Multifaceted roles of FHY3 and FAR1 in light signaling and beyond

•FHY3 and FAR1 were initially identified as positive regulators of phyA signaling. •FHY3 and FAR1 are transcription factors derived from Mutator-like transposases. •FHY3 and FAR1 play multifaceted roles in regulating light signaling and beyond. FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), initially identified as crucial components of phytochrome A (phyA)-mediated far-red (FR) light signaling in Arabidopsis thaliana, are the founding members of the FAR1-related sequence (FRS) family of transcription factors present in most angiosperms. These proteins share extensive similarity with the Mutator-like transposases, indicative of their evolutionary history of 'molecular domestication'. Here we review emerging multifaceted roles of FHY3/FAR1 in diverse developmental and physiological processes, including UV-B signaling, circadian clock entrainment, flowering, chloroplast biogenesis, chlorophyll biosynthesis, programmed cell death, reactive oxygen species (ROS) homeostasis, abscisic acid (ABA) signaling, and branching. The domestication of FHY3/FAR1 may enable angiosperms to better integrate various endogenous and exogenous signals for coordinated regulation of growth and development, thus enhancing their fitness and adaptation. FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), initially identified as crucial components of phytochrome A (phyA)-mediated far-red (FR) light signaling in Arabidopsis thaliana, are the founding members of the FAR1-related sequence (FRS) family of transcription factors present in most angiosperms. These proteins share extensive similarity with the Mutator-like transposases, indicative of their evolutionary history of 'molecular domestication'. Here we review emerging multifaceted roles of FHY3/FAR1 in diverse developmental and physiological processes, including UV-B signaling, circadian clock entrainment, flowering, chloroplast biogenesis, chlorophyll biosynthesis, programmed cell death, reactive oxygen species (ROS) homeostasis, abscisic acid (ABA) signaling, and branching. The domestication of FHY3/FAR1 may enable angiosperms to better integrate various endogenous and exogenous signals for coordinated regulation of growth and development, thus enhancing their fitness and adaptation. refers to a scenario in which a TE evolved into a functional host gene. a DNA sequence that resembles a functional gene but lost its protein-coding ability, often due to accumulation of random mutations. Most pseudogenes are nonfunctional but some have been found to harbor regulatory roles. sunlight can be a luxury in natural environments, since seeds and newly emergent seedlings are often confronted with dim canopy light in which R light has been depleted by their neighbors, leaving mostly FR light unfavorable for photosynthesis. To survive the shade, plants evolved a FR-specific photoreceptor called phyA. On activation by FR light, phyA promotes seed germination, inhibits seedling hypocotyl elongation, and stimulates cotyledon expansion. These effects in sum enhance the fitness of plants in vegetatively shaded environments. DNA sequences that can change their positions (transpose) within the genome. According to the mechanism of transposition, they can be divided into Class I (retrotransposons) and Class II (DNA transposons). Transposition of Class II TEs is catalyzed by transposase enzymes. Some Class II TEs contain the coding sequences of transposases within them and therefore are able to transpose autonomously, while nonautonomous Class II TEs lack transposases and cannot transpose by themselves.