ArticleBMC biology2025
Single-cell transcriptomics and time-series metabolite profiling reveal the spatiotemporal regulation of flavonoid biosynthesis genes and phytohormone homeostasis by PAP1 in Arabidopsis.
Article in BMC biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Anthocyanin-Driven Dark Phenotypes in Stress Adaptation.Plants (Basel, Switzerland) · 2026Review
- MaMYB12 and MaMYB308 antagonistically regulate flavonoid biosynthesis in mulberry (Food chemistry. Molecular sciences · 2026Article
- RNA-seq and ATAC-seq reveal candidate genes and regulatory networks underlying exogenous ABA-enhanced abiotic stress tolerance in Gossypium hirsutum.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Comparative Profiling of Aroma Volatiles and Flavonoid Biosynthesis in Crimson Seedless, Red Globe, and Shine Muscat Table Grapes Using GC-IMS and RNA-Seq.Foods (Basel, Switzerland) · 2026Article
- Hormone-Specific Reprogramming of the Phenylpropanoid Network in JuvenilePlants (Basel, Switzerland) · 2026Article
- Network-Driven Insights into Plant Immunity: Integrating Transcriptomic and Proteomic Approaches in Plant-Pathogen Interactions.International journal of molecular sciences · 2026Review
- Integrated transcriptomic and metabolomic profiles analysis reveals a potential gene-metabolite network associated with anthocyanin-mediated color variation in maize kernels.Frontiers in plant science · 2026Article
- Responses and adaptations of plants to abiotic stress: transcriptional regulation of secondary metabolic pathways, metabolomics, and nanobiological approaches.Frontiers in genetics · 2026Review
- The regulatory roles of flavonoids, melatonin, and glycine betaine in plant salt stress response.Frontiers in plant science · 2026Review
- The effects of clonal integration and earthworms on the growth, active constituent accumulation inFrontiers in plant science · 2025Article
- Opportunities and challenges in the application of spatiotemporal transcriptomics in plant research.Frontiers in plant science · 2025Review
- Spatial and Temporal Dynamics of Phenylpropanoid Pathway-Derived Secondary Metabolites Under Abiotic Stress.Physiologia plantarumReview
- A Metabolomics and Transcriptomics Resource for Identifying Candidate Genes in the Biosynthesis of Specialised Metabolites in Populus tremula.Physiologia plantarumArticle
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Abstract
backgroundUnderstanding the spatiotemporal regulation of specialized metabolism in plants is critical for advancing both basic plant biology and biotechnological applications. PRODUCTION OF ANTHOCYANIN PIGMENT 1 (PAP1) is a well-known transcription factor that plays a key regulatory role in the biosynthesis pathway of plant flavonoids. Similar to other secondary metabolites, flavonoid biosynthesis displays cell heterogeneity. However, the cell-specific regulation network of the flavonoid biosynthetic pathway remains unclear.
resultsIn this study, we utilized single-cell RNA sequencing (scRNA-seq) and time-series metabolite profiling to investigate the regulation of flavonoid biosynthesis and phytohormone homeostasis in Arabidopsis thaliana by PAP1. By comparing single-cell transcriptomes of the pap1-D mutant and wild-type plant leaves, we constructed a cell-type-specific atlas of gene expression and high-resolution dynamics of metabolites across developmental stages. Our findings reveal that PAP1 overexpression induces distinct spatiotemporal regulation of phenylpropanoid pathway genes in different cell types and widespread upregulation of glycosylation processes. Metabolomic profiling validated these transcriptional patterns and showed significant changes of metabolites in phenylalanine metabolic processes as pap1-D leaf matures. Additionally, PAP1 overexpression leads to significant changes in phytohormone levels, particularly jasmonate and salicylate, indicating complex crosstalk between flavonoid biosynthesis and hormone homeostasis.
conclusionsThis integrated multi-omics approach provides unprecedented insights into the cell-specific regulatory networks controlling specialized metabolism and establishes a valuable framework for optimizing metabolic engineering strategies to enhance the production of bioactive plant compounds.
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