The ancillary N-terminal region of the yeast AP-1 transcription factor Yap8 contributes to its DNA binding specificity.

Anna Reymer,Ewa Maciaszczyk-Dziubinska,Katarzyna Mizio,Markus J Tamás,Nallani Vijay Kumar,Robert Wysocki,Wojciech Białek

doi:10.1093/nar/gkaa316

Anna Reymer, Ewa Maciaszczyk-Dziubinska + Show 5 more

Open Access

https://doi.org/10.1093/nar/gkaa316

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Abstract

Activator protein 1 (AP-1) is one of the largest families of basic leucine zipper (bZIP) transcription factors in eukaryotic cells. How AP-1 proteins achieve target DNA binding specificity remains elusive. In Saccharomyces cerevisiae, the AP-1-like protein (Yap) family comprises eight members (Yap1 to Yap8) that display distinct genomic target sites despite high sequence homology of their DNA binding bZIP domains. In contrast to the other members of the Yap family, which preferentially bind to short (7–8 bp) DNA motifs, Yap8 binds to an unusually long DNA motif (13 bp). It has been unclear what determines this unique specificity of Yap8. In this work, we use molecular and biochemical analyses combined with computer-based structural design and molecular dynamics simulations of Yap8–DNA interactions to better understand the structural basis of DNA binding specificity determinants. We identify specific residues in the N-terminal tail preceding the basic region, which define stable association of Yap8 with its target promoter. We propose that the N-terminal tail directly interacts with DNA and stabilizes Yap8 binding to the 13 bp motif. Thus, beside the core basic region, the adjacent N-terminal region contributes to alternative DNA binding selectivity within the AP-1 family.

Highlights

Yap8 protein is one of eight members of the yeast Activator protein 1 (AP-1) (Yap) family [1] that belongs to the fungal specific Pap1 subfamily of basic leucine zipper transcription factors [2] (Figure 1)
We recently showed that the Yap8 ortholog from Kluyveromyces lactis binds to multiple variants of Yap8 response element (Y8RE) with different 7 bp core sequences flanked by conserved TGA bases [17]
Yap8 contains several amino acid substitutions within its basic region at positions conserved in other members of yeast AP-1 (Yap) family (Figure 1); these amino acid residues may contribute to the specificity of Yap8 towards the extended Y8RE motif as well as its inability to bind to short Yap response element (YRE) motifs

Summary

Introduction

Yap protein is one of eight members of the yeast AP-1 (Yap) family [1] that belongs to the fungal specific Pap subfamily of basic leucine zipper (bZIP) transcription factors [2] (Figure 1). The crystal structure of the Pap bZIP domain bound to the 8 bp YRE revealed that five amino acid residues of the basic region make direct contacts with a TTAC half-site, and these residues constitute the signature DNA recognition NxxAQxxFR sequence [2]. This motif is highly conserved among members of the Pap subfamily suggesting that Yap proteins share a common mechanism of DNA binding (Figure 1). Despite the high similarity of DNA binding regions and corresponding recognition elements of 7-8 bp, little is known how individual Yap proteins achieve their specificity of transcriptional regulation

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