{"title":"基于质谱的水稻蛋白质组图谱揭示了 N6-甲基腺苷的转录后调控作用","authors":"Shang-Tong Li, Yunzhuo Ke, Yunke Zhu, Tian-Yi Zhu, Huanwei Huang, Linxia Li, Zhiyang Hou, Xuemin Zhang, Yaping Li, Chaofan Liu, Xiulan Li, Mengjia Xie, Lianqi Zhou, Chen Meng, Faming Wang, Xiaofeng Gu, Bing Yang, Hao Yu, Zhe Liang","doi":"10.1038/s41477-024-01745-5","DOIUrl":null,"url":null,"abstract":"Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome. This proteomic landscape study reveals proteins associated with the functional specificity of rice tissues, and further multi-omics analysis shows that N6-methyladenosine in untranslated regions is negatively correlated with protein abundance.","PeriodicalId":18904,"journal":{"name":"Nature Plants","volume":null,"pages":null},"PeriodicalIF":15.8000,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine\",\"authors\":\"Shang-Tong Li, Yunzhuo Ke, Yunke Zhu, Tian-Yi Zhu, Huanwei Huang, Linxia Li, Zhiyang Hou, Xuemin Zhang, Yaping Li, Chaofan Liu, Xiulan Li, Mengjia Xie, Lianqi Zhou, Chen Meng, Faming Wang, Xiaofeng Gu, Bing Yang, Hao Yu, Zhe Liang\",\"doi\":\"10.1038/s41477-024-01745-5\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome. This proteomic landscape study reveals proteins associated with the functional specificity of rice tissues, and further multi-omics analysis shows that N6-methyladenosine in untranslated regions is negatively correlated with protein abundance.\",\"PeriodicalId\":18904,\"journal\":{\"name\":\"Nature Plants\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":15.8000,\"publicationDate\":\"2024-07-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Nature Plants\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.nature.com/articles/s41477-024-01745-5\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nature Plants","FirstCategoryId":"99","ListUrlMain":"https://www.nature.com/articles/s41477-024-01745-5","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine
Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and tissue-enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome. This proteomic landscape study reveals proteins associated with the functional specificity of rice tissues, and further multi-omics analysis shows that N6-methyladenosine in untranslated regions is negatively correlated with protein abundance.
期刊介绍:
Nature Plants is an online-only, monthly journal publishing the best research on plants — from their evolution, development, metabolism and environmental interactions to their societal significance.