Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Structure Pub Date : 2024-07-30 DOI:10.1016/j.str.2024.07.004

引用次数: 0

Abstract

Two retinal transcription factors, cone-rod homeobox (CRX) and neural retina leucine zipper (NRL), cooperate functionally and physically to control photoreceptor development and homeostasis. Mutations in CRX and NRL cause severe retinal diseases. Despite the roles of NRL and CRX, insight into their functions at the molecular level is lacking. Here, we have solved the crystal structure of the CRX homeodomain in complex with its cognate response element (Ret4) from the rhodopsin proximal promoter region. The structure reveals an unexpected 2:1 stoichiometry of CRX/Ret4 and unique orientation of CRX molecules on DNA, and it explains the mechanisms of pathogenic mutations in CRX. Mutations R41Q and E42K disrupt the CRX protein-protein contacts based on the structure and reduce the CRX/Ret4 binding stoichiometry, suggesting a novel disease mechanism. Furthermore, we show that NRL alters the stoichiometry and increases affinity of CRX binding at the rhodopsin promoter, which may enhance transcription of rod-specific genes and suppress transcription of cone-specific genes.

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Ret4 反应元件上 CRX/DNA 识别和化学计量的分子基础

两种视网膜转录因子--视锥-视杆细胞同源染色体（CRX）和神经视网膜亮氨酸拉链（NRL）--在功能和物理上相互配合，控制感光细胞的发育和稳态。CRX 和 NRL 的突变会导致严重的视网膜疾病。尽管 NRL 和 CRX 发挥着重要作用，但人们对它们在分子水平上的功能还缺乏深入了解。在这里，我们解析了 CRX 同源结构域与其来自视网膜近端启动子区域的同源反应元件（Ret4）复合物的晶体结构。该结构揭示了 CRX/Ret4 意外的 2:1 比例和 CRX 分子在 DNA 上的独特取向，并解释了 CRX 致病突变的机制。基于该结构，突变 R41Q 和 E42K 破坏了 CRX 蛋白与蛋白之间的接触，降低了 CRX/Ret4 结合的化学计量，提示了一种新的疾病机制。此外，我们还发现，NRL改变了CRX在视网膜启动子上的结合比例并增加了其亲和力，这可能会增强杆状特异性基因的转录并抑制视锥特异性基因的转录。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Structure 生物-生化与分子生物学

CiteScore

8.90

自引率

1.80%

发文量

155

审稿时长

3-8 weeks

期刊介绍： Structure aims to publish papers of exceptional interest in the field of structural biology. The journal strives to be essential reading for structural biologists, as well as biologists and biochemists that are interested in macromolecular structure and function. Structure strongly encourages the submission of manuscripts that present structural and molecular insights into biological function and mechanism. Other reports that address fundamental questions in structural biology, such as structure-based examinations of protein evolution, folding, and/or design, will also be considered. We will consider the application of any method, experimental or computational, at high or low resolution, to conduct structural investigations, as long as the method is appropriate for the biological, functional, and mechanistic question(s) being addressed. Likewise, reports describing single-molecule analysis of biological mechanisms are welcome. In general, the editors encourage submission of experimental structural studies that are enriched by an analysis of structure-activity relationships and will not consider studies that solely report structural information unless the structure or analysis is of exceptional and broad interest. Studies reporting only homology models, de novo models, or molecular dynamics simulations are also discouraged unless the models are informed by or validated by novel experimental data; rationalization of a large body of existing experimental evidence and making testable predictions based on a model or simulation is often not considered sufficient.