ARF Genomic sequences

Minimum number of tobacco ARF genes: 12

Count of tobacco ARF sequences: 14

Pfam accession: Auxin_resp

SHOULD possess Auxin_resp domain and COULD possess AUX_IAA B3 domains

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 .

Papers

Guilfoyle, TJ; Ulmasov, T; Hagen, G. The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell. Mol. Life Sci. 1998. 54(7):619-27 PMID: 9711229

Ulmasov, T; Hagen, G; Guilfoyle, TJ. ARF1, a transcription factor that binds to auxin response elements. Science 1997. 276(5320):1865-8 PMID: 9188533



Number of contigs: 11

Number of singlets: 3

Number of N terminal – 3

Number of C terminal – 2

Number of full – 9

Total minimum number – 12




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
ARF_1 [comment=N terminal] ET042646
ET042647
ARF_2 [comment=full] ET044549
ET044550
ARF_3 [comment=N terminal] ET043332
ET043790
ARF_4 [comment=full] ET045897
ET045384
ARF_5 [comment=full] ET045297
ET049419
ARF_6 [comment=full] ET051403
ET045164
ARF_7 [comment=full] ET045481
ET045525
ET048603
ARF_8 [comment=full] ET049221
ET044191
ET044179
ET046373
ARF_9 [comment=full] ET050562
ET043964
ET043975
ET044823
ET043974
ARF_10 [comment=full] ET044891
ET044892
ET048648
ET044893
ET048647
ARF_11 [comment=full] ET042667
ET042666
ET050501
ET050605
ET051350
ET042669
ET042668
ARF_12 [comment=N terminal] ET045502
ARF_13 [comment=C terminal] ET051132
ARF_14 [comment=C terminal] ET051597


Tobacco published genes related to transcription factor family ARF
Family Genbank ID Name
ARF DQ340258.1 ARF2-like protein
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu