Multiprotein complexes execute and coordinate diverse cellular processes such as organelle biogenesis, vesicle trafficking, cell signaling, and metabolism. Knowledge about their composition and localization provides useful clues about the mechanisms of cellular homeostasis and system-level control. This is of great biological importance and practical significance in heterotrophic rice (Oryza sativa) endosperm and aleurone–subaleurone tissues, which are a primary source of seed vitamins and stored energy. Dozens of protein complexes have been implicated in the synthesis, transport, and storage of seed proteins, lipids, vitamins, and minerals. Mutations in protein complexes that control RNA transport result in aberrant endosperm with shrunken and floury phenotypes, significantly reducing seed yield and quality. The purpose of this study was to broadly predict protein complex composition in the aleurone–subaleurone layers of developing rice seeds using co-fractionation mass spectrometry. Following orthogonal chromatographic separations of biological replicates, thousands of protein elution profiles were subjected to distance-based clustering to enable large-scale multimerization state measurements and protein complex predictions. The predicted complexes had predicted functions across diverse functional categories, including novel heteromeric RNA binding protein complexes that may influence seed quality. This effective and open-ended proteomics pipeline provides useful clues about system-level posttranslational control during the early stages of rice seed development.

中文翻译：

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基于共分馏质谱的水稻糊粉-亚糊粉蛋白复合物组装预测

多蛋白复合物执行和协调不同的细胞过程，例如细胞器生物发生、囊泡运输、细胞信号传导和新陈代谢。关于它们的组成和定位的知识为细胞稳态和系统级控制的机制提供了有用的线索。这在异养水稻 (Oryza sativa) 胚乳和糊粉-亚糊粉组织中具有重要的生物学意义和实际意义，它们是种子维生素和储存能量的主要来源。数十种蛋白质复合物与种子蛋白质、脂质、维生素和矿物质的合成、运输和储存有关。控制 RNA 转运的蛋白质复合物的突变导致异常胚乳具有收缩和粉化的表型，从而显着降低种子产量和质量。本研究的目的是使用共分馏质谱法广泛预测发育中的水稻种子的糊粉层-亚糊粉层中的蛋白质复合物组成。在生物复制品的正交色谱分离之后，对数千个蛋白质洗脱曲线进行基于距离的聚类，以实现大规模多聚化状态测量和蛋白质复合物预测。预测的复合物预测了不同功能类别的功能，包括可能影响种子质量的新型异聚 RNA 结合蛋白复合物。这种有效且开放的蛋白质组学管道为水稻种子发育早期的系统级翻译后控制提供了有用的线索。