The UWA Institute of Agriculture, The University of Western Australia, M082, Perth, 6009, Australia.
The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, M316 Perth, Perth, 6009, Australia.
Planta. 2020 Feb 10;251(3):62. doi: 10.1007/s00425-020-03354-w.
Genome-wide identification, together with gene expression patterns and promoter region analysis of FYVE and PHOX proteins in Physcomitrella patens, emphasized their importance in regulating mainly developmental processes in P. patens. Phosphatidylinositol 3-phosphate (PtdIns3P) is a signaling phospholipid, which regulates several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through effector proteins have been partially explored in plants, with main focus on Arabidopsis thaliana. In this study, we searched for genes coding for PtdIns3P-binding proteins such as FYVE and PHOX domain-containing sequences from different photosynthetic organisms to gather evolutionary insights on these phosphoinositide binding domains, followed by an in silico characterization of the FYVE and PHOX gene families in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor (TF) binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2 to 3D growth. These studies would identify ancestral regulatory players undertaken during plant evolution.
对Physcomitrella patens 中的 FYVE 和 PHOX 蛋白进行全基因组鉴定，以及与基因表达模式和启动子区域分析，强调了它们在调节 P. patens 中主要发育过程中的重要性。磷脂酰肌醇 3-磷酸（PtdIns3P）是一种信号磷脂，它调节植物生长和发育的几个方面，以及对生物和非生物胁迫的反应。在植物中，已经部分探索了 PtdIns3P 作用模式的机制见解，特别是通过效应蛋白，主要集中在拟南芥上。在这项研究中，我们从不同的光合生物中搜索编码 PtdIns3P 结合蛋白（如 FYVE 和 PHOX 结构域）的基因，以收集这些磷酸肌醇结合结构域的进化见解，随后对苔藓 Physcomitrella patens 中的 FYVE 和 PHOX 基因家族进行了计算机模拟特征描述。系统发育分析表明，PpFYVE 蛋白可以分为 7 个亚类，其中一个亚类的 FYVE 结构域在进化为高等植物的过程中丢失了。另一方面，PpPHOX 蛋白分为 5 个亚类。基于 RNAseq 数据的表达分析以及顺式作用调节元件和启动子区域转录因子（TF）结合位点的分析表明，这些蛋白在调节应激反应方面非常重要，但主要在 P. patens 的发育过程中起作用。研究结果为未来的功能分析提供了有价值的信息和稳健的候选基因，旨在进一步探索该信号通路在顶端生长细胞生长和从 2D 到 3D 生长的转变过程中的主要作用。这些研究将确定在植物进化过程中执行的古老调控因子。
