Activation domains

Two domains, t1 and t2, exist which affect the GR post-DNA binding transcription activity (37). The major (t1) transactivation domain is 185 amino acid residues ia length with a 58-tesidue a-heUcal functional cote (38). The t1 domain is located at the N terminus of the proteia the minor (t2) trans activation domain residues on the carboxy-terminal side of the DNA binding domain. 

The polypeptide chain of p53 is divided in three domains, each with its own function (Figure 9.16). Like many other transcription factors, p53 has an N-terminal activation domain followed by a DNA-binding domain, while the C-terminal 100 residues form an oligomerization domain involved in the formation of the p53 tetramers. Mutants lacking the C-terminal domain do not form tetramers, but the monomeric mutant molecules retain their sequence-specific DNA-binding properties in vitro. 

Rel homology domain (RHD) that encompasses a sequence-specific DNA-binding domain, a dimerization domain and a nuclear translocation signal (NLS) (Fig. la). RelA, cRel, and RelB contain a transcription activation domain (TAD). NF-kB 1 and NF-kB2 are synthesized as large precursors, pi 05 and pi 00, that are posttranslationnally processed to generate the mature forms, p50 and p52, which lack a TAD. 

Eight exons of the AR gene encode a protein of around 917 aa depending on two polymorphic regions of polyglutamines (CAG) and polyglycines (GGN) in the N-terminal activation domain. Two isoforms are detected in tissues the predominant (80%) 110 kD (B isoform) and 87 kD (A isoform). It is not clear whether the two isoforms also serve different functions. 

The most ingenious exocytosis toxins, however, come from the anaerobic bacteria Clostridium botulinum and Clostridium tetani. The former produces the seven botulinum neurotoxins (BoNTs) A-G the latter produces tetanus neurotoxin (TeNT). All eight toxins consist of a heavy (H) chain and a light (L) chain that are associated by an interchain S-S bond. The L-chains enter the cytosol of axon terminals. Importantly, BoNT L-chains mainly enter peripheral cholinergic terminals, whereas the TeNT L-chain mainly enters cerebral and spinal cord GABAergic and glycinergic terminals. The L-chains are the active domains of the toxins. They are zinc-endopeptidases and specifically split the three core proteins of exocytosis, i.e. the SNAREs (Fig. 1 inset). Each ofthe eight toxins splits a... 

While activation of HSFl and HSF2 results in the increased expression of HS genes, recent studies indicate that there are distinct differences between these transcription factors. As noted previously, HSFl is the heat-inducible form of the HS factors, whereas HSF2 is activated by hemin (Sistonen et al., 1992). This observation has indicated a possible role of HSF2 in cellular differentiation. It also indicates that the activation domains of the two transcription factors are quite different. Presumably the DNA binding properties of the two transcription factors are similar, but recent experiments indicate otherwise (Kroger and Morimoto,... 

Fig. 3.17 Activation of gene transcription by artificial transcription factors. (Top) The artificial activator is composed of three separate functional domains. The DNA binding domain consists of the pyrrole/imidazole polyamides (shown as connected arrows). A tethered linker domain (shown as a coil) connects the DNA binding domain to the peptide activation domain (AD, shown as an oval).

Upon binding, the artificial transcription factor recruits the necessary transcriptional machinery for gene activation. (Bottom, left) Ball-and-stick model for a polyamide conjugated to the VP2 activation domain. Symbols are as in Fig. 3.4. (Bottom, right) Structure of the polyamide-VP2 conjugate with the polyproline linker domain in brackets... 

Sequences farther upstream from the start site determine how frequently the transcription event occurs. Mutations in these regions reduce the frequency of transcriptional starts tenfold to twentyfold. Typical of these DNA elements are the GC and CAAT boxes, so named because of the DNA sequences involved. As illustrated in Figure 37—7, each of these boxes binds a protein, Spl in the case of the GC box and CTF (or C/EPB,NF1,NFY) by the CAAT box both bind through their distinct DNA binding domains (DBDs). The frequency of transcription initiation is a consequence of these protein-DNA interactions and complex interactions between particular domains of the transcription factors (distinct from the DBD domains—so-called activation domains ADs) of these proteins and the rest of the transcription machinery (RNA polymerase II and the basal factors TFIIA, B, D, E, F). (See... 

The formation of the PIC described above is based on the sequential addition of purified components in in vitro experiments. An essential feature of this model is that the assembly takes place on the DNA template. Accordingly, transcription activators, which have autonomous DNA binding and activation domains (see Chapter 39), are thought to function by stimulating either PIC formation or PIC function. The TAF coactivators are viewed as bridging factors that communicate between the upstream activators, the proteins associated with pol II, or the many other components of TFIID. This view, which assumes that there is stepwise assembly of the PIC—promoted by various interactions between activators, coactivators, and PIC components— is illustrated in panel A of Figure 37-10. This model was supported by observations that many of these proteins could indeed bind to one another in vitro. 

THE DNA BINDING TRANS-ACTIVATION DOMAINS OF MOST REGULATORY PROTEINS ARE SEPARATE NONINTERACTIVE... 

Figure 39-17. Proteins that regulate transcription have several domains. This hypothetical transcription factor has a DNA-binding domain (DBD) that is distinct from a ligand-binding domain (LBD) and several activation domains (ADs) (1-4). Other proteins may lack the DBD or LBD and all may have variable numbers of domains that contact other proteins, including co-regulators and those of the basal transcription complex (see also Chapters 42 and 43).

Lastly, in order to use Eq. (A. 12) to compute the phonon absorption due to this particular mechanism, we need to estimate the density of the active domain walls. It will suffice for our purposes here to consider as active the defects that contribute to the specihc heat, that is, roughly, n /Tg. A more... 

Figure 5.1. Yeast two-hybrid system. Interaction of proteins X and Y upstream of a reporter gene leads to transcriptional activation. Protein X is part of a fusion protein that binds to a site on DNA upstream of the reporter gene by means of a DNA binding domain. Protein Y is part of a fusion protein that contains a transcriptional activation domain. Interaction of proteins X and Y places the activation domain in the vicinity of the reporter gene and stimulates its transcription.

Repeat 16 times to assay all 6,000 activation domain fusions... 

Figure 5.3. Systematic mating ofyeast two-hybrid bait and prey pools. Each yeast ORF was cloned individually into both as a DNA binding domain fusion (bait) and activation domain fusion (prey). The bait fusions were introduced into a MATa strain and the prey fusions were introduced into a MATa strain. The bait and prey fusions were pooled in sets of 96 clones to generate a total of 62 pools of each. The pools were systematically mated (62 x 62) in a total of 3844 crosses. Interacting clones were selected and the bait and prey inserts were PCR amplified and sequenced to determine their identify. Figure adapted from Ito et al. (2001).

The genome of the Helicobacterpylori bacterium is 1.6 million base pairs in size and encodes 1590 ORFs (Tomb et al., 1997). The comprehensive two-hybrid library screen performed with these ORFs differs from the yeast experiments described above in that the Gal4 activation domain library used consisted of over ten million random genomic fragments (Rain et al., 2001). Thus, the potential problem of full-size ORFs masking protein-protein interactions is reduced. A total of 261 ORFs were fused to the Gal4 DNA binding domain to create a set of baits. These ORFs... 

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