The PHYTOCHROME INTERACTING FACTOR 3, a bHLH transcription factor, promotes thermosensory growth by directly activating PIF4 transcription and its protein accumulation in Arabidopsis

The role of PHYTOCHROME INTERACTING FACTOR 3 (PIF3) in thermomorphogenesis, despite being a crucial regulator of photosensory hypocotyl growth in Arabidopsis, remains unknown. Here, we demonstrate PIF3 as a key and novel component of the thermosensory pathway. pif3 mutants show reduced sensitivity to warm temperature-induced hypocotyl elongation, which is more pronounced at higher light intensities. pif3 mutant exhibits moderate impairment in petiole elongation and flowering. By contrast, PIF3 overexpression lines show constitutive thermomorphogenic responses. Whole-genome transcriptome analysis revealed that genes induced by warm temperature are significantly downregulated in the pif3 mutant but are constitutively upregulated in the PIF3 overexpression line. Moreover, PIF3 directly activates PIF4 transcription by binding to the PIF-binding element (PBE-box) in a temperature-dependent manner. Chromatin immunoprecipitation (ChIP) and biochemical data indicate that PIF4 binding to its target genes requires PIF3. The physical interaction between PIF3 and PIF4 is likely required for the optimal expression of downstream genes involved in metabolism and growth. Epistatic and gene regulation analysis further revealed that PIF3 functions in PIF4-dependent and PIF4-independent pathways to regulate gene expression. This study unravels the novel role, and mechanism through which, PIF3 promotes thermomorphogenic growth in Arabidopsis.