A Comprehensive Analysis of Structural and Sequence Conservation in the TetR Family Transcriptional Regulators
A Comprehensive Analysis of Structural and Sequence Conservation in the TetR Family Transcriptional Regulators
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DOI：
10.1016/j.jmb.2010.05.062
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发表时间：
2010-07-23
影响因子：
5.6
通讯作者：
Davidson, Alan R.
中科院分区：
文献类型：
--
作者：
Yu, Zhou;Reichheld, Sean E.;Davidson, Alan R.
四环素抑制因子家族转录调节因子(TFR)是一类同源二聚体DNA结合蛋白，通常作为转录抑制因子发挥作用。它们的DNA结合活性因小分子配体的结合而变构失活。TFR是在细菌中发现的第三个最常见的转录调控家族，在非冗余蛋白质数据库中有10,000多个代表。此外，100多个独特的TFR结构已经用X射线结晶学进行了解析。在这项研究中，我们使用计算和实验方法来揭示TFR中存在的变化和守恒。虽然TFR结构非常多样化，但我们能够在它们的配体结合结构域中识别出一个保守的中心三角形，它构成了该结构的基础和配体结合腔的框架。尽管TFR的DNA结合域序列在整个家族中高度保守，但其配体结合域的序列是如此的多样化，以至于通常无法检测到成对的序列相似性。然而，通过分析TFR亚家族，我们能够确定配体结合域中可能对变构重要的不同保守区。为了帮助对TFR功能的大规模分析，我们开发了一种简单而可靠的计算方法来预测TFR操纵子序列，一种基于温度熔融的分析来测量DNA结合，以及一种可能适用于大多数TFR的通用配体结合分析。最后，我们对TFR结构的分析突出了它们的灵活性，并为该家族提供了一种保守的变构机制。(C)2010爱思唯尔有限公司。保留所有权利。
The tetracycline repressor family transcriptional regulators (TFRs) are homodimeric DNA-binding proteins that generally act as transcriptional repressors. Their DNA-binding activity is allosterically inactivated by the binding of small-molecule ligands. TFRs constitute the third most frequently occurring transcriptional regulator family found in bacteria with more than 10,000 representatives in the nonredundant protein database. In addition, more than 100 unique TFR structures have been solved by X-ray crystallography. In this study, we have used computational and experimental approaches to reveal the variations and conservation present within TFRs. Although TFR structures are very diverse, we were able to identify a conserved central triangle in their ligand-binding domains that forms the foundation of the structure and the framework for the ligand-binding cavity. While the sequences of DNA-binding domains of TFRs are highly conserved across the whole family, the sequences of their ligand-binding domains are so diverse that pairwise sequence similarity is often undetectable. Nevertheless, by analyzing subfamilies of TFRs, we were able to identify distinct regions of conservation in ligand-binding domains that may be important for allostery. To aid in large-scale analyses of TFR function, we have developed a simple and reliable computational approach to predict TFR operator sequences, a temperature melt-based assay to measure DNA binding, and a generic ligand-binding assay that will likely be applicable to most TFRs. Finally, our analysis of TFR structures highlights their flexibility and provides insight into a conserved allosteric mechanism for this family. (C) 2010 Elsevier Ltd. All rights reserved.