The FHY3/FAR1 Gene Family in Plants: Transposase-Derived Transcription Factors as Master Integrators of Light Signaling and Plant Development

The FAR-RED IMPAIRED RESPONSE 1 (FAR1) and FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) transcription factors, together with other members of the FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) families, represent a striking example of transposable element domestication in plants. Derived from ancient Mutator-like element (MULE) transposases, these proteins have been repurposed as transcriptional regulators throughout the plant kingdom. FHY3 and FAR1 were first identified in Arabidopsis thaliana as positive regulators of phytochrome A (phyA) signaling. They participate in the coordination of light signaling with the circadian clock, chlorophyll biosynthesis, hormone pathways, stress responses, flowering time, shoot branching, leaf senescence, seed dormancy, and phosphate homeostasis. At the molecular level, FHY3 and FAR1 regulate gene expression mainly by binding to the conserved FHY3/FAR1-binding site, FBS, with the sequence CACGCGC, in the promoters of target genes. They also act through protein interactions with key signaling regulators, including HY5, PIFs, EIN3, TOC1, and SPL transcription factors. In this review, we summarize the molecular basis of FHY3/FAR1 gene family function, discuss the roles and mutant phenotypes of characterized family members, and highlight recent advances from other plant species beyond Arabidopsis. Collectively, this gene family illustrates how domesticated transposase-derived proteins have evolved into key regulators of plant development and environmental adaptation.