Panda, M. K. | Search bioRxiv

bioRxiv2025

PIF4-mediated regulation of H2O2 homeostasis controls Arabidopsis seedling thermomorphogenesis

Thermomorphogenesis under high ambient temperature involves extensive developmental changes, including hypocotyl elongation at the seedling stage, in Arabidopsis. Reactive Oxygen Species (ROS), particularly hydrogen peroxide (H2O2), are important signaling molecules, playing crucial roles in plant development and stress responses. While ROS-homeostasis is shown to be crucial for maintaining cellular functions and mediating various developmental responses, the involvement of ROS-homeostasis in the regulation of thermomorphogenic responses and the underlying genetic basis remains poorly understood. In this study, comprehensive transcriptomic analyses revealed strong induction of ROS homeostasis and signaling genes in Arabidopsis seedlings under high ambient temperature. Pharmacological and genetic experiments showed that maintaining H2O2 homeostasis is crucial for seedling thermomorphogenesis. We identified PHYTOCHROME INTERACTING FACTOR 4 (PIF4) as a key regulator of H2O2 homeostasis via direct transcriptional activation of CAT2 and CAT3 genes, which are involved in the regulation of H2O2 levels, to modulate hypocotyl elongation under high temperature. Genetic and biochemical experiments confirmed that CATs act downstream to PIF4 in the same signaling pathway to regulate high-temperature-responsive hypocotyl elongation. Interestingly, elevated H2O2 levels reduced PIF4 protein abundance under high temperature. Together, our findings establish a PIF4-CAT-H2O2 regulatory module, functioning alongside the canonical PIF4-Auxin module, that integrates to auxin signaling to fine-tune hypocotyl elongation under high temperature by maintaining H2O2 homeostasis. HighlightsO_LIHigh ambient temperature significantly affects ROS homeostasis and signaling genes in Arabidopsis seedlings. C_LIO_LIH2O2 homeostasis is crucial for high-temperature-mediated hypocotyl elongation, a signature feature of Arabidopsis thermomorphogenesis. C_LIO_LIPHYTOCHROME INTERACTING FACTOR 4 (PIF4) regulates the expression of CATALASE genes in a temperature-dependent manner to maintain H2O2 levels for seedling thermomorphogenesis. C_LIO_LIElevated H2O2 level reduces PIF4 protein abundance, thus forming a PIF4-CAT-H2O2 regulatory module that integrates with auxin to fine-tune hypocotyl elongation under high temperature. C_LI

plant biology↗

bioRxiv2025

Integrative comparative transcriptomics using cultivated and wild rice reveals key regulators of developmental and photosynthetic progression along the rice leaf developmental gradient

A comprehensive understanding of gene regulatory networks and the key regulators underlying developmental and physiological progression along the leaf developmental gradient is crucial for optimizing photosynthetic competence. Comparisons of developmental and photosynthetic features across successive leaf developmental stages revealed pronounced differences between wild rice (Oryza australiensis) and three cultivated rice accessions. Global gene expression profiling identified three major transcriptional phases across leaf stages: a predominance of developmental genes at SAM+Pi (initiating primordia) and P3; genes for photosynthetic transition at P3 and P4; and enriched core photosynthetic genes at P4 and P5. O. australiensis showed a more prominent expression of developmental and photosynthetic genes than cultivated accessions across leaf stages. Multivariate analysis further supported a distinct transcriptional landscape in O. australiensis compared with cultivated accessions. Integration of gene expression with species-specific variations in regulatory sequences, derived from synteny-anchored orthology analysis, generated stage-resolved gene regulatory networks and identified key transcription factors (TFs) mediating the developmental and physiological progression. A cross-species comparison of TF-target regulatory networks revealed extensive stage- and accession-dependent rewiring of the regulatory networks of key TFs, with strong regulatory divergence in O. australiensis. Gene silencing of two candidate TFs, OsDOF8 and OsARID2, altered the rice photosynthetic competence with accession-specific effects. Taken together, the study highlights promoter-driven regulatory divergence as a potential mechanism underlying developmental and photosynthetic differences among the rice accessions. The resource is available through an interactive public database, Rice DEV-LEAF (https://nipgr.ac.in/DEV-LEAF/), enabling exploration of gene expression dynamics and regulatory networks across the rice leaf developmental gradient.

plant biology↗