Peanut LC-MS/MS, part 1 of 3 - Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages

Cultivated peanut (Arachis hypogaea. L) is one of the most important oil crops in the world. After flowering, the peanut plant forms aboveground pegs (gynophores) that penetrate the soil, giving rise to underground pods. This means of reproduction, referred to as geocarpy, distinguishes peanuts from most other plants. The molecular mechanism underlying geocarpic pod development in peanut is poorly understood. To gain insight into the mechanism of geocarpy, we extracted proteins from aerial gynophores, subterranean unswollen gynophores, and gynophores that had just started to swell into pods. We analyzed the protein profiles in each of these samples by combining 1 DE with nanoLC-MS/MS approaches. In total, 2766, 2518, and 2280 proteins were identified from the three samples, respectively. An integrated analysis of proteome and transcriptome data revealed specifically or differentially expressed genes in the different developmental stages at both the mRNA and protein levels. A total of 69 proteins involved in the gravity response, light and mechanical stimulus, hormone biosynthesis, and transport were identified as being involved in geocarpy. Furthermore, we identified 91 genes that were specifically or abundantly expressed in aerial gynophores, including pectin methylesterase and expansin, which were presumed to promote the elongation of aerial gynophores. In addition, we identified 35 proteins involved in metabolism, defense, hormone biosynthesis and signal transduction, nitrogen fixation, and transport that accumulated in subterranean unswellen gynophores. Furthermore, 26 specific or highly abundant proteins related to fatty acid metabolism, starch synthesis, and lignin synthesis were identified in the early swelling pods. We identified thousands of proteins in the aerial gynophores, subterranean gynophores, and early swelling pods of peanut. This study provides the basis for examining the molecular mechanisms underlying peanut geocarpy pod development.

栽培花生（Arachis hypogaea L.）是全球最重要的油料作物之一。花生开花后会形成地上果针（aerial gynophores，子房柄），果针穿透土壤后发育为地下荚果。这种被称为地下结实（geocarpy）的生殖策略，使得花生区别于绝大多数其他植物。目前学界对花生地下结实过程中荚果发育的分子机制尚缺乏深入认知。为解析花生地下结实的分子机制，本研究分别从地上果针、未膨大的地下果针以及刚刚开始膨大形成荚果的果针中提取蛋白质。本研究结合一维凝胶电泳（1 DE）与纳升液相色谱-串联质谱（nanoLC-MS/MS）技术，对上述三类样本的蛋白质组谱进行分析。三类样本分别鉴定得到2766、2518及2280种蛋白质。通过对蛋白质组与转录组数据的整合分析，本研究在mRNA与蛋白质两个层面，筛选得到了不同发育阶段特异性表达或差异表达的基因。共计鉴定得到69种与重力响应、光与机械刺激、激素生物合成及转运相关的蛋白质，这些蛋白质均参与花生地下结实过程。此外，本研究还鉴定得到91种在地上果针中特异性或高丰度表达的基因，其中包括果胶甲酯酶（pectin methylesterase）与扩张蛋白（expansin），推测二者可促进地上果针的伸长生长。另外，在未膨大的地下果针中，本研究鉴定得到35种参与代谢、防御、激素生物合成与信号转导、固氮及转运过程的积累型蛋白质。而在早期膨大的荚果中，本研究则鉴定得到26种与脂肪酸代谢、淀粉合成及木质素合成相关的特异性或高丰度表达蛋白质。本研究在花生的地上果针、地下未膨大果针及早期膨大荚果中共计鉴定得到数千种蛋白质。本研究为解析花生地下结实荚果发育的分子机制奠定了重要基础。