The bHLH transcription factor IBL1 fine-tunes growth and development via restraining cell elongation/expansion in Arabidopsis

bHLH proteins regulate plant development, hormone responses, and stress adaptation; however, the precise functions of most bHLHs remain unclear. In this study, we explored the functions and mechanism of a bHLH gene, IBH1-LIKE 1 (IBL1), in Arabidopsis. IBL1 negatively controlled root growth, hypocotyl elongation, and leaf expansion, as indicated by larger or longer cells in ibl1 compared with Col-0 in the early vegetative process. IBL1 promoted photomorphogenesis and participated in various hormone pathways. In later vegetative stages, ibl1 plants were smaller and weaker than Col-0. During the reproductive stage, the deficiency of IBL1 led to earlier bolting and unhealthy shoots but did not obviously impair gametogenesis and embryogenesis. Longer pistils occurred in ibl1 plants, while stamens exhibited normal length, indicating that IBL1 restricted pistil cell elongation. The unsynchronized sexual organs led to substantial incomplete pollination and vacant seats in siliques. Transcriptomic analysis implied that IBL1 functions via affecting the expression of cell expansion-related genes. Yeast two-hybrid, bimolecular fluorescence complementation, in vitro protein pull-down, electrophoretic mobility shift assays, and dual luciferase assays indicated that IBL1 interacts with other bHLHs, including PRE5, HBI1, and CIL2. These bHLH proteins could constitute a tri-antagonistic system to regulate plant cell elongation/expansion. In a proposed model, IBL1 and PRE5 antagonistically regulate the activity of HBI1/CIL2 to control target gene expression and eventually fine-tune cell elongation/expansion. This study reveals physiological roles and the working mode of IBL1 and provides insights into the regulation of plant growth and development.