A fungal family of transcriptional regulators: the zinc cluster proteins

Abstract

The trace element zinc is required for proper functioning of a large number of proteins, including various enzymes. However, most zinc-containing proteins are transcription factors capable of binding DNA and are named zinc finger proteins. They form one of the largest families of transcriptional regulators and are categorized into various classes according to zinc-binding motifs. This review focuses on one class of zinc finger proteins called zinc cluster (or binuclear) proteins. Members of this family are exclusively fungal and possess the well-conserved motif CysX(2)CysX(6)CysX(5-12)CysX(2)CysX(6-8)Cys. The cysteine residues bind to two zinc atoms, which coordinate folding of the domain involved in DNA recognition. The first- and best-studied zinc cluster protein is Gal4p, a transcriptional activator of genes involved in the catabolism of galactose in the budding yeast Saccharomyces cerevisiae. Since the discovery of Gal4p, many other zinc cluster proteins have been characterized; they function in a wide range of processes, including primary and secondary metabolism and meiosis. Other roles include regulation of genes involved in the stress response as well as pleiotropic drug resistance, as demonstrated in budding yeast and in human fungal pathogens. With the number of characterized zinc cluster proteins growing rapidly, it is becoming more and more apparent that they are important regulators of fungal physiology.

FIG. 1.

Functional domains of zinc cluster proteins. Zinc cluster proteins can be separated into three functional domains: the DBD, the regulatory domain, and the acidic region. In addition, the DBD is compartmentalized into subregions: the zinc finger, the linker, and the dimerization domain. These regions contribute to DNA-binding specificity and to protein-DNA and protein-protein interactions (267). MHR, middle homology region.

FIG. 2.

Crystal structures of the DBDs of some Zn(II)₂Cys₆ regulators. AlcR binds as a monomer (28), while Gal4p, Put3p, Ppr1p, Leu3p, and Hap1p bind as homodimers. Gal4p, Put3p, and Ppr1p recognize inverted DNA repeats (168, 169, 253, 278). Leu3p and Hap1p bind to everted and direct repeats, respectively (72, 89, 98, 124, 294). Yellow spheres correspond to zinc atoms.

FIG. 3.

A model for zinc cluster protein DNA recognition. Zinc cluster proteins preferentially bind to CGG triplets that can be oriented in three different configurations: the inverted, everted, and direct repeats. The orientation of CGG triplets and the nucleotide spacing between the triplets are the two major determinants of DNA-binding specificity (166). Zinc cluster proteins can also bind as monomers (in green) as well as homodimers (two molecules in blue) and heterodimers (one molecule in blue and one in orange).

FIG. 4.

Zinc cluster proteins involved in the PDR network in S. cerevisiae. Zinc cluster proteins (left column) and their target genes involved in PDR and the stress response (right column) are represented. Dashed lines point to genes that are not known to be direct or indirect targets of zinc cluster proteins. Only the most important ABC transporters and major facilitator superfamily members are shown. ERG genes are included because they are also involved in drug resistance.

FIG. 5.

Interplay among zinc cluster proteins implicated in PDR in budding yeast. A network of characterized zinc cluster proteins cooperatively coordinate the transcriptional regulation of PDR genes in S. cerevisiae. Pdr1p (in blue) can form homodimers as well as heterodimers with Pdr3p (in yellow) and Stb5p (in red) (3, 167). Pdr3p, Rdr1p (in gray), and Yrr1p (in green) are able to form homodimers (, ; S. MacPherson et al., unpublished data). These different combinations may differentially regulate the expression of PDR5 and SNQ2 ABC transporters. A direct binding of Rdr1p to PDR5 has not been demonstrated, and the mode of binding (e.g., monomer or heterodimer) of Yrm1p (in orange) is not known. 4NQO, 4-nitroquinoline-1-oxide.