“Of the many intricate and beautiful control mechanisms living organisms have evolved to optimize their survival in a variable and changing environment， none is more elegant than the phytochrome system of plants.”—This is a quote by Warren L. Butler who made seminal contributions to the discovery of the pigment in plants previously described to control a wide range of physiological responses， including red/far-red light reversible seed germination or photoperiodic flowering. I fully share Warren L. Butler’s fascination and excitement for this pigment， which was later named phytochrome. This pigment has been part of my daily life since 2003， when I met Eberhard Schäfer， another great and inspiring mind of phytochrome research. Mutant screens， genome sequencing and other genetic or molecular approaches pioneered by phytochrome enthusiasts all over the world paved the way to the model for phytochrome signalling that we have today. In short， the activity of phytochromes is controlled by light in the red/far-red spectral range， and they accumulate in the nucleus in the active state and control the expression of genes involved in seed germination， growth， flowering and other responses by regulating the activity of a number of transcription factors （
Fig.1）. The recent finding that photobodies， subnuclear structures formed by phytochromes， are the result of liquid-liquid phase separation and the structure of full-length phytochromes provide further insight into phytochrome action， but also lead to new questions. So the more we know about phytochromes， the more we realise what we don’t know. The following list is a summary of questions related to phytochromes， phytochrome signalling and evolution of phytochromes to which I would love to have an answer – both to satisfy my curiosity and to provide a basis for addressing challenges in agriculture and plant breeding：
• Is the model for phytochrome signalling that we have based on research in Arabidopsis really representative for all seed plants？ Is it good enough to draw conclusions on phytochrome signalling in important crop plants？ How can knowledge on phytochromes be transferred to applications in agriculture？
• Are there physiological responses mediated by phytochromes that we have missed so far because we have used the wrong model or the wrong conditions？
• How do phytochromes coordinate light， temperature， and hormonal signalling pathways to control adaptation of plants to the environment？
• How conserved are phytochrome signalling mechanisms？ Which factors are common to all land plants （or even land plants and streptophyte algae） and which mechanisms are specific to a subgroup， e.g. a particular family， monocots or dicots， seed plants， ferns or mosses？ This is an important aspect when it comes to transferring knowledge from model species to non-model species （including many crops）.
• What is the molecular basis for the diversification of phytochromes into phytochromes that are most active in red light （e.g. phyB in seed plants， PHY5 in mosses） and phytochromes that are most active in far-red light （e.g. phyA in seed plants， PHY1/3 in mosses） and is it conserved between seed plants and mosses？
• What were the properties of the phytochrome in the last common ancestor of land plants？
• How do differences in the structure of phytochromes in the active and inactive states trigger downstream events？
• What is the role of phytochrome photobodies， i.e. the subnuclear structures formed by liquid-liquid phase separation， in phytochrome signalling？
Suggested further reading
Burgie E S， Li H， Gannam Z T K，
et al. The structure of
Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms. Nature Plants 2023， 9： 1116-1129.
https：//doi.org/10.1038/s41477-023-01435-8.Chen D， Lyu M， Kou X，
et al. Integration of light and temperature sensing by liquid-liquid phase separation of phytochrome B. Molecular Cell， 2022， 82： 3015-3029.
https：//doi.org/10.1016/j.molcel. 2022.05.026.
Legris M， Ince Y Ç， Fankhauser C. Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nature Communications， 2019， 10： 5219.
https：//doi.org/10.1038/s41467-019-13045-0.Li H， Burgie E S， Gannam Z T K，
et al. Plant phytochrome B is an asymmetric dimer with unique signalling potential. Nature， 2022， 604： 127-133.
https：//doi.org/10.1038/s41586-022-04529-z.Sage L C. Pigment of the imagination： a history of phytochrome research， 1992. Academic Press， p.562.
https：//doi.org/10.1016/C2009-0-03196-1.Wang Z， Wang W， Zhao D，
et al. Light-induced remodeling of phytochrome B enables signal transduction by phytochrome-interacting factor. Cell， 2024， 187： 6235-6250.
https：//doi.org/10.1016/j.cell.2024.09.005.“生物有机体不断优化和完善自身以适应多变的环境，在其进化产生的复杂机制中，植物体内光敏色素系统的精妙调控是无与伦比的”——这句话引自沃伦·L·巴特勒（Warren L. Butler）。人们最初认为这个色素分子参与植物体内广泛的生理反应，包括红光/远红光可逆调控的种子萌发或光周期性开花，后来被命名为光敏色素。Butler先生是光敏色素研究的先行者，在植物光敏色素发现及研究中做出了开创性的贡献。Butler先生对光敏色素研究的兴趣浓厚、几近痴迷，我也深有同感。2003年，我有幸遇到了埃伯哈德·沙弗（Eberhard Schafer）先生，他也是植物光敏素色素研究领域一位杰出的研究者。自那时起，光敏色素的研究逐渐成为我日常生活的一部分。借助于突变体筛选、基因组测序和世界各地光敏色素研究人员开发的遗传学或分子生物学方法，目前已逐渐构建起光敏色素信号转导途径。简言之，植物光敏色素的活性受红光/远红光可逆调控；光敏色素被光激活并在细胞核中不断积累，调控种子萌发、植物生长、开花等过程相关的基因表达，并通过调节多种转录因子的活性来介导其他重要的生理响应（
图1）。最近的研究发现，光敏色素形成的光体是液-液相分离产生亚细胞核结构，此外，完整光敏色素的结构解析则为我们进一步阐释其作用机制提供了全新的视角。随着研究的不断深入，我们越发认识到对这种色素仍然充满了很多未知。以下谨总结了在光敏色素、光敏色素信号转导及光敏色素进化研究中我非常关注并希望得到答案的一些问题，破解这些问题可能为农业和植物育种领域面临的挑战提供应对之策。
• 基于模式植物拟南芥建立的光敏色素信号转导模型是否适用于所有种子植物？是否对构建重要作物光敏色素信号转导途径有指导意义？如何利用光敏色素知识为农业生产做出贡献？
• 到目前为止，我们是否遗漏或错过发现光敏色素介导的生理反应？而这可能是由于我们使用了错误的模型或不恰当的试验条件造成的。
• 光敏色素如何协调光、温度和激素信号通路来调控植物适应环境？
• 光敏色素信号转导机制的保守性如何？在光敏素色素信号转导途径中，哪些遗传组分因子是陆生植物（或陆生植物和丝状藻类）所共有的？哪些机制是某个植物亚类群（例如某个植物门、单子叶植物或双子叶植物、种子植物、蕨类植物或苔藓植物）所特有的？这方面的研究和探索，对于我们从模式物种拓展到非模式物种（包括许多作物）来认知光敏色素是非常重要的。
• 有的光敏色素（例如种子植物中phyB和苔藓植物中 PHY5）在红光诱导下活性更高，而有的光敏色素（例如种子植物中phyA和苔藓植物中PHY1/3）则在远红光诱导下表现出更高的活性。那么，这种红光或远红光诱导的光敏色素功能分化的分子基础是什么呢？这种多样化在种子植物和苔藓植物中是保守的吗？
• 陆地植物最后的共同祖先的光敏色素特性是什么呢？
• 光敏色素在活性和非活性状态下的结构差异如何触发下游信号转导的发生？
• 光敏色素光小体，即液-液相分离形成的亚核结构，在光敏色素信号转导中起什么作用？
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