Leucine-zipper proteins

The ability of the leucine zipper proteins to form heterodimers greatly expands the repertoire of DNA-binding specificities that these proteins can display. As illustrated in Figure 10.19, for example, three distinct DNA-binding specificities could, in principle, be generated from two types of monomer, while six could be created from three types of monomer and so on. This is an example of combinatorial control, in which combinations of proteins, rather than individual proteins, control a cellular process. It is one of the most important mechanisms used by eucaryotic cells to control gene expression. 

Figure 10.19 Heterodimerization of leucine zipper proteins can alter their DNA-binding specificity. Leucine zipper homodimers bind to symmetric DNA sequences, as shown In the left-hand and center drawings. These two proteins recognize different DNA sequences, as indicated by the red and blue regions in the DNA. The two different monomers can combine to form a heterodimer that recognizes a hybrid DNA sequence, composed of one red and one blue region.

Figure 5.10. Protein complementation assay using murine DHFR. The F[l,2] and F[3] fragments are each fused to the homodimerizing GCN4 leucine zipper protein. A. Transformation of both Z-F[l,2] and Z-F[3] constructs results in reconstituted DHFR and growth of E. coh on agar plates containing trimethoprim. B. Transformation of Z-F[l,2] or Z-F[3] alone does not result in trimethoprim resistant E. coli cells. Figure adapted from Pelletier et al. (1998).

Subunit Mixing in Eukaryotic Regulatory Proteins Several families of eukaryotic transcription factors have been defined based on close structural similarities. Within each family, dimers can sometimes form between two identical proteins (a homodimer) or between two different members of the family (a heterodimer). A hypothetical family of four different leucine-zipper proteins could thus form up to ten different dimeric species. In many cases, the different combinations appear to have distinct regulatory and functional properties. 

FIGURE 28-14 Leucine zippers, (a) Comparison of amino acid sequences of several leucine zipper proteins. Note the Leu (L) residues at every seventh position in the zipper region, and the number of Lys (K) and Arg (R) residues in the DNA-binding region. 

Leucine zipper proteins. Several transcription factors have the leucine zipper structure, which has been described in Chapter 2 and was illustrated there by the structure of transcription factor Max (Fig. 2-21).417 Related structures include those of the transcription... 

Figure 5-36 Stereoscopic diagrams showing some of the interactions between an N-terminal helical domain of the yeast transcription factor GCN4-bZIP, a leucine zipper protein, and a specific palindromic DNA binding site ...

Several mammalian leucine zipper proteins bind to the CCAAT sequence (Table 28-1) and are, therefore, as a family designated C/EBP.361 366 367 A 30-residue segment of C/EBP contains four leucine residues at 7-residue intervals. When plotted as a helical wheel (Fig. 2-20) the four leucines are aligned on one side.368 Similar sequences are present in the proteins cMyc, cjun, and cFos and in GCN4. These observations suggested that if the peptide sequence forms an a helix, the leucine side chain from two identical subunits or closely related proteins might interdigitate in... 

The helix-loop-helix motif appears to be another way of creating heterodimers that can bind to asymmetric sites on the DNA. Like the leucine zipper proteins, the helix-loop-helix proteins have a basic region that contacts the DNA and a neighboring region that mediates dimer formation. Based on sequence patterns, it has been proposed that this dimerization region forms an a helix, a loop, and a second a helix. Like the leucine zipper protein, the activity of the helix-loop-helix proteins is modulated by heterodimer formation. For example, the MyoD protein, which appears to be the primary signal for differentiation of muscle cells, binds DNA most tightly when it forms a heterodimer with the ubiquitously expressed E2A protein. 

New York, 1991, p. 126. Adapted from C. R. Vinson, P. B. Sigler, and S. L. McKnight, Scis-sors-grip model for DNA recognition by a family of leucine zipper proteins, Science 246 911, 1989. Copyright 1989 by the AAAS. Reprinted by permission. 

Guiltinan, M.J., Marcotte, W.R., Jr Quatrano, R.S. (1990). A plant leucine zipper protein that recognizes an abscisic acid response element. Science 250, 267-71. 

Leucine zipper proteins have been shown to interact with their cognate recognition sites as dimers (Landschulz et al., 1988). This dimer formation is mediated by the leucine zipper domain and is absolutely required for DNA binding (Hu et al., 1990 and references therein). We employed the method of Hope Struhl (1987) to investigate the ability of GBF-1 to form dimers in the presence of DNA. Different portions of the cDNA... 

DNA binding domains called basic domains (rich in basic amino acids), occur in transcription factors in combination with leucine zipper or helix-loop-helix (HLH) dimerization domains (see below). The combination of basic domain and dimerization domain gives these proteins their names of basic leucine zipper proteins (bZIP) or basic HLH proteins, respectively. In each case the dimerization means that two basic domains (one from each monomer) interact with the target DNA. 

CNC Cap n Collar family of basic leucine zipper proteins... 

Walker A Motif A motif described in SKN-1, a transcription factor in Caenorhabditis ele-gans. See Walker, A.K., See, R., Batchelder, C. et al., A conserved transcription motif suggesting functional parallels between Caenorhabitis ele-gans SKN-1 and Cap n Collar-related basic leucine zipper proteins, J. Biol. Chem. 275, 22166-22171, 2000. 

Andrews NC, Erdjument-Bromage H, Davidson MB, Temspt P, Orkin SH. 1993. Erythroid transcription factor NF-E2 is a haematopoietic-specific basic-leucine zipper protein. Nature 362 722-28... 

Chan, J. Y. and Kwong, M. (2000) Impaired expression of glutathione synthetic enzyme genes in mice with targeted deletion of the Nrf2 basic-leucine zipper protein. Biochim. Biophys. Acta 1517, 19-26. 

Leucine-Zipper Proteins Another structural motif present in the DNA-binding domains of a large class of transcription factors contains the hydrophobic amino acid leucine at every seventh position in the sequence. These proteins bind to DNA as dimers, and mutagenesis of the leucines showed that they were required for dimerization. Consequently, the name leucine zipper was coined to denote this structural motif. 

---