Structural Basis of Alternative DNA Recognition by Maf Transcription Factors

Abstract

Maf transcription factors constitute a family of the basic region-leucine zipper (bZip) factors and recognize unusually long DNA motifs (13 or 14 bp), termed the Maf recognition element (MARE). The MARE harbors extended GC sequences on each side of its core motif, which is similar to TRE or CRE (7 or 8 bp) recognized by the AP1 and CREB/ATF families, respectively. To ascertain the structural basis governing the acquirement of such unique DNA recognition, we determined the crystal structure of the MafG-DNA complex. Each MafG monomer consists of three helices in which the carboxyl-terminal long helix organizes one DNA-contacting element and one coiled-coil dimer formation element. To our surprise, two well-conserved residues, Arg57 and Asn61 in the basic region, play critical roles in Maf-specific DNA recognition. These two residues show unique side-chain orientations and interact directly with the extended GC bases. Maf-specific residues in the aminoterminal and basic regions appear to indirectly stabilize MARE recognition through DNA backbone phosphate interactions. This study revealed an alternative DNA recognition mechanism of the bZip factors that bestows specific target gene profiles upon Maf homodimers or Maf-containing heterodimers.

Bach2 maintains T cells in a naive state by suppressing effector memory-related genes

“…A basic leucine zipper domain and an adjacent conserved CNC domain are the defining features of this family. The CNC proteins form heterodimers with small maf proteins (MafK/F/G), and those dimers bind to a specific DNA sequence, the antioxidant response element (ARE) (8). The CNC proteins have important roles in stress responses.…”

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses

“…Although most bZIP transcription factors are thought to bind relatively compact binding sites (SI Appendix, Fig. S21), Maf subfamily transcription factors recognize unusually long motifs (13-14 bp) via an unconventional conformation of the invariant arginine and asparagine residues within the basic region of all bZIP proteins (4). Similarly, a crystal structure of Pap1, a S. pombe bZIP transcription factor, complexed with DNA demonstrated that Pap1 target site specificity was also due to alternate positioning of these two residues (2).…”

“…In a manner analogous to the Maf proteins, we propose that the extended homology region could stabilize invariant bZIP residues in the conformation required for UPRE-2 recognition. With the exception of MafG, most bZIP crystal structures have been based on constructs truncated to include only 1-9 nucleotides N-terminal to the basic DNA binding region (4,(25)(26)(27)(28) (SI Appendix, Fig. S22).…”

“…If this is the case, it should be possible to create Hac1 i mutants that disrupt binding to one site while largely preserving binding to the other. In the Maf subfamily of bZIP transcription factors, a region of extended homology positioned N-terminal to the basic DNA binding domain is critical for recognition of extended (13-14 nucleotide) target sites (4). Phylogenetic alignment of Hac1 orthologs across ascomycetes reveals a similar region of extended homology (SI Appendix, Fig.…”

“…Invariant arginine and asparagine residues within the basic DNA binding region (NXAAXXCR) make direct contact with DNA bases within the major groove and drive binding specificity to palindromic or semipalindromic target sites (2,3). Although considered to be the simplest known protein-DNA recognition motif, crystal structures of bZIP domains bound to DNA have revealed functional variability in how these conserved residues contact DNA (2,4), and no universal code linking basic region sequence with target DNA preferences has been developed.…”