Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism

IF 4.4 2区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Structure Pub Date : 2024-08-30 DOI:10.1016/j.str.2024.08.008

Szabolcs Bódizs, Petra Mészáros, Lukas Grunewald, Heikki Takala, Sebastian Westenhoff

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Abstract

Phytochromes are photoreceptor proteins in plants, fungi, and bacteria. They can adopt two photochromic states with differential biochemical responses. The structural changes transducing the signal from the chromophore to the biochemical output modules are poorly understood due to challenges in capturing structures of the dynamic, full-length protein. Here, we present cryoelectron microscopy (cryo-EM) structures of the phytochrome from Pseudomonas aeruginosa (PaBphP) in its resting (Pfr) and photoactivated (Pr) state. The kinase-active Pr state has an asymmetric, dimeric structure, whereas the kinase-inactive Pfr state opens up. This behavior is different from other known phytochromes and we explain it with the unusually short connection between the photosensory and output modules. Multiple sequence alignment of this region suggests evolutionary optimization for different modes of signal transduction in sensor proteins. The results establish a new mechanism for light-sensing by phytochrome histidine kinases and provide input for the design of optogenetic phytochrome variants.

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一种水底植物色素组氨酸激酶的低温电子显微镜结构揭示了一种独特的光依赖性激活机制

植物色素是植物、真菌和细菌中的感光蛋白质。它们可以采用两种光致变色状态，并做出不同的生化反应。由于难以捕捉动态全长蛋白质的结构，人们对从发色团向生化输出模块传递信号的结构变化知之甚少。在这里，我们展示了铜绿假单胞菌的植物色素（PaBphP）在静止（Pfr）和光激活（Pr）状态下的冷冻电子显微镜（cryo-EM）结构。激酶激活状态的 Pr 具有不对称的二聚体结构，而激酶不激活状态的 Pfr 则是开放的。这种行为不同于其他已知的植物色素，我们用光敏模块和输出模块之间异常短的连接来解释这种行为。该区域的多重序列比对表明，传感器蛋白质中不同的信号转导模式在进化过程中得到了优化。这些结果为植物色素组氨酸激酶的光感应建立了一种新的机制，并为设计光遗传植物色素变体提供了参考。

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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.