ARF Family from Brachypodium

Brachypodium families updated 2023 based on Maize family rules

Required domains for ARF family:PF02362PF06507

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The plant hormone auxin, or indole-3-acetic acid, controls many physiological and developmental processes in land plants including but not limited to organogenesis, tissue differentiation, apical dominance,and  gravitropism.  Genes for auxin biosynthesis, perception and signaling are present in the common ancestor of all embryophytes and most were present in mosses (Gao et al., 2020). Auxin response factors or ARFs are a family of transcription factors that bind with specificity to auxin response elements (AuxREs TGTCTC) in promoters of primary or early auxin-responsive genes.  Generally, ARF proteins can be functionally divided into transcriptional activators (ARF5-8 and 19 in A. thaliana) and repressors (remaining ARFs in A. thaliana) with well-characterized functional domain architectures (Gao et al., 2020).

ARFS can be identified by two signature domains: the amino-terminal B3 (PF02362) domain (related to the AB!-VP1 TF family) and the auxin-response (PF06507) domain, although some ARF proteins (e.g. ARF23 in A. thaliana) may be truncated and lack the auxin-response domain. All but one ARF identified to date contain a carboxyl-terminal protein-protein interaction domain that forms a putative amphipathic alpha-helix. A similar carboxyl-terminal protein protein interaction domain is found in the Aux/IAA class of auxin-inducible proteins. Some ARFs contain transcriptional activation domains while others contain repression domains.

A 2011 study revealed 31 maize genes that encode ARF proteins (Xing et al., 2011). Out of these 31 ZmARF genes, 14 possess auxin-responsive element in their promoter region, among which 7 appear to show small or negligible response to exogenous auxin. 18 ZmARF genes were predicted to be the potential targets of small RNAs. Transgenic analysis revealed that increased miR167 level could cause degradation of transcripts of six potential targets (ZmARF3, 9, 16, 18, 22 and 30) (Xing et al., 2011).

A 2012 study revealed 36 maize genes that encode ARF proteins (Wang et al., 2012). Eleven maize ARF proteins were observed to lack homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaptation were located in promoters of maize ARF genes. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic.

Overexpression of ZmARF4 in Arabidopsis confers tolerance of Pi deficiency with better root morphology than wild-type. Overexpressed ZmARF4 can also partially restore the absence of lateral roots in the Arabidopsis double mutant arf7 arf19.  ZmARF4 overexpression also conferred salinity and osmotic stress tolerance in Arabidopsis. Overall, ZmARF4, appears to be a pleiotropic gene that modulates multiple stress signaling pathways (Li et al., 2022).

Last updated June 2023 by John Gray


Xing H, Pudake RN, Guo G, Xing G, Hu Z, Zhang Y, Sun Q, Ni Z. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize. BMC Genomics. 2011 Apr 7;12:178. doi: 10.1186/1471-2164-12-178. PMID: 21473768; PMCID: PMC3082248.

Wang Y, Deng D, Shi Y, Miao N, Bian Y, Yin Z. Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. Mol Biol Rep. 2012 Mar;39(3):2401-15. doi: 10.1007/s11033-011-0991-z. Epub 2011 Jun 11. PMID: 21667107.

Gao B, Wang L, Oliver M, Chen M, Zhang J. Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants. Plant Methods. 2020 May 14;16:70. doi: 10.1186/s13007-020-00609-1. PMID: 32467718; PMCID: PMC7226935.

Li J, Wu F, He Y, He B, Gong Y, Yahaya BS, Xie Y, Xie W, Xu J, Wang Q, Feng X, Liu Y, Lu Y. Maize Transcription Factor ZmARF4 Confers Phosphorus Tolerance by Promoting Root Morphological Development. Int J Mol Sci. 2022 Feb 21;23(4):2361. doi: 10.3390/ijms23042361. PMID: 35216479; PMCID: PMC8880536.




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