Dimeric Transcription Factors

It is believed that many transcription factors bind DNA as dimers ( dimeric transcription factors) in either the same or opposite orientation. The DNA sites therefore can look like two direct repeat sequences or like palindromes. The interaction of the subunits with each other must obviously be specific and be mediated by dimerization domains. Specificity and stability of the dimers (dimeric transcription factors) is mostly promoted by hydrophobic or ionic inteiphases, e.g. a... 

L-Dihydroxyphenylalanine 4-Dihydroxyphenylethylamine Dimeric Transcription Factors Dioxins Dipeptidase Dipeptidylpeptidase Dipeptidylpeptidase IV Direct Thrombin Inhibitors Discharge of Neurons... 

The helix-loop-helix (HLH) dimerization domain is quite distinct from the helix-turn-helix motif described above (which is involved in DNA binding not dimerization) and must not be confused with it. The HLH domain consists of two a-helices separated by a nonhelical loop. The C-terminal a-helix has hydrophobic amino acids on one face. Thus two transcription factor monomers, each with an HLH motif, can dimerize by interaction between the hydrophobic faces of the two C-terminal a-helices. Like the leucine zipper (see above), the HLH motif is often found in transcription factors that contain basic DNA binding domains. Again, like the leucine zipper, the HLH motif can dimerize transcription factor monomers to form either homodimers or heterodimers. This ability to form heterodimers markedly increases the variety of active transcription factors that are possible and so increases the potential for gene regulation. 

The interaction of NF-kB with IkB provides a wealth of examples of several different kinds of order-disorder processes. This work was started in our lab as a collaboration with Dr. E.A. Komives at the University of California, San Diego. Nuclear factor-kappaB (NF-kB) is a dimeric transcription factor widely employed for the transcription of stress-response genes, as it binds to kB upstream enhancer DNA sequences, where it recruits the transcriptional activator CBP. In an unstressed cell, the majority of the NF-kB resides in the cytoplasm, in complex with the inhibitor of NF-kB (IkB). Response to stress involves phosphorylation and ubiquitination of IkB and its subsequent degradation by the proteasome. The free NF-kB is transported to the nucleus, where it binds to the kB enhancer sequences and mediates the transcription of genes that include that of IkB, which acts subsequently to remove NF-kB from the DNA and return it to the cytoplasm as the NF-kB-IkB complex. 

How do the distantly bound transcription factors contact the basic transcriptional machinery and instruct Pol II when to start transcription Although there are linkers to establish these contacts, the chromatin complex itself helps to make the contacts. DNA is highly condensed, suprahelical, and often bends on binding a dimeric transcription factor, bringing the transcriptional regulators closer together (Fig. 9.4). 

An important eukaryotic transcription factor is the nuclear factor, NF-kB (NF-xB). This factor binds to DNA through i-sheets. The i-sheets of the dimeric transcription factor wrap around the DNA like a mantle. Contacts are made, as in the case of a-helices, with die major groove of the DNA. The structure is shown in Plate 18. 

Basic Helix-Loop-Helix (bHLH) Proteins The DNA-binding domain of another class of dimeric transcription factors contains a structural motif very similar to the basic-zipper motif except that a nonhelical loop of the polypeptide chain separates two a-helical regions in each monomer (Figure 1 l-22b). Termed a basic helix-loop-helix (bHLH), this motif was predicted from the amino acid sequences of these proteins, which contain an N-terminal a helix with basic residues that interact with DNA, a middle loop region, and a C-termlnal region with hydrophobic amino acids spaced at intervals characteristic of an amphipathic a helix. As with basic-zipper proteins, different bHLH proteins can form heterodimers. 

There are two other technologies stiU in development with similar potentials. So-called yeast three hybrid screens are related to the better known two-hybrid screens, where the binding interaction that is being hunted for triggers the assembly of a dimeric transcription factor. The functional transcription factor then stimulates expression of a reporter gene. One half of the transcription factor is fused to a known smaU-molecule receptor (say for a dmg), whilst the other is fused to memhers... 

Residues 50-64 of the GAL4 fragment fold into an amphipathic a helix and the dimer interface is formed by the packing of these helices into a coiled coil, like those found in fibrous proteins (Chapters 3 and 14) and also in the leucine zipper families of transcription factors to be described later. The fragment of GAL4 comprising only residues 1-65 does not dimerize in the absence of DNA, but the intact GAL4 molecule does, because in the complete molecule residues between 65 and iOO also contribute to dimer interactions. 

Leucine zippers provide dimerization interactions for some eucaryotic transcription factors... 

The coiled-coil structure of the leucine zipper motif is not the only way that homodimers and heterodimers of transcription factors are formed. As we saw in Chapter 3 when discussing the RNA-binding protein ROP, the formation of a four-helix bundle structure is also a way to achieve dimerization, and the helix-loop-helix (HLH) family of transcription factors dimerize in this manner. In these proteins, the helix-loop-helix region is preceded by a sequence of basic amino acids that provide the DNA-binding site (Figure 10.23), and... 

Figure 10.23 Domain arrangement along the polypeptide chains of three families of transcription factors b/z, b/HLH and b/HLH/z. All three have a basic region (blue) that binds DNA. Dimerization is achieved by the zipper region (purple) in the b/z family, by the Hl-loop-H2 region (red-yellow-green) in the b/HLH family and by a combination of both the zipper and the HLH regions in the b/HLH/z family.

The b/HLH/zip family of transcription factors have both HLH and leucine zipper dimerization motifs... 

Figure 10.28 Schematic diagram of the binding of the transcription factor Max to DNA. The two monomers of Max (blue and green) form a dimer through both the helix-loop-helLx regions which form a four-helix bundle like MyoD, and the zipper regions, which are arranged in a coiled coil. The N-terminal basic regions bind to DNA in a way similar to GCN4 and MyoD. (Adapted from A.R. Ferre-D Amare et al., Nature 363 38-4S, 1993.)...

Dimerization of the Ce-zinc cluster transcription factors involves an a-helical coiled coil in the dimerization region. Coiled coils, often called leucine zippers, are also found in a large group of transcription factors that do not contain zinc. The leucine zipper is made up of two a helices in a coiled coil with every seventh residue leucine or some other large hydrophobic residue, such as isoleucine or valine. Leucine zipper transcription factors (b/zip) include factors characterized by heterodimerization, for example Fos and Jun. The a-helical DNA-binding motifs of the heterodimers recognize quite different base sequences and are continous with the a helices of the zipper. 

Helix-loop-helix (b/HLH) transcription factors are either heterodimers or homodimers with basic a-helical DNA-binding regions that lie across the major groove, rather than along it, and these helices extend into the four-helix bundle that forms the dimerization region. A modification of the b/HLH structure is seen in some transcription factors (b/HLH/zip) in which the four-helix bundle extends into a classic leucine zipper. 

Activator Protein-1 (API) comprises transcriptional complexes formed by dimers of members oftheFos, Jun, and ATF family of transcription factors. These proteins contain basic leucine zipper domains that mediate DNA binding and dimerization. They regulate many aspects of cell physiology in response to environmental changes. 

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