Dimerization specificity of all 67 B-ZIP motifs in Arabidopsis thaliana: a comparison to Homo sapiens B-ZIP motifs

Abstract

Basic region-leucine zipper (B-ZIP) proteins are a class of dimeric sequence-specific DNA-binding proteins unique to eukaryotes. We have identified 67 B-ZIP proteins in the Arabidopsis thaliana genome. No A.thaliana B-ZIP domains are homologous with any Homo sapiens B-ZIP domains. Here, we predict the dimerization specificity properties of the 67 B-ZIP proteins in the A.thaliana genome based on three structural properties of the dimeric alpha-helical leucine zipper coiled coil structure: (i) length of the leucine zipper, (ii) placement of asparagine or a charged amino acid in the hydrophobic interface and (iii) presence of interhelical electrostatic interactions. Many A.thaliana B-ZIP leucine zippers are predicted to be eight or more heptads in length, in contrast to the four or five heptads typically found in H.sapiens, a prediction experimentally verified by circular dichroism analysis. Asparagine in the a position of the coiled coil is typically observed in the second heptad in H.sapiens. In A.thaliana, asparagine is abundant in the a position of both the second and fifth heptads. The particular placement of asparagine in the a position helps define 14 families of homodimerizing B-ZIP proteins in A.thaliana, in contrast to the six families found in H.sapiens. The repulsive interhelical electrostatic interactions that are used to specify heterodimerizing B-ZIP proteins in H.sapiens are not present in A.thaliana. Instead, we predict that plant leucine zippers rely on charged amino acids in the a position to drive heterodimerization. It appears that A.thaliana define many families of homodimerizing B-ZIP proteins by having long leucine zippers with asparagine judiciously placed in the a position of different heptads.

Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice

“…IdentiWcation and sequence analysis of the bZIP group A genes in rice Sequences of Arabidopsis bZIP transcription factors previously identiWed (Deppmann et al 2004) were downloaded from TAIR (http://www.arabidopsis.org/wublast/index2. jsp).…”

“…All hits with E-value below 0.001 were selected for further analysis. False hits were removed by manual inspection based on two criteria: (1) a well-deWned basic region including a near invariant asparagine critical for sequencespeciWc DNA binding and (2) a canonical leucine zipper region with obvious amphipathic qualities (Deppmann et al 2004). Multiple protein alignment was performed with ClustalX 1.81 using default parameters (Thompson et al 1997).…”

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

“…Additionally, the Tyr and Gln residues of the SKYQ motif occupy the g and a positions, respectively, in the Leu zipper after this last Leu. The a, e, and g positions in the helix of Leu zippers determine the specificity of dimerization between Leu zippers (Acharya et al, 2002;Deppmann et al, 2004). Additionally, the presence of a positively charged amino acid in the a position of one of the heptads-Lys in ig1, ial1, Sbig1, Osig1, and AS2 and Arg in ial2, ial3, and Osial1-suggests that these proteins do not homodimerize.…”

The Potential of Transcription Factor-Based Genetic Engineering in Improving Crop Tolerance to Drought

“…The basic region leucine zipper (bZIP) family of TFs is exclusively present in eukaryotes and regulates diverse functions such as plant development and stress responses (Deppmann et al, 2004;Ying et al, 2012). This family of TFs is characterized by a 40-80 amino acid long conserved bZIP domain, hence its name (Correa et al, 2008;Nijhawan et al, 2008).…”