Transcription factors and transporters in zinc homeostasis: lessons learned from fungi

Abstract

Zinc is an essential nutrient for all organisms because this metal serves as a critical structural or catalytic cofactor for many proteins. These zinc-dependent proteins are abundant in the cytosol as well as within organelles of eukaryotic cells such as the nucleus, mitochondria, endoplasmic reticulum, Golgi, and storage compartments such as the fungal vacuole. Therefore, cells need zinc transporters so that they can efficiently take up the metal and move it around within cells. In addition, because zinc levels in the environment can vary drastically, the activity of many of these transporters and other components of zinc homeostasis is regulated at the level of transcription by zinc-responsive transcription factors. Mechanisms of post-transcriptional control are also important for zinc homeostasis. In this review, the focus will be on our current knowledge of zinc transporters and their regulation by zinc-responsive transcription factors and other mechanisms in fungi because these organisms have served as useful paradigms of zinc homeostasis in all organisms. With this foundation, extension to other organisms will be made where warranted.

Keywords: Zinc; homeostasis; regulation; transcription factors; transporters.

Figure 1.

Functional domains of the canonical zinc-responsive transcription factors of fungi, Zap1 of S. cerevisiae and Loz1 of S. pombe. A) Zap1 contains seven zinc finger domains numbered 1-7 indicated by the black boxes. Zinc fingers 3-7 comprise the DNA binding domain (DBD). Zap1 also contains two transcription activation domains, AD1 and AD2 (blue boxes). AD1 is located within a larger domain, ZRD^AD1 (dashed box) that confers zinc responsiveness on AD1 function. AD2 is located within zinc finger domains 1 and 2 that are required for AD2 zinc responsiveness and this region is designated as ZRD^AD2. B) The DNA binding domain of Loz1 contains two zinc fingers and the zinc responsive domain (ZRD) of this protein contains those fingers and an adjacent accessory domain (dashed box). A conserved region between residues 128 and 169 that has numerous potential metal-binding histidines and cysteines is also present but of unknown function (gray box). The N- and C-termini are indicated and the numbers refer to the domain boundaries in the amino acid sequences.

Figure 2.

Variations in gene regulation mediated by Zap1. Expression under zinc-replete and zinc-deficient conditions are depicted for A) ZRT1, B) ZRT2, C) ADH1, D) RTC4 and GIS2, and E) ADH6. For ZRT2, an intermediate condition of mild zinc deficiency is also shown. Gene open reading frames are indicated by the open boxes, ZREs are indicated by orange boxes, TATA boxes are indicated by filled circles, RNA transcripts are shown by black arrows, repressive effects on gene expression are depicted by red T-bars. Zap1 is indicated by blue circles and other transcription factors are depicted by purple circles and their binding sites are indicated by gray boxes.

Figure 3.

Topology and structure of ZIP transporters. A) Transmembrane α-helices are numbered α1-α8, and the N- and C-termini and other features are indicated (ECD = extracellular domain). B) Side view and top view of BbZIP. Transmembrane α-helices are shown and the metal binding sites are indicated by the yellow spheres. Panel B is reproduced with permission from (Zhang et al., 2017) with some modifications.

Figure 4.

Topology and structure of CDF transporters. A) Transmembrane α-helices are numbered α1-α6, and the N- and C-termini and other features are indicated (CTD = carboxy terminal domain). B) Side view and top view of YiiP. Transmembrane α-helices are shown in a YiiP dimer and the metal binding sites are indicated by the purple spheres circled in red. The arrows mark the predicted path of zinc exit during transport. On the top view, the central red dashed oval indicates the hydrophobic dimer interface and the red dashed diamonds highlight the four-helix bundles (α1-α2-α4-α5) in each monomer. Panel B is reproduced with permission from (Lu et al., 2009) with some modifications

Figure 5.

Competitive advantage of having both high and low affinity transporter systems. A) Dual transport system causes a prolonged preparation phase. Zinc influx (red arrows) is plotted relative to external zinc concentration. When abundant, nutrient influx is mediated by the Zrt2 low affinity system. As available zinc levels drop, activation of the starvation response occurs (“regulon activation”) which leads to induction of ZRT1 (blue arrow) and other starvation response genes. ZRT1 induction maintains influx until external levels drop to near the K_m of the high affinity system at which point growth inhibition occurs. The “preparation phase” is thus defined by the K_m’s of the low and high affinity transporters. B) A solo high affinity transport system has a much narrower preparation phase. As nutrient influx drops, growth limitation follows soon after induction of the starvation response, thereby shortening the time the cells have to respond to and prepare for severe deficiency. This figure is reproduced with permission from (Levy et al., 2011) with some modifications.