Phytochromes: Structural Perspectives on Photoactivation and Signaling

光敏色素：光活化和信号传导的结构视角

• 批准号: 10708835
• 负责人: RICHARD DAVID VIERSTRA
• 金额: $ 32.34万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10708835
• 关键词: Acceleration; Advanced Development; Agriculture; Architecture; Back; Behavior; Bilin; Binding; Biochemical; Biology; Biotechnology; Collection; Coupled; Cryoelectron Microscopy; Crystallography; Data; Deuterium; Ecosystem; Electrons; Engineering; Environment; Event; Evolution; Family; Genetic Transcription; Goals; Growth and Development function; Head; Health; Human; Hydrogen; Influentials; Isomerism; Kinetics; Knowledge; Length; Life; Light; Link; Maps; Mass Spectrum Analysis; Measures; Medical; Membrane Proteins; Microscopic; Mission; Modality; Modeling; Molecular Conformation; Nature; Organism; Output; Paint; Pathway interactions; Perception; Performance; Photochemistry; Photons; Photoperiod; Photoreceptors; Physiological Processes; Phytochrome; Plant Model; Plants; Positioning Attribute; Process; Protein Isoforms; Proteins; Reaction; Reagent; Research; Signal Transduction; Source; Structure; Surface; Synchrotrons; Tail; Temperature; Temperature Sense; Tetrapyrroles; Time; Time Perception; Tissue imaging; Transcription Repressor; United States National Institutes of Health; Variant; Work; X-Ray Crystallography; absorption; chromophore; comparative; conformer; dimer; driving force; fluorophore; human pathogen; improved; information gathering; light intensity; member; microbial; microorganism; novel; optogenetics; oxidation; particle; pathogen; photoactivation; plant growth/development; protein-histidine kinase; three dimensional structure; three-dimensional modeling; tool; transcription factor; x-ray free-electron laser

PROJECT SUMMARY Almost all cellular organisms employ an array of photoreceptors to detect their light environment. Arguably the most influential are the phytochromes (Phys), a diverse group essential for plant development and the behavior of many bacterial, fungal, and algal species. By reversible photointerconversion of their bilin (or open-chain tetrapyrrole) chromophores between red light-absorbing Pr and far-red light-absorbing Pfr states, Phys act as photoswitches in various signaling cascades responsive to light intensity, duration, direction, and spectral quality. Moreover, through the thermal reversion of Pfr back to Pr, some Phys sense temperature through enthalpic effects on this reaction, and perceive photoperiod through the nighttime depletion of Pfr. The cumulative effects of this Pr/Pfr interconversion impact numerous physiological processes important to agriculture and the biology of harmful plant and human pathogens. In addition, their unique photochemistries provide invaluable optogenetic tools, including novel fluorophores for tissue imaging, and engineered photoswitches for regulating cellular events with remarkable temporal and spatial precision. Recently, we made great strides in understanding how Phys signal, with emerging structures suggesting that microbial and plant Phys use two distinct output modalities. Both start with light-triggered isomerization of the bilin, which drives a - stranded to -helical rearrangement of a hairpin loop that links the signature PHY and GAF domains. While photoactivated microbial Phys then connect torsional strain generated within the dimer to regulate an appended output domain (typically with histidine kinase activity), plant Phys have rearranged their domain organization to create a photosensitive dimeric platform that likely enables reversible binding and eventual degradation of the family of PIF transcriptional repressors. While current models helped illuminate gross changes required for endstate conversion, the intermediates of photoexcitation and ensuing structural changes necessary for creating a signaling-competent Pfr state remain uncertain. The objectives of this proposal are to complete these pictures through continued X-ray crystallographic and cryo-electron microscopic approaches followed by informed biochemical analyses of representatives in their inactive and active states. Specific aims are to: (1) exploit time-resolved serial X-ray crystallography to structurally define the intermediates generated by Phys after photon absorption; (2) generate more comprehensive structures of bacterial Phys, including models of full- length dimeric photoreceptors with their signal output modules; (3) develop a model for how plant Phys signal through structural studies on Pfr; (4) apply steady-state and time-resolved protein surface mapping to support the Phy photoconversion pathway(s) seen structurally; (5) develop models of Phys interacting with their downstream effectors, and (6) appreciate how diversity among plant Phy enables thermal/time perception by specific isoforms. Taken together, this project will provide an essential framework to better appreciate the structure, allosteric mechanisms, and evolution of the Phy superfamily. Understanding how microorganisms and plants sense light, temperature, and time would then have important ramifications for improving the agricultural performance of crop plants, understanding microbial ecosystems, controlling medically-relevant pathogens, and furthering the application of Phys as optogenetic reagents.

