Guo Huihui, Qi Xiushan, Zhang Li, Guo Haixia, Gao Fan, Tian Xindi, Wu Jianfei, Li Tongtong, Yan Tongdi, Cui Xiwang, Xu Jiawei, Zeng Fanchang
State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
BMC Biol. 2025 Apr 30;23(1):116. doi: 10.1186/s12915-025-02218-7.
Phosphorylation is one of the most common post-translational modifications and is central to many cellular signaling events; however, little is currently known about the phosphorylation landscape during somatic embryogenesis (SE) for plant regeneration.
Here, we systematically analyzed the phosphoproteomic profile of three typical developmentally staged cultures of SE, non-embryogenic calli (NEC), primary embryogenic calli (PEC), and globular embryos (GE), in cotton (Gossypium hirsutum L.), the pioneer crop for genetic biotechnology applications. Our data revealed a total of 6301 quantifiable phosphorylation sites in 2627 quantifiable phosphoproteins from 5548 modified peptides, of which 1105 phosphoproteins (2147 sites) were differentially phosphorylated. Functional enrichment analyses revealed that differentially regulated phosphoproteins (DRPPs) were significantly enriched in DNA mismatch repair and peroxisome during callus embryogenic differentiation (PEC vs. NEC) and somatic embryo initiation (GE vs. PEC), respectively. Notably, six dynamic trajectory patterns of DRPP enrichment were observed. In addition, preferentially activated DRPPs with specific phosphorylation patterns were identified at different developmental stages. These DRPPs were mainly involved in hormone-responsive and photosystem events during initiation of plant regeneration.
Overall, this study identified a series of potential phosphoproteins responsible for SE trans-differentiation and plant regeneration, providing a valuable resource and molecular basis for understanding the regulatory pathways underlying cell totipotency at the post-translational modification level.
磷酸化是最常见的翻译后修饰之一，是许多细胞信号转导事件的核心；然而，目前对于植物再生过程中体细胞胚胎发生（SE）期间的磷酸化格局知之甚少。
在此，我们系统地分析了棉花（陆地棉）中SE的三种典型发育阶段培养物、非胚性愈伤组织（NEC）、初级胚性愈伤组织（PEC）和球形胚（GE）的磷酸化蛋白质组概况，棉花是遗传生物技术应用的先锋作物。我们的数据显示，来自5548个修饰肽段的2627个可定量磷酸化蛋白质中共鉴定出6301个可定量磷酸化位点，其中1105个磷酸化蛋白质（2147个位点）存在差异磷酸化。功能富集分析表明，在愈伤组织胚性分化（PEC与NEC）和体细胞胚胎起始（GE与PEC）过程中，差异调节的磷酸化蛋白质（DRPPs）分别显著富集于DNA错配修复和过氧化物酶体中。值得注意的是，观察到DRPP富集的六种动态轨迹模式。此外，在不同发育阶段鉴定出具有特定磷酸化模式的优先激活的DRPPs。这些DRPPs在植物再生起始过程中主要参与激素应答和光系统事件。
总体而言，本研究鉴定出了一系列负责SE转分化和植物再生的潜在磷酸化蛋白质，为在翻译后修饰水平理解细胞全能性的调控途径提供了有价值的资源和分子基础。
