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Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum

by Wu, Shaolong , Yang, Jiashuo , Yan, Jianbin , Li, Yangyang , Liu, Pingping , Gao, Junping , Liu, Tianbo , Zhou, Zhicheng , Zhou, Huina , Sheng, Song , Hu, Risheng , Duan, Shuhui , Wang, Shuaibin , Zheng, Qingxia , Xiao, Qinzhi , Li, Jiaming , Li, Xiaoxu , Liao, Qinggang , Lu, Zhongshan , Yu, Bei , Hu, Zhengrong , Pu, Wenxuan , Liu, Yongjun , Xiao, Hanqian

in 38 / 38/39 / 38/91 / 631/208/200 / 631/449/2667 / 631/61/320 / 631/61/447/8 / Abscisic acid / Aroma / Biosynthesis / Carotenoids / Cosmetics / Flavonoids / Food / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Plant / Gene Regulatory Networks / Hubs / Humanities and Social Sciences / Hydroxycinnamic acid / Industrial crops / Lignin / Lipids / Metabolic Engineering / Metabolic flux / Metabolic Networks and Pathways - genetics / Metabolism / Metabolites / Metabolome / Metabolomics / Metabolomics - methods / multidisciplinary / Multiomics / Nicotiana - genetics / Nicotiana - metabolism / Plant growth / Plant Leaves - genetics / Plant Leaves - metabolism / Plant Proteins - genetics / Plant Proteins - metabolism / Radiation / Raw materials / Science / Science (multidisciplinary) / Tobacco / Transcription / Transcriptome / Transcriptomics / VOCs / Volatile organic compounds

2025

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2025

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2025

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Journal Article

Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum

Wu, Shaolong,

Yang, Jiashuo,

Yan, Jianbin,

Li, Yangyang,

Liu, Pingping,

Gao, Junping,

Liu, Tianbo,

Zhou, Zhicheng,

Zhou, Huina,

Sheng, Song,

Hu, Risheng,

Duan, Shuhui,

Wang, Shuaibin,

Zheng, Qingxia,

Xiao, Qinzhi,

Li, Jiaming,

Li, Xiaoxu,

Liao, Qinggang,

Lu, Zhongshan,

Yu, Bei,

Hu, Zhengrong,

Pu, Wenxuan,

Liu, Yongjun,

Xiao, Hanqian

2025

Overview

Tobacco is a significant industrial crop, serving as a model for plant science and a promising specie for the production of proteins and small molecules. However, system biology studies of tobacco under natural field cultivation conditions remain scarce. Here, we construct a genome-scale metabolic regulatory network through integration of dynamic transcriptomic and metabolomic profiles from field-grown tobacco leaves across two ecologically distinct regions. We map 25,984 genes and 633 metabolites into 3.17 million regulatory pairs using multi-algorithm integration. This network reveals three pivotal transcriptional hubs, including NtMYB28 (promoting hydroxycinnamic acids synthesis by modifying Nt4CL2 and NtPAL2 expression), NtERF167 (amplifying lipid synthesis via NtLACS2 activation) and NtCYC (driving aroma production through NtLOX2 induction). These transcriptional hubs achieve substantial yield improvements of target metabolites by rewiring metabolic flux. The present work provides a systems-level atlas of tobacco metabolic regulation and may help to guide metabolic engineering. Tobacco is not only an important industrial crop but also severs as a model for plant science research and chassis for plant metabolic engineering. Here, the authors report genome-scale metabolic regulatory network and reveal key transcriptional hubs for different metabolite biosynthesis.

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Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

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