State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.
Genes (Basel). 2024 Aug 15;15(8):1079. doi: 10.3390/genes15081079.
Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and post-translational modifications. Here, we performed association analysis of high-throughput proteomics and phosphoproteomics in three representative samples (non-embryogenic calli, NEC; primary embryogenic calli, PEC; globular embryos, GE) during the initiation of plant regeneration in cotton, a pioneer crop for genetic biotechnology applications. Our results showed that protein accumulation is positively regulated by phosphorylation during SE, as revealed by correlation analyses. Of the 1418 proteins that were differentially accumulated in the proteome and the 1106 phosphoproteins that were differentially regulated in the phosphoproteome, 115 proteins with 229 phosphorylation sites overlapped (co-differential). Furthermore, seven dynamic trajectory patterns of differentially accumulated proteins (DAPs) and the correlated differentially regulated phosphoproteins (DRPPs) pairs with enrichment features were observed. During the initiation of plant regeneration, functional enrichment analysis revealed that the overlapping proteins (DAPs-DRPPs) were considerably enriched in cellular nitrogen metabolism, spliceosome formation, and reproductive structure development. Moreover, 198 DRPPs (387 phosphorylation sites) were specifically regulated at the phosphorylation level and showed four patterns of stage-enriched phosphorylation susceptibility. Furthermore, enrichment annotation analysis revealed that these phosphoproteins were significantly enriched in endosomal transport and nucleus organization processes. During embryogenic differentiation, we identified five DAPs-DRPPs with significantly enriched characteristic patterns. These proteins may play essential roles in transcriptional regulation and signaling events that initiate plant regeneration through protein accumulation and/or phosphorylation modification. This study enriched the understanding of key proteins and their correlated phosphorylation patterns during plant regeneration, and also provided a reference for improving plant regeneration efficiency.
体细胞胚胎发生 (SE) 是一种用于产生新个体的生物技术工具，是快速植物再生的首选方法。然而，通过 SE 进行体细胞再生的分子基础尚未完全理解，特别是关于蛋白质组和翻译后修饰之间的相互作用。在这里，我们对棉花植物再生起始过程中的三个代表性样本（非胚胎发生愈伤组织，NEC；初级胚胎发生愈伤组织，PEC；球形胚胎，GE）进行了高通量蛋白质组学和磷酸化蛋白质组学的关联分析，棉花是遗传生物技术应用的先驱作物。我们的结果表明，通过相关性分析，SE 过程中蛋白质的积累受到磷酸化的正向调节。在蛋白质组和磷酸化蛋白质组中差异积累的 1418 种蛋白质和 1106 种差异调节的磷酸化蛋白质中，有 115 种蛋白质具有 229 个磷酸化位点重叠（共差异）。此外，观察到 7 种差异积累蛋白质 (DAP) 和相关差异调节磷酸化蛋白质 (DRPP) 对的动态轨迹模式，具有富集特征。在植物再生起始过程中，功能富集分析表明，重叠蛋白（DAP-DRPP）在细胞氮代谢、剪接体形成和生殖结构发育中显著富集。此外，198 个 DRPP（387 个磷酸化位点）在磷酸化水平上受到特异性调节，表现出 4 种阶段富集磷酸化易感性模式。此外，富集注释分析表明，这些磷酸化蛋白在核内体运输和核组织过程中显著富集。在胚胎发生分化过程中，我们鉴定了五个具有显著富集特征模式的 DAP-DRPP。这些蛋白质可能在通过蛋白质积累和/或磷酸化修饰启动植物再生的转录调控和信号事件中发挥重要作用。本研究丰富了对植物再生过程中关键蛋白质及其相关磷酸化模式的认识，为提高植物再生效率提供了参考。
