Drought-activated BZR1 reprograms flavonoid metabolism via transcriptional cascades to amplify baicalin biosynthesis in Scutellaria baicalensis.

Environmental stress triggers a dual response in medicinal plants by inhibiting growth while enhancing secondary metabolite production. However, the regulatory mechanism of this trade-off remains unclear. Here, we identified SbBZR1 as a brassinosteroid (BR)-responsive transcription factor that orchestrates drought resilience and baicalin biosynthesis in Scutellaria baicalensis through integrated multi-omics and metabolic flux analysis. In general, drought stress upregulated BR signaling and SbBZR1 expression. Transgenic Arabidopsis expressing SbBZR1 and its hyperactive mutant (Sbbzr1-1D) exhibited enhanced drought tolerance: 57 % greater biomass, 43 % increased root density, and 62 % reduced lipid peroxidation via antioxidant gene activation (AtDHAR1, AtCAT2, AtSOD1). In S. baicalensis hairy roots, SbBZR1 overexpression increased biomass (68 %) and anthocyanins (2.3-fold), while upregulating flavonoid genes (SbPAL, SbCHS, SbCHI). Under gradient drought, SbBZR1 reprogrammed metabolism dose-dependently: mild stress (1 % PEG) elevated both glycosides (baicalin +128 %) and aglycones (baicalein +196 %), whereas Sbbzr1-1D prioritized glycoside production (3.42-fold baicalin; glycoside-aglycone ratio 15.02 vs. WT 3.93). Mechanistically, Sbbzr1-1D amplified phenylpropanoid flux via SbPAL and SbF8H (4.1-6.3 fold) while suppressing deglycosylation (β-glucuronidase, SbGUS 72 % down-expression). Exogenous epibrassinolide (eBL) treatment confirmed SbBZR1 amplifies BR sensitivity, boosting baicalin yields 2.1-3.8 fold. The BR-SbBZR1 axis dynamically coordinates drought-induced transcriptional bursts (SbFNSII-2, SbF6H) with flavonoid accrual, while differentially regulating glycosylation (SbUBGAT up-expression) and deglycosylation (SbGUS down-expression). Collectively, these results first reveal the transcriptional logic of stress-driven phytochemical enhancement and provide valuable references for engineering drought-resistant crops through precision metabolic regulation.