Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland.
Genomics. 2021 Sep;113(5):3185-3197. doi: 10.1016/j.ygeno.2021.06.031. Epub 2021 Jun 25.
Group A PP2C (PP2CA) genes form a gene subfamily whose members play an important role in regulating many biological processes by dephosphorylation of target proteins. In this study we examined the effects of evolutionary changes responsible for functional divergence of BnaABI1 paralogs in Brassica napus against the background of the conserved PP2CA gene subfamily in Brassicaceae. We performed comprehensive phylogenetic analyses of 192 PP2CA genes in 15 species in combination with protein structure homology modeling. Fundamentally, the number of PP2CA genes remained relatively constant in these taxa, except in the Brassica genus and Camelina sativa. The expansion of this gene subfamily in these species has resulted from whole genome duplication. We demonstrated a high degree of structural conservation of the PP2CA genes, with a few minor variations between the different PP2CA groups. Furthermore, the pattern of conserved sequence motifs in the PP2CA proteins and their secondary and 3D structures revealed strong conservation of the key ion-binding sites. Syntenic analysis of triplicated regions including ABI1 paralogs revealed significant structural rearrangements of the Brassica genomes. The functional and syntenic data clearly show that triplication of BnaABI1 in B. napus has had an impact on its functions, as well as the positions of adjacent genes in the corresponding chromosomal regions. The expression profiling of BnaABI1 genes showed functional divergence, i.e. subfunctionalization, potentially leading to neofunctionalization. These differences in expression are likely due to changes in the promoters of the BnaABI1 paralogs. Our results highlight the complexity of PP2CA gene subfamily evolution in Brassicaceae.
A 组 PP2C（PP2CA）基因形成一个基因亚家族，其成员通过靶蛋白的去磷酸化在调节许多生物过程中发挥重要作用。在本研究中，我们研究了导致油菜 BnaABI1 同源物功能分化的进化变化对 Brassicaceae 中保守的 PP2CA 基因亚家族的影响。我们对 15 个物种的 192 个 PP2CA 基因进行了综合系统发育分析，并结合蛋白质结构同源建模。从根本上讲，除了芸薹属和荠属以外，这些分类群中的 PP2CA 基因数量相对保持不变。该基因亚家族在这些物种中的扩张是由于全基因组复制造成的。我们证明了 PP2CA 基因具有高度的结构保守性，不同的 PP2CA 组之间存在一些较小的变异。此外，PP2CA 蛋白中的保守序列基序模式及其二级和 3D 结构揭示了关键离子结合位点的强烈保守性。包括 ABI1 同源物在内的三倍体区域的共线性分析显示出芸薹属基因组的显著结构重排。功能和共线性数据清楚地表明，B. napus 中 BnaABI1 的三倍体化对其功能以及相应染色体区域中相邻基因的位置产生了影响。BnaABI1 基因的表达谱显示出功能分化，即亚功能化，可能导致新功能化。这些表达差异可能是由于 BnaABI1 同源物的启动子发生了变化。我们的研究结果强调了 Brassicaceae 中 PP2CA 基因亚家族进化的复杂性。
