Taxonomic distribution of proteins containing B3 domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing B3 domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

RAV1, a novel DNA-binding protein, binds to bipartite recognition sequencethrough two distinct DNA-binding domains uniquely found in higher plants.

Kagaya Y, Ohmiya K, Hattori T
Nucleic Acids Res. 1999; 27: 470-8

We have cloned and characterized two novel DNA binding proteins designatedRAV1 and RAV2 from Arabidopsis thaliana. RAV1 and RAV2 contain twodistinct amino acid sequence domains found only in higher plant species.The N-terminal regions of RAV1 and RAV2 are homologous to the AP2DNA-binding domain present in a family of transcription factorsrepresented by the Arabidopsis APETALA2 and tobacco EREBP proteins, whilethe C-terminal region exhibits homology to the highly conserved C-terminaldomain, designated B3, of VP1/ABI3 transcription factors. Binding siteselection assays using a recombinant glutathione S-transferase fusionprotein have revealed that RAV1 binds specifically to bipartiterecognition sequences composed of two unrelated motifs, 5'-CAACA-3' and5'-CACCTG-3', separated by various spacings in two different relativeorientations. Analyses using various deletion derivatives of the RAV1fusion protein show that the AP2 and B3-like domains of RAV1 bindautonomously to the CAACA and CACCTG motifs, respectively, and togetherachieve a high affinity and specificity of binding. From these results, wesuggest that the AP2 and B3-like domains of RAV1 are connected by a highlyflexible structure enabling the two domains to bind to the CAACA andCACCTG motifs in various spacings and orientations.

The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA bindingactivity.

Suzuki M, Kao CY, McCarty DR
Plant Cell. 1997; 9: 799-807

The biochemical activities that underlie the genetically defined activatorand repressor functions of the VIVIPAROUS1 (VP1) protein have resisted invitro analysis. Here, we show that a glutathione S-transferase (GST)fusion protein, including only the highly conserved B3 domain of VP1, hasa highly cooperative, sequence-specific DNA binding activity. GST fusionproteins that include larger regions of the VP1 protein have very lowactivity, indicating that removal of the flanking protein sequences isnecessary to elicit DNA binding in vitro. DNA competition and DNase Ifootprinting analyses show that B3 binds specifically to the Sph elementinvolved in VP1 activation of the C1 gene, whereas binding to theG-box-type VP1-responsive element is of low affinity and is nonspecific.Footprint analysis of the C1 promoter revealed that sequences flanking thecore TCCATGCAT motif of Sph also contribute to the recognition of the Sphelement in its native context. The salient features of the in vitro GST-B3DNA interaction are in good agreement with the protein and DNA sequencerequirements defined by the functional analyses of VP1 and VP1-responsiveelements in maize cells.

ARF1, a transcription factor that binds to auxin response elements.

Ulmasov T, Hagen G, Guilfoyle TJ
Science. 1997; 276: 1865-8

The plant hormone auxin regulates plant physiology by modulating theinteraction of transcription factors with auxin response elements (AuxREs)of the affected genes. A transcription factor, Auxin Response Factor 1(ARF1), that binds to the sequence TGTCTC in AuxREs was cloned fromArabidopsis by using a yeast one-hybrid system. ARF1 has an amino-terminalDNA-binding domain related to the carboxyl terminus of the maizetransactivator Viviparous-1. Sequence requirements for ARF1 binding invitro are identical to those that confer auxin responsiveness in vivo. Thecarboxyl terminus of ARF1 contains two motifs found in the Aux/IAA classof proteins and appears to mediate protein-protein interactions.