Photomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (e.g., HY5, HFR1, PAP1 and others) in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic basis for the constitute photomorphogenic phenotype of spaQ remains unknown. Here, we show that >7200 genes are differentially expressed in the spaQ background compared to wild type in the dark. Comparison of the RNA Sequencing (RNA-Seq) data between cop1 and spaQ revealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling gene expression in concert with COP1, likely through regulating the abundance of downstream transcription factors in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and -independent manner in regulating many biological processes and developmental pathways in Arabidopsis. This article is protected by copyright. All rights reserved.

中文翻译：

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基因组证据揭示了暗生长的拟南芥幼苗中 SPA 调节的发育和代谢途径

光形态发生在黑暗中主要受到 E3 泛素连接酶复合物的抑制，该复合物包含 CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) 和四种称为 SUPPRESSOR OF PHYA-105 (SPA1-SPA4) 的拟南芥。该复合物在黑暗中诱导具有积极作用的转录因子（例如 HY5、HFR1、PAP1 等）的泛素化和随后的降解，以抑制光形态发生。基因组证据表明，在黑暗中存在大量受COP1调控的基因，其中许多是HY5的直接靶点。然而，spaQ 构成光形态发生表型的基因组基础仍然未知。在这里，我们表明与黑暗中的野生型相比，> 7200 个基因在 spaQ 背景中差异表达。cop1 和 spaQ 之间的 RNA 测序 (RNA-Seq) 数据的比较揭示了由 COP1-SPA 复合物调节的大量重叠基因。此外，许多由COP1-SPA复合体协同调控的基因也直接或间接受到HY5调控。总之，我们的数据表明 SPA 蛋白通过与 COP1 协同控制基因表达来抑制光形态发生，可能是通过调节光信号通路中下游转录因子的丰度。此外，SPA 蛋白可能以 COP1 依赖性和非依赖性方式在调节拟南芥中的许多生物过程和发育途径中发挥作用。本文受版权保护。版权所有。许多由 COP1-SPA 复合物协同调控的基因也直接或间接受到 HY5 的调控。总之，我们的数据表明 SPA 蛋白通过与 COP1 协同控制基因表达来抑制光形态发生，可能是通过调节光信号通路中下游转录因子的丰度。此外，SPA 蛋白可能以 COP1 依赖性和非依赖性方式在调节拟南芥中的许多生物过程和发育途径中发挥作用。本文受版权保护。版权所有。许多由 COP1-SPA 复合物协同调控的基因也直接或间接受到 HY5 的调控。总之，我们的数据表明 SPA 蛋白通过与 COP1 协同控制基因表达来抑制光形态发生，可能是通过调节光信号通路中下游转录因子的丰度。此外，SPA 蛋白可能以 COP1 依赖性和非依赖性方式在调节拟南芥中的许多生物过程和发育途径中发挥作用。本文受版权保护。版权所有。此外，SPA 蛋白可能以 COP1 依赖性和非依赖性方式在调节拟南芥中的许多生物过程和发育途径中发挥作用。本文受版权保护。版权所有。此外，SPA 蛋白可能以 COP1 依赖性和非依赖性方式在调节拟南芥中的许多生物过程和发育途径中发挥作用。本文受版权保护。版权所有。