Molecular dynamics simulations reveal the disparity in specific recognition of GCC‐box by AtERFs transcription factors super family in Arabidopsis

Abstract

Arabidopsis ethylene responsive element binding factors (AtERFs) form a transcription factor super family. While the functions of most AtERFs are unknown, a number of AtERFs appear to be involved in regulation of stress-related genes through their DNA binding domains (DBD), namely ERF domains, which recognize a consensus motif GCC-box at the regulatory region. In this study, molecular dynamics simulations were performed on the four ERF domain-GCC-box complexes, AtERF1, AtERF4, AtEBP and CFBF1, to determine disparity in specific binding to the GCC-box by the AtERFs. Our results suggested that three amino acid residues Arg29, Glu39 and Arg41, played a vital role in direct readout of DNA. The position of the consensus sequence GCCGCC has an intrinsic disparity on binding with ERF domains. The third C, fourth G and the last C in the GCC motif was compulsory for recognition by ERF domains. Our results provide structural evidence for a sequence-dependent recognition mechanism for AtERFs.

Divergent DNA-Binding Specificities of a Group of ETHYLENE RESPONSE FACTOR Transcription Factors Involved in Plant Defense

“…Amino acid residues, mainly Arg and Trp, that directly contact base moieties of DNA are found in the b-sheet (Fig. 1B) and are important, along with other residues in the DBD, for DNA-binding properties (Allen et al, 1998;Sakuma et al, 2002;Hao et al, 2002;Liu et al, 2006;Wang et al, 2009).…”

Expression and functional analysis of the transcription factor-encoding Gene CsERF004 in cucumber during Pseudoperonospora cubensis and Corynespora cassiicola infection

“…ERF transcription factors are capable of binding to the GCC-box or DRE/CRT cis-acting elements of the gene promoter region to regulate gene expression [31, 32, 48, 54, 55]. Previous studies have shown that the over-expression of ERFs in plants enhances plant disease resistance by increasing the expression of PR genes.…”

“…Zhang et al showed that LeERF2 binds to the CCGCC box [48]. Wang et al reported that the third, fourth, and sixth bases of the conserved GCCGCC sequence of the GCC box are essential for ERF protein binding and that other base alterations may affect their binding efficiency [55]. Therefore, the low binding efficiency of CsERF004 and the CsPR1 promoter may have affected the expression level of CsPR1 .…”

Differential expression of peach ERF transcriptional activators in response to signaling molecules and inoculation with Xanthomonas campestris pv. pruni

“…Although all these residues are conserved among Pp-ERFs, the divergence in other regions within the AP2/ERF domain might be the reason for different transactivation capabilities of Pp-ERFs. On the other hand, molecular dynamic simulations have predicted some disparity among Arabidopsis ERFs in terms of their binding specificity to the GCC-box (Wang et al, 2009). While the interactions of Arg29, Glu39 and Arg41 to G7, C6 and G4, respectively, were conserved among the four studied AP2/ERF domain-GCC complexes, three residues Arg31, Arg49 and Trp51 exhibited different binding preferences to DNA bases or the phosphate backbone (Wang et al, 2009).…”

“…On the other hand, molecular dynamic simulations have predicted some disparity among Arabidopsis ERFs in terms of their binding specificity to the GCC-box (Wang et al, 2009). While the interactions of Arg29, Glu39 and Arg41 to G7, C6 and G4, respectively, were conserved among the four studied AP2/ERF domain-GCC complexes, three residues Arg31, Arg49 and Trp51 exhibited different binding preferences to DNA bases or the phosphate backbone (Wang et al, 2009). Possibly such differences exist among Pp-ERFs as well, explaining their different capacities in triggering GUS expression (Fig.…”