved base-pairs within the response element while residues of least importance interact with the most variable base-pairs. The correlation averages 0.74 over 12 unrelated families of transcriptional regulators, including nuclear hormone receptors, basic helix–loop–helix, ETS- and homeo-domain family. To test the predictive power of this correlation, we targeted a mutational swap of top-ranked ET residues in a transcription factor, LRH-1. This redirects LRH-1 binding as predicted and showed that, in this case, evolutionary importance and binding specificity are coupled sufficiently strongly for the Evolutionary Trace to guide the computational design of DNA binding specificity. This establishes the existence of evolutionary importance correlation at protein–DNA interfaces, and demonstrates that it is a useful principle for the rational engineering of binding specificity.