bZIPs and WRKYs: two large transcription factor families executing two different functional strategies

Abstract

bZIPs and WRKYs are two important plant transcription factor (TF) families regulating diverse developmental and stress-related processes. Since a partial overlap in these biological processes is obvious, it can be speculated that they fulfill non-redundant functions in a complex regulatory network. Here, we focus on the regulatory mechanisms that are so far described for bZIPs and WRKYs. bZIP factors need to heterodimerize for DNA-binding and regulation of transcription, and based on a bioinformatics approach, bZIPs can build up more than the double of protein interactions than WRKYs. In contrast, an enrichment of the WRKY DNA-binding motifs can be found in WRKY promoters, a phenomenon which is not observed for the bZIP family. Thus, the two TF families follow two different functional strategies in which WRKYs regulate each other's transcription in a transcriptional network whereas bZIP action relies on intensive heterodimerization.

Keywords: DNA-binding; G/C box accumulation; W-box accumulation; WRKYs; bZIPs; heterodimerization; regulatory mechanisms.

FIGURE 1

Outline of a section through two a helices interacting via leucine zippers. The amino acids in positions a and d configure the hydrophobic core, which is indicated with the yellow halo. Charged residues in positions e and g generate electrostatic forces, represented by the dashed green lines. The hydrophilic surface is formed by the amino acids in positions b, c, and f.

FIGURE 2

Schematic drawing of a bZIP dimer bound to the DNA. The two proteins form a Y-shape structure which embraces a perpendicularly disposed DNA molecule. The major groove is contacted by both bZIPs via their DNA-binding domains. L represents the leucines forming the interface in the bZIP dimer.

FIGURE 3

Diagram of a WRKY C-terminal domain interacting with the DNA. The C-terminal WRKY domain consists of a four-stranded antiparallel β-sheet (1–4). The DNA recognition takes place along the major grove by the β1-strand containing the WRKYQK motif.

FIGURE 4

Frequency of cis-element distribution within the 3-kb upstream of coding sequences. The occurrence of the cis-elements was calculated only for the positive strand using the Patmatch tool in the TAIR website. Red bars refer to the whole set of 33,602 annotations of the TAIR10 Genome Release, while green and blue bars indicate the subsets including only bZIPs or only WRKYs genes, respectively. (A) The occurrence of W-boxes was determined using a TTGACY motif, where Y indicates pyrimidine. The enrichment of W-boxes in the WRKY promoters is remarkable, while only few WRKY promoters carry no W-boxes. (B) The occurrence of the G- and C-boxes, the preferred cis-elements bound by plant bZIPs, was determined using a SACGTS motif, where S indicate strong bases (C and G). In contrast, no increase of bZIP-binding sites in their promoters can be observed.

FIGURE 5

Model featuring the main differences between the regulatory strategies of the two families. (A) The expression of WRKY TFs is strongly regulated at the transcriptional level. The promoters of the WRKY genes are enriched in W-boxes, which are bound by WRKY proteins indicating transcriptional networking and also feed-back regulations. The dotted lines indicate that WRKY possibly interact with the DNA also in a monomeric stage. In addition, WRKYs can form dimers and thereby increase the variability in regulating specific target genes. (B) In the bZIP family heterodimerization is extensively used to increase variability in target gene regulation. The activity of the bZIPs is regulated via specific dimerization which determines the target specificity. There are no indications for transcriptional networking.