ARF Transcription Factor Family
Auxin response factors or ARFs are a family of transcription factors that bind with specificity to auxin response elements
(AuxREs) in promoters of primary or early auxin-responsive genes. ARFs have an amino-terminal DNA-binding domain related to
the carboxyl-terminal DNA-binding domain in the maize transactivator VIVIPAROUS1. 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. ARFs appear to play a pivotal role in
auxin-regulated gene expression of primary response genes .
Auxin-response factors (ARFs) bind to TGTCTC auxin-response elements(AuxREs), which are found in promoters of primary/early
auxin-response genes. The ARF1 protein contains an amino-terminal DNA-binding domain (DBD), which has some sequence
similarity to a carboxyl-terminal B3 domain found in the maize transcription factor VIVIPAROUS 1 (VP1) and its relatives.
ARF1 contains a carboxyl-terminal domain (CTD) related to motifs III and IV found in the CTDs of Aux/IAA proteins, which are
short-lived nuclear proteins encoded by a family of primary/early auxin-response genes. The CTDs in ARF1 and Aux/IAA
proteins facilitate dimerization among the members of both ARF and Aux/IAA protein families. Transcriptional activation or
repression domains in ARFs have not been identified in previous studies.
Here, we show that some ARFs contain middle regions (i.e., regions separating the DBD from the CTD) that function as
activation domains. Our results suggest that TGTCTC AuxREs are occupied regardless of the auxin status in cells and that
auxin is unlikely to directly affect the targeting of ARFs to their DNA-binding sites. These prebound transcription factors
facilitate activated transcription when auxin levels are elevated or when ARF activators are overexpressed in transfected
protoplasts. Our results also suggest that ARF CTDs facilitate interactions between ARF activators that are not bound to DNA
and transcription factors (e.g., ARFs) that are bound to AuxREs to further enhance transcription .
Auxin response factors (ARFs) are transcription factors that bind with specificity to TGTCTC auxin response elements
(AuxREs) found in promoters of primary/early auxin response genes. ARFs are encoded by a multi-gene family, consisting of
more than 10 genes. Ten ARFs have been analyzed by Northern analysis and were found to be expressed in all major plant
organs and suspension culture cells of Arabidopsis. The predicted amino acid sequences indicate that the 10 ARFs contain a
novel amino-terminal RNA binding domain and a carboxyl-terminal dimerization domain, with the exception of ARF3 which lacks
this dimerization domain. All ARFs tested bind with specificity to the TGTCTC AuxRE, but there are subtle variations in the
sequence requirements at positions 5 (T) and 6 (C) of the AuxRE. While the amino-terminal domain of about 350 amino acids is
sufficient for binding ARF1 to TGTCTC AuxREs, this domain is not sufficient for the binding of some other ARFs to
palindromic AuxREs. Our results suggest that ARFs must form dimers on palindromic TGTCTC AuxREs to bind stably, and this
dimerization may be facilitated by conserved motifs found in ARF carboxyl-terminal domains. Dimerization in at least some
cases may dictate which ARF(s) are targeted to AuxREs .
73 putative ARF peptide,
CDS, and cDNA sequences;
blast HSP output, and globe multiple sequence alignment for validating the sequences in the family.
73 Auxin_resp domain peptide sequences with
alignment, and phylogeny tree.
13 ARF protein
and DNA
sequences with
annotations for soybean in PlantTFDB. Most are partial sequences.
This page was setup on May 27, 2009, last updated by Dr. Jeff Chen on
June 16, 2009.