项目摘要 几乎所有的细胞生物都使用一系列的光感受器来检测它们的光环境。可以说是最 有影响力的是光敏色素（Phys），一种对植物发育和许多细菌的行为至关重要的不同群体， 真菌和藻类物种。通过它们的胆色素（或开链四吡咯）发色团的可逆光互变 在红光吸收Pr和远红光吸收Pfr状态之间，Phys在各种信号中充当光开关 级联响应光的强度，持续时间，方向和光谱质量。此外，通过热回复， Pfr返回到Pr，一些Phys通过对该反应的光效应来感知温度，并且通过 Pfr的夜间消耗。这种Pr/Pfr相互转换的累积效应影响了许多生理功能 对农业以及有害植物和人类病原体的生物学具有重要意义的过程。此外，其独特的 光化学提供了宝贵的光遗传学工具，包括用于组织成像的新型荧光团， 光开关以显著的时间和空间精度调节细胞事件。 最近，我们在理解Phys信号的方式方面取得了很大进展，新出现的结构表明微生物和 植物物理学使用两种不同的输出模式。两者都是从光引发的胆色素异构化开始的，这会驱动一个β- 链到连接签名PHY和GAF结构域的发夹环的β-螺旋重排。当被光活化时 然后微生物Phys连接二聚体内产生的扭转应变以调节附加的输出结构域（通常 具有组氨酸激酶活性），植物Phys已经重排了它们的结构域组织以产生光敏二聚体， 该平台可能使PIF转录抑制因子家族可逆结合并最终降解。 虽然目前的模型有助于阐明终态转换所需的总体变化， 和随后的结构变化所需的创造一个信号能力的Pfr状态仍然不确定。 本提案的目标是通过连续的X射线晶体学和低温电子学来完成这些图片 微观方法，然后在其非活性和活性状态下对代表进行知情的生化分析。 具体目标是：（1）利用时间分辨连续X射线晶体学来确定所产生的中间体的结构 通过光子吸收后的Phys;（2）生成更全面的细菌Phys结构，包括完整的 长度二聚体光感受器及其信号输出模块;（3）开发植物Phys信号如何通过 Pfr的结构研究;（4）应用稳态和时间分辨蛋白质表面图谱来支持Phy （5）开发Phys与其下游效应物相互作用的模型，以及 (6)了解植物Phy之间的多样性如何通过特定的同种型实现热/时间感知。 总之，这个项目将提供一个重要的框架，以更好地了解结构，变构机制， 和Phy超家族的进化。了解微生物和植物如何感知光、温度和时间 将对改善作物的农业性能，了解微生物， 生态系统、控制医学相关病原体以及促进Phys作为光遗传学试剂的应用。

项目成果

The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms.

• DOI: 10.1038/s41477-023-01435-8
• 发表时间: 2023-07
• 期刊: NATURE PLANTS
• 影响因子: 18
• 作者: Burgie, E. Sethe;Li, Hua;Gannam, Zachary T. K.;McLoughlin, Katrice E.;Vierstra, Richard D.;Li, Huilin
• 通讯作者: Li, Huilin

Plant phytochrome B is an asymmetric dimer with unique signalling potential.

• DOI: 10.1038/s41586-022-04529-z
• 发表时间: 2022-04
• 期刊: Nature
• 影响因子: 64.8