Transcription factors enable cells to quickly and adequately respond and adapt to environmental changes by reprogramming their transcription pattern, that is, by activating or repressing gene expression in a spatially and temporally controlled manner. The GCN4 protein was originally identified as a positive regulator of genes encoding enzymes required for amino acid biosynthesis (Hinnebusch 1992), but it has since been implicated in various other biosynthetic pathways as well (Hinnebusch and Natarajan 2002). Upon amino acid, purine, or nitrogen starvation, the GCN4 protein level is upregulated through several mechanisms, and GCN4 homodimers bind to a consensus sequence (TGACTC) found upstream of target genes, thus derepressing their transcription. These targets include more than 35 genes encoding enzymes involved in amino acid biosynthesis (Hinnebusch 1992); furthermore, transcription of at least 10% of all genes of the entire yeast genome is directly or indirectly stimulated by GCN4 (Hinnebusch and Natarajan 2002).

The GCN4 dimer belongs to the family of basic region leucine zipper (bZip) transcription factors, which are of paramount importance in all eukaryotic cells (Hurst 1994, 1995). The two vital functions of these proteins - that is, dimerization and ensuing DNA binding - are reflected in the structure of their bZip domain, which is about 60-80 amino acid residues long and consists of two distinct regions (Vinson et al. 1989): an N-terminal basic region responsible for binding to the major groove of double-stranded DNA and a C-terminal leucine zipper mediating dimerization (Ellenberger et al. 1992; Keller et al. 1995; Konig and Richmond 1993). The dimeric quaternary structure of GCN4 and other bZip transcription factors bears several advantages over transcription regulators acting as monomers. Trivially, although monomeric or multimeric proteins can serve the same purpose, binding to double-stranded DNA inherently reveals some bias in favor of dimeric protein complexes. More importantly, however, the dimeric nature of the active state brings about a more pronounced concentration dependence as compared with a biologically active protein monomer. This is due to the fact that the concentration of protein dim-ers is not a linear function of the concentration of monomeric subunits, but reveals a steeper dependence. Finally, the modular architecture of bZip transcription factors allows for a huge number of conceivable homo- and heterodimeric combinations resulting from a rather limited set of polypeptide chains. GCN4 natively self-associates into a homodimeric protein assembly, but other members of the bZip family are involved in simultaneous, competing homo- and heterodimeric association processes, giving rise to transcription factors differing in DNA-binding avidity and even target-gene specificity (O'Shea et al. 1989, 1992; Hurst 1994, 1995; Glover and Harrison 1995; Newman and Keating 2003).

1.2 Structure

The GCN4 protein is 281 amino acid residues long and contains a bZip domain at its C-terminus (O'Shea et al. 1991). The 31-residue coiled-coil leucine zipper spans residues 249-279 of the full-length protein; its sequence reads

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