Reconstruction of protein networks from an atlas of maize seed proteotypes
Reconstruction of protein networks from an atlas of maize seed proteotypes
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DOI：
10.1073/pnas.1319113110
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发表时间：
2013-12-03
影响因子：
11.1
通讯作者：
Briggs, Steven P.
中科院分区：
文献类型：
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作者：
Walley, Justin W.;Shen, Zhouxin;Briggs, Steven P.
蛋白质组状态的全面知识对于理解生物系统是必不可少的。利用质谱仪，我们绘制了玉米种子发育的蛋白质图谱，包括14,165个蛋白质和18,405个磷酸多肽(由4,511个蛋白质组成)，量化了8个组织。我们发现，许多最丰富的蛋白质与可检测到的mRNAs水平无关，我们为三种可能的解释提供了证据：蛋白质在组织之间的运输；mRNAs和同源蛋白的昼夜异相积累；以及mRNAs与蛋白质相比的不同寿命。同样，许多最丰富的mRNAs与可检测到的蛋白质水平无关。在整个数据集中，蛋白质丰度与信使核糖核酸水平的相关性很差，并且在很大程度上与磷酸化状态无关。蛋白质类型之间的比较揭示了特定蛋白质和磷酸化事件对空间和时间调节的淀粉和油脂生物合成途径的定量贡献。信号网络的重建建立了蛋白质和磷蛋白与种子发育过程中不同的生物学过程之间的联系。此外，还重建了蛋白激酶底物网络，从而能够识别762种特定蛋白激酶的潜在底物。最后，对694个转录因子的检测显示，转录因子家族中的表达模式和磷酸化受到显著的限制。这些结果为理解作为现代农业基础的作物的种子发育提供了资源。
A comprehensive knowledge of proteomic states is essential for understanding biological systems. Using mass spectrometry, we mapped an atlas of developing maize seed proteotypes comprising 14,165 proteins and 18,405 phosphopeptides (from 4,511 proteins), quantified across eight tissues. We found that many of the most abundant proteins are not associated with detectable levels of their mRNAs, and we provide evidence for three potential explanations: transport of proteins between tissues; diurnal, out-of-phase accumulation of mRNAs and cognate proteins; and differential lifetimes of mRNAs compared with proteins. Likewise, many of the most abundant mRNAs were not associated with detectable levels of their proteins. Across the entire dataset, protein abundance was poorly correlated with mRNA levels and was largely independent of phosphorylation status. Comparisons between proteotypes revealed the quantitative contribution of specific proteins and phosphorylation events to the spatially and temporally regulated starch and oil biosynthetic pathways. Reconstruction of signaling networks established associations of proteins and phosphoproteins with distinct biological processes acting during seed development. Additionally, a protein kinase substrate network was reconstructed, enabling the identification of 762 potential substrates of specific protein kinases. Finally, examination of 694 transcription factors revealed remarkable constraints on patterns of expression and phosphorylation within transcription factor families. These results provide a resource for understanding seed development in a crop that is the foundation of modern agriculture.