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The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins

Figure 4

Structural explorations of yeast AP-1 transcription factor DNA recognition properties.

(A) Structure of the Pap1p bZIP dimer as defined in the PDB file 1GD2. Pap1p is the closest Yap1p functional homologue in the yeast S. pombe (see Main Text). Two identical chains of Pap1p proteins are represented. They are labeled E and F and colored in blue. Only the leucine-zipper domains and the DNA-binding regions are shown here. They are surrounding with dashed black boxes. Leucine residues in the coiled coil region responsible for the dimerization are colored in red. The DNA fragment at which the Pap1p proteins are associated is represented in orange and is surrounding with a dashed orange box. The sequence is indicated below: AGGTTACGTAACC. Note that this sequence contains the motif TTACGTAA that is the exact YRE-A motif identified in promoter of Cgap1p-dependant genes (Figure 3). (B) Predicted interactions between Pap1p TF and DNA in the 1GD2 structure presented in (A). Three types of interactions are represented: “Salt bridge” with a pink lines, “Hydrogen bound” with a green dashed lines and “Water-mediated hydrogen bound in grey dashed lines. These interactions were identified using the MONSTER web tool (see Materials and Methods). Nine residues of the Pap1p protein interact with DNA: R82, K83, Q85, N86, R87, A89, Q90, R94 and R96. (C) Comparison of the DNA-binding domains of the AP-1 proteins Ypap1p (in S. cerevisiae), Cgap1p (in C. glabrata) and Cap1p (in C. albicans) with the DNA-binding domain of Pap1p (in S. pombe). Protein residues that are conserved in the four species analyzed in this study are labeled with a black star. In Pap1p protein, the 9 residues that are predicted to interact with DNA (see B) are underlined. From these 9 interacted residues, 8 are strictly conserved in other species, they are surrounding with a black box. Note that in the protein Cgap1p, the residue 12 described by Kuo et al. (see Main Text) is highlighted in pink.

Figure 4

doi: https://doi.org/10.1371/journal.pone.0020924.g004