To promote photomorphogenesis, including plastid development and metabolism, the phytochrome (phy) and the cryptochrome (cry) photoreceptors orchestrate genome wide changes in gene expression in response to Red (R) and Blue (B) light cues. While phys and crys have a clear role in modulating photosynthesis, their role in the coordination of the nuclear genome and the plastome, essential for functional chloroplasts, remains underexplored. Using publicly available genome datasets for WT and phyABCDE or cry1cry2 Arabidopsis seedlings, grown respectively under R- or B-light, we bioinformatically analyzed the influence of light inputs and photoreceptors in the control of nuclear genes with a function in the chloroplast, and evaluated the role of phyB in the modulation of plastome-encoded genes. We show gene co-induction by R-phys and B-crys for genes with a chloroplastic function, but also apparent photoreceptor-driven preferential responses. Evidence from phyB in Arabidopsis together with published evidence from CRY2 in tomato also supports the participation of both photoreceptor families in the global modulation of the plastome genes. To begin addressing how these light-sensors orchestrate changes in an organellar genome, we evaluated their effect over genes with potential functions in plastid gene-expression regulation based on their TAIR annotation. Results indicate that both crys and phys modulate "plastome-regulatory genes" with enrichment in the contribution of crys to all processes and of phys to post-transcription and transcription. Furthermore, we identified a new role for HY5 as a relevant light-signaling component in photoreceptor-based anterograde signaling leading to plastome gene regulation. This article is protected by copyright. All rights reserved.

中文翻译：

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协调细胞核和叶绿体之间的光反应，植物隐花色素和光敏色素的作用

为了促进光形态发生，包括质体发育和代谢，光敏色素 (phy) 和隐花色素 (cry) 光感受器协调基因组范围内的基因表达变化，以响应红 (R) 和蓝 (B) 光线索。虽然phys 和crys 在调节光合作用方面具有明显的作用，但它们在核基因组和塑性体（对功能性叶绿体必不可少）的协调中的作用仍未得到充分探索。使用分别在 R 或 B 光下生长的 WT 和 phyABCDE 或 cry1cry2 拟南芥幼苗的公开可用基因组数据集，我们生物信息学分析了光输入和光感受器对控制具有叶绿体功能的核基因的影响，并评估了phyB 在调节质体编码基因中的作用。我们展示了 R-phys 和 B-crys 对具有叶绿体功能的基因的基因共诱导，以及明显的光感受器驱动的优先反应。来自拟南芥中 phyB 的证据以及来自番茄中 CRY2 的已发表证据也支持两个光感受器家族参与塑性体基因的全局调节。为了开始解决这些光传感器如何协调细胞器基因组中的变化，我们根据它们的 TAIR 注释评估了它们对在质体基因表达调控中具有潜在功能的基因的影响。结果表明，crys 和 phys 都调节“塑性体调节基因”，丰富了 crys 对所有过程的贡献以及 phys 对转录后和转录的贡献。此外，我们确定了 HY5 作为相关光信号组分在基于光感受器的顺行信号中的新作用，导致塑性体基因调控。本文受版权保护。版权所有。