Abstract
BackgroundThe auxin response factor (ARF) gene family is involved in plant development and hormone regulation. Although the ARF gene family has been studied in some plant species, its structural features, molecular evolution, and expression profiling in Brachypodium distachyon L. are still not clear.ResultsGenome-wide analysis identified 19 ARF genes in B. distachyon. A phylogenetic tree constructed with 182 ARF genes from seven plant species revealed three different clades, and the ARF genes from within a clade exhibited structural conservation, although certain divergences occurred in different clades. The branch-site model identified some sites where positive selection may have occurred, and functional divergence analysis found more Type II divergence sites than Type I. In particular, both positive selection and functional divergence may have occurred in 241H, 243G, 244 L, 310 T, 340G and 355 T. Subcellular localization prediction and experimental verification indicated that BdARF proteins were present in the nucleus. Transcript expression analysis revealed that BdARFs were mainly expressed in the leaf and root tips, stems, and developing seeds. Some BdARF genes exhibited significantly upregulated expression under various abiotic stressors. Particularly, BdARF4 and BdARF8 were significantly upregulated in response to abiotic stress factors such as salicylic acid and heavy metals.ConclusionThe ARF gene family in B. distachyon was highly conserved. Several important amino acid sites were identified where positive selection and functional divergence occurred, and they may play important roles in functional differentiation. BdARF genes had clear tissue and organ expression preference and were involved in abiotic stress response, suggesting their roles in plant growth and stress resistance.
Highlights
The auxin response factor (ARF) gene family is involved in plant development and hormone regulation
The basic information containing gene name, locus, protein length, intron number, predicted isoelectric point, and molecular weight (MW) are shown in Additional file 1: Table S1, and their conserved motifs identified by SMART and Pfam are listed in Additional file 1: Table S2
We found that functional disproportionation occurred between each pair of clades, Expression and functions of B. distachyon ARFs in response to abiotic stressors Auxin plays an important role in the response to abiotic stressors, and ARF is an important transcription factor in the auxin signaling pathway [65]
Summary
The auxin response factor (ARF) gene family is involved in plant development and hormone regulation. The auxin gene family is involved in plant stress response, and includes Aux/IAA, Small Auxin Up RNA (SAUR), and Gretchen Hagen 3 (GH3) [2, 3]. Auxin response factors (ARFs), a critical family of transcription factors in the auxin-mediated pathway, are involved in hormone. A CTD, similar to the PB1 domain of the Aux/IAA protein, includes motifs III and IV that involve protein-protein interactions and mediate the homodimerization of ARFs or the heterodimerization of ARF and Aux/IAA [7, 10, 11]. When the concentration of auxin is low, the heterodimerization of Aux/ IAA and ARF inhibits the transcription activity of ARF, thereby preventing the transcription of related genes. When the auxin concentration reaches a certain level, the ubiquitin ligase SCFTIR1/AFB subunit ubiquitinates Aux/IAA and degrades it via the 26S proteasome pathway, weakening the inhibitory effect of Aux/IAA on ARF [7, 8]
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