Van Itallie Elizabeth, Sonnett Matthew, Kalocsay Marian, Wühr Martin, Peshkin Leonid, Kirschner Marc W
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Dev Biol. 2025 Sep;525:155-171. doi: 10.1016/j.ydbio.2025.05.022. Epub 2025 Jun 2.
Vertebrate development from an egg to a complex multi-cell organism is accompanied by multiple phases of genome-scale changes in the repertoire of proteins and their post-translational modifications. While much has been learned at the RNA level, we know less about changes at the protein level. In this paper, we present a deep analysis of changes of ∼15,000 proteins and ∼11,500 phospho-sites at 11 developmental time points in Xenopus laevis embryos ranging from the stage VI oocyte to the juvenile tadpole. We find that the most dramatic changes to the proteome occur during the transition to functional organ systems, which occurs as the embryo becomes a tadpole. At that time, the absolute amount of non-yolk protein increases two-fold, and there is a shift in the balance of expression from proteins regulating gene expression to receptors, ligands, and proteins involved in cell-cell and cell-environment interactions. Between the early and late tadpole, the median increase for membrane and secreted proteins is substantially higher than that of nuclear proteins. To begin to appreciate changes at the post-translational level, we have measured quantitative phospho-proteomic data across the same developmental stages. In contrast to the significant protein changes that are concentrated at the end of the time series, the most significant phosphorylation changes are concentrated in the very early stages of development. A clear exception are phosphorylations of proteins involved in gene expression: these increase just after fertilization, with patterns that are highly correlated with the underlying protein changes. To facilitate the interpretation of this unique phospho-proteome data set, we created a pipeline for identifying homologous human phosphorylations from the measured Xenopus phospho-proteome. Collectively, our data reveal multiple coordinated transitions in protein and phosphorylation profiles, reflecting distinct developmental strategies and providing an extensive resource to further explore developmental biology at the proteomic and phospho-proteomic levels.
从卵子发育成复杂的多细胞脊椎动物，伴随着蛋白质库及其翻译后修饰在基因组规模上的多个变化阶段。虽然我们在RNA水平上已经了解了很多，但对蛋白质水平的变化却知之甚少。在本文中，我们对非洲爪蟾胚胎从VI期卵母细胞到幼体蝌蚪的11个发育时间点上约15,000种蛋白质和约11,500个磷酸化位点的变化进行了深入分析。我们发现，蛋白质组最显著的变化发生在向功能器官系统的转变过程中，即胚胎变成蝌蚪的时候。此时，非卵黄蛋白的绝对量增加了两倍，并且表达平衡从调节基因表达的蛋白质转向受体、配体以及参与细胞间和细胞与环境相互作用的蛋白质。在蝌蚪早期和晚期之间，膜蛋白和分泌蛋白的中位数增加幅度明显高于核蛋白。为了开始了解翻译后水平的变化，我们测量了相同发育阶段的定量磷酸化蛋白质组数据。与集中在时间序列末尾的显著蛋白质变化不同，最显著的磷酸化变化集中在发育的非常早期阶段。一个明显的例外是参与基因表达的蛋白质的磷酸化：这些在受精后立即增加，其模式与基础蛋白质变化高度相关。为了便于解释这个独特的磷酸化蛋白质组数据集，我们创建了一个管道，用于从测量的爪蟾磷酸化蛋白质组中识别同源的人类磷酸化。总体而言，我们的数据揭示了蛋白质和磷酸化谱中的多个协调转变，反映了不同的发育策略，并提供了一个丰富的资源，以在蛋白质组学和磷酸化蛋白质组学水平上进一步探索发育生物学。
