FAR1-like Family from Maize

Required domains for FAR1-like family:PF03101

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FHY3 (far red elongated hypocotyl) and FAR1 (Far red-impaired response) are transcription factors that have separable DNA binding and transcriptional activation domains that are highly conserved in Mutator-like transposases, act as transcription factors essential for activating the expression by directly binding to a CACGCGC motif present in the promoters of FHY1 and FHL (for FHY1-like), whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses. FHY3, FAR1, and Mutatorlike transposases also share a similar domain structure, including an N-terminal C2H2 zinc finger domain (PF03101), a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases, of the sequence CxCxnCXH, where x stands for any amino acid residue). The N-terminal C2H2 domain has been shown to be involved in direct DNA-binding, while the transposase domain and C-terminal SWIM motif are required for transcriptional activity (Hudson et al., 1999, Lin et al., 2008).  FHY3 and FAR1 also act in an age gating mechanism to prevent precocious leaf senescence by integrating light and ethylene signaling with developmental aging (Kie et al., 2021).  In maize there are at least 2 members of the FARL (FAR1-like) family exhibiting a PF03101 domain.

FHY3 is an example of TE exaptation, a process whereby TEs (transposable elements), which persist by replicating in the genome, transform into novel host genes, which then persist by conferring phenotypic benefits. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms (Joly-Lopez et al., 2016).

Last updated June 2023 by John Gray


Hudson M, Ringli C, Boylan MT, Quail PH. The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling. Genes & Development. 1999 Aug;13(15):2017-2027. DOI: 10.1101/gad.13.15.2017. PMID: 10444599; PMCID: PMC316922.

Lin R, Teng Y, Park HJ, Ding L, Black C, Fang P, Wang H. Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction. Plant Physiol. 2008 Oct;148(2):981-92. doi: 10.1104/pp.108.120436. Epub 2008 Aug 20. PMID: 18715961; PMCID: PMC2556831.

Joly-Lopez Z, Hoen DR, Blanchette M, Bureau TE. Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements. Mol Biol Evol. 2016 Aug;33(8):1937-56. doi: 10.1093/molbev/msw067. Epub 2016 Apr 28. PMID: 27189548; PMCID: PMC4948706.

Xie Y, Ma M, Liu Y, et al. Arabidopsis FHY3 and FAR1 Function in Age Gating of Leaf Senescence. Frontiers in Plant Science. 2021 ;12:770060. DOI: 10.3389/fpls.2021.770060. PMID: 34777451; PMCID: PMC8584998.



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