Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Eco-Chongming (IEC), School of Life Sciences, Fudan University, Shanghai, 200438, China.
Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
Plant Cell Rep. 2022 May;41(5):1209-1227. doi: 10.1007/s00299-022-02850-5. Epub 2022 Feb 26.
Plant PIFs have been characterized, WGDs contributed to the expansion of class II PIFs; BdPIFs localized in the nucleus; BdPIF4/5C most likely response to high temperature and light stress. Phytochrome interacting factors (PIFs) belong to a small subset of basic helix-loop-helix (bHLH) transcription factors (TFs). As cellular signaling hubs, PIFs integrate multiple external and internal signals to orchestrate the regulation of the transcriptional network, thereby actuating the pleiotropic aspects of downstream morphogenesis. Nevertheless, the origin, phylogeny and function of plant PIFs are not well understood. To elucidate their evolution history and biological function, the comprehensive genomic analysis of the PIF genes was conducted using 40 land plant genomes plus additionally four alga lineages and also performed their gene organizations, sequence features and expression patterns in different subfamilies. In this study, phylogenetic analysis displayed that 246 PIF gene members retrieved from all embryophytes could be divided into three main clades, which were further felled into five distinct classes (Class I-V). The duplications of Class II PIFs were associated specially with whole genome duplication (WGD) events during the plant evolution process. Sequence analysis showed that PIF proteins had a conserved APB motif, and its crucial amino acid residues were relatively high proportion in the average abundance. As expected, subcellular localization analysis revealed that all BdPIF proteins were localized to the nucleus. Especially, BdPIF4/5C showed the highest expression level at high temperature, and the most significant hypocotyl elongation phenotype of overexpression of BdPIFs in Arabidopsis, which was consistent with the function and phenotype of AtPIF4. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant PIFs, and lays a foundation for further investigation on its functions in plant growth and development.
植物 PIFs 已被鉴定，WGD 导致了 II 类 PIFs 的扩张；BdPIFs 定位于细胞核；BdPIF4/5C 可能对高温和光胁迫有反应。
光受体相互作用因子（PIFs）属于少数基本螺旋-环-螺旋（bHLH）转录因子（TFs）之一。作为细胞信号枢纽，PIFs 整合多种外部和内部信号，协调转录网络的调节，从而激活下游形态发生的多效性方面。然而，植物 PIFs 的起源、系统发育和功能尚不清楚。为了阐明它们的进化历史和生物学功能，使用 40 种陆地植物基因组加上另外 4 种藻类谱系对 PIF 基因进行了全面的基因组分析，并对不同亚家族的基因组织、序列特征和表达模式进行了分析。在这项研究中，系统发育分析显示，从所有胚胎植物中检索到的 246 个 PIF 基因成员可分为三个主要分支，进一步分为五个不同的类（I-V 类）。II 类 PIFs 的复制与植物进化过程中的全基因组复制（WGD）事件特别相关。序列分析表明，PIF 蛋白具有保守的 APB 基序，其关键氨基酸残基在平均丰度中相对较高。正如预期的那样，亚细胞定位分析表明，所有 BdPIF 蛋白都定位于细胞核。特别是，BdPIF4/5C 在高温下表现出最高的表达水平，并且在拟南芥中过表达 BdPIFs 表现出最显著的下胚轴伸长表型，这与 AtPIF4 的功能和表型一致。
总之，我们的研究结果为植物 PIFs 的起源和进化历史提供了新的视角，并为进一步研究其在植物生长和发育中的功能奠定了基础。
