Single-cell Transcriptomics and Time-series Metabolite Profiling Reveal the Spatiotemporal Regulation of Flavonoid Biosynthesis Genes and Phytohormone Homeostasis by PAP1 in Arabidopsis

ABSTRACT: Understanding the spatiotemporal regulation of specialized metabolism in plants is critical for advancing both basic plant biology and biotechnological applications. In 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 (PRODUCTION OF ANTHOCYANIN PIGMENT 1). By comparing single-cell transcriptomes of the pap1-D mutant and wild-type plants, 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 mature. Additionally, PAP1 overexpression leads to significant changes in phytohormone levels, particularly jasmonate and salicylate, indicating complex crosstalk between flavonoid biosynthesis and hormone homeostasis. This 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.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS12459 | MetaboLights | 2025-05-27

REPOSITORIES: MetaboLights