{"title":"大豆蛋白质组的景观和m6A转录后调控。","authors":"Qing Yang, Zhi-Yang Hou, Linxia Li, Leili Wang, Shang-Tong Li, Yaping Li, Xuemin Zhang, Huanwei Huang, Yunzhuo Ke, Xiaofei Ma, Zexuan Wu, Zhi Liu, Xiaolei Shi, Chaofan Liu, Chen Meng, Hai Du, Mingxun Chen, Xiaofeng Gu, Zhe Yan, Faming Wang, Xiao Luo, Long Yan, Zhe Liang","doi":"10.1016/j.xgen.2025.100926","DOIUrl":null,"url":null,"abstract":"<p><p>The soybean is a critical source of vegetable protein, but its proteome remains undercharacterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity with significant differences in protein-transcript abundance across organs. We also map N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of the proteome and m<sup>6</sup>A methylome identifies a novel regulator in m<sup>6</sup>A methylation. This comprehensive proteomic and m<sup>6</sup>A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100926"},"PeriodicalIF":11.1000,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Landscape and m<sup>6</sup>A post-transcriptional regulation of soybean proteome.\",\"authors\":\"Qing Yang, Zhi-Yang Hou, Linxia Li, Leili Wang, Shang-Tong Li, Yaping Li, Xuemin Zhang, Huanwei Huang, Yunzhuo Ke, Xiaofei Ma, Zexuan Wu, Zhi Liu, Xiaolei Shi, Chaofan Liu, Chen Meng, Hai Du, Mingxun Chen, Xiaofeng Gu, Zhe Yan, Faming Wang, Xiao Luo, Long Yan, Zhe Liang\",\"doi\":\"10.1016/j.xgen.2025.100926\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The soybean is a critical source of vegetable protein, but its proteome remains undercharacterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity with significant differences in protein-transcript abundance across organs. We also map N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of the proteome and m<sup>6</sup>A methylome identifies a novel regulator in m<sup>6</sup>A methylation. This comprehensive proteomic and m<sup>6</sup>A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.</p>\",\"PeriodicalId\":72539,\"journal\":{\"name\":\"Cell genomics\",\"volume\":\" \",\"pages\":\"100926\"},\"PeriodicalIF\":11.1000,\"publicationDate\":\"2025-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Cell genomics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1016/j.xgen.2025.100926\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/7/7 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"CELL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cell genomics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1016/j.xgen.2025.100926","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/7/7 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"CELL BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
大豆是植物蛋白的重要来源，但其蛋白质组仍未被充分描述。在这里，我们使用4D数据独立采集质谱（4D- dia - ms）量化了14个大豆器官中的12,855个蛋白质，创建了迄今为止最广泛的大豆蛋白质组数据集。器官特异性蛋白表达和共表达分析强调了功能特异性，不同器官的蛋白转录丰度存在显著差异。我们还绘制了n6 -甲基腺苷（m6A）修饰图，确定了它们在转录后蛋白调控中的关键作用。对蛋白质组和m6A甲基化组的综合分析发现了一个新的m6A甲基化调节因子。这一全面的蛋白质组学和m6A图谱促进了我们对大豆生物学的认识，并为作物改良提供了宝贵的资源。
Landscape and m6A post-transcriptional regulation of soybean proteome.
The soybean is a critical source of vegetable protein, but its proteome remains undercharacterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of the proteome and m6A methylome identifies a novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.
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