Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Korea.
Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea.
Plant Cell Rep. 2024 May 15;43(6):142. doi: 10.1007/s00299-024-03226-7.
111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.
111 个 PHD 基因在黑麦基因组中被新鉴定出来，并提出 ScPHD5 在调节耐冷性和开花时间中的作用。植物同源结构域（PHD）-手指蛋白调节染色质的物理性质，并控制植物发育和应激耐受性。尽管黑麦（Secale cereale L.）是一种主要的冬季作物，但黑麦中的 PHD 手指蛋白尚未得到研究。在这里，我们在黑麦基因组中鉴定出 111 个 PHD 基因，它们表现出多样化的基因和蛋白质序列结构。系统发育树分析表明，PHD 在单子叶植物中具有遗传亲缘关系，并与双子叶植物中的 PHD 分化开来。复制和共线性分析表明，ScPHDs 在进化过程中经历了多次复制，并且在三叶草属物种中保持了高度的共线性。组织特异性和非生物胁迫响应基因表达分析表明，ScPHDs 在小穗和发育种子中高度表达，并对冷和干旱胁迫有反应。其中一个基因 ScPHD5 被选择进行进一步的功能表征。ScPHD5 在穗组织中高度表达，并在黑麦原生质体和烟草叶片的核中定位。与野生型（WT）相比，ScPHD5 过表达的拟南芥对冷冻胁迫更具耐受性，CBF 和 COR 基因的表达增加。此外，这些转基因植物表现出极早开花的表型，比 WT 早开花两周以上，并且在 WT 中增加了春化基因，而不是光周期基因。RNA-seq 分析显示，包括 HSPs、HSFs、LEAs 和 MADS-box 基因在内的多种应激响应基因也在转基因植物中上调。我们的研究将有助于阐明 PHD 基因在黑麦植物发育和非生物胁迫耐受性中的作用。
