TFIID structure

The purification of TFIID was soon followed by the identification of its subunits (reviewed in Albright and Tjian, 2000 Burley and Roeder, 1996). The amino acid sequences of many TAFs revealed a high level of conservation. TFIID structure has changed little through evolution, with all... 

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

Figure 37-9. The eukaryotic basal transcription complex. Formation of the basal transcription complex begins when TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA and protein-protein interactions. The entire complex spans DNA from position -30 to +30 relative to the initiation site (+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and ofTBP bound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 A resolution. The structure of TFIID complexes have been determined by electron microscopy at 30 A resolution. Thus, the molecular structures of the transcription machinery are beginning to be elucidated. Much of this structural information is consistent with the models presented here.

There are also indications that the composition of TFIID is not fixed, but may vary depending on the detailed structure of the promoter. This idea is corroborated by the isolation of a transcription-competent TFIID that supports transcription without requiring TBP binding (Apone Green, 1998). 

TFIIA and TFIIB support TFIID in the formation of a stable complex with the promotor. TFllB is necessary for the downstream selection of the start site for RNA polymerase 11. Interactions with TFllB ensure correct positioning of the RNA polymerase 11 on the promoter. Crystal structures have been solved for several of the intermediates of the pre-initiation complex (review Sokolev and Burley, 1997), showing, for example, that TBP affects a predominant kink in the DNA (see Fig. 1.16). TFIIB binds to the TBP-DNA complex, contacting both TBP and the DNA. 

Burley, S.K. and Roeder, R.G. Biochemistry and structural biology of transcription factor IID (TFIID) (1996) Annu Rev Biochem. 65, 769-799. 

The effects of DNA-binding transactivators on Pol II are mediated by coactivator protein complexes such as TFIID or mediator. The modular structures of the transactivators have distinct activation and DNA-binding domains. Other protein complexes, including histone acetyltransferases such as GCN5-ADA2-ADA3 and ATP-dependent complexes such as SWI/SNF and NURF, reversibly remodel chromatin structure. 

Interaction of the TATA-box-binding protein (TBP) with promoter DNA is rather inefficient and appears to be the rate-limiting step for the start of transcription. TBP must actually dissociate first from the TFIID complex before it can bind to the TATA-box DNA. Dissociation of TBP is facilitated by the dimeric structure of TFIID, when it is not bound to DNA, and by the interaction of TBP with TFIIA. 

Finally, in Plate 21, the structure of the yeast TFIIA-TBP-DNA complex is shown. TFIIA interacts with TBP and the TFIID complex and stimulates transcription of the Pol II gene.29-32 TFIIA has two characteristic structural motife. One is a six-stranded (i-sand-wich, the other is a left-handed four-helix bundle. The P-sandwich domain of TFUA is alone responsible for all of the interactions with the DNA, whereas its helix-bundle domain projects away and is free to interact with signal-responsive transcription factors. These interactions are important for regulation of transcription. Little conformational change occurs in TBP when it binds to TFIIA. The main difference between the TFIIA-TPB complex and the TFIIB-TBP complex is that TFIIA binds upstream of the TATA box, away from the transcriptional start site, whereas TFIIB binds downstream of the TATA box. Moreover, TFIIB is positioned on the side opposite to TFIIA. 

The largest TAP included in TFIID has an inhibitory action on TBP binding to DNA. The structure of a domain located in the N-terminus of D. melanogaster TAF230 complexed with S.cerevisiae TBP was obtained by NMR... 

D.B. Nikolov, et al. Crystal structure of TFIID TATA-box binding protein. Nature 360 (1992) 40-6. 

Transcriptional activators or repressors can intervene as regulators at various steps in the initiation of transcription. They can interact with components of TFIID, as well as with components of the RNA polymerase II holoenzyme to stimulate transcription. Furthermore, contacts to chromatin proteins are formed to change the structure of chromatin during transcription initiation and ongoing elongation. Regulated transcription and chromatin modification generally requires the aid of further protein components, which are commonly termed coactivators (see Section 1.4.4.2). 

TFIID and its individual subunits have been subjected to intense study. As will be discussed below, complementary information from biochemical, genetic, and structural studies has shown, and will continue to give, a clearer picture of the forms and functions of this crucial component of the transcription machinery. 

Fig. 1. Possible subunit structure of TFIID. On the basis of immuno-EM studies (Leurent et al., 2002), yeast two-hybrid data (Andel et al., 1999 Brand et al., 1999 Yatherajam et al., 2003), and in vitro protein interaction data (see text), a model of TFIID interactions was constructed. TAFs that appear in both TFIID and the SAGA HAT complex are shaded. BD1 and BD2 signify the bromodomains found in higher eukaryotic TAF1 or in yeast Bdfl. The exact stoichiometry of histone-like TAFs within each lobe is unclear some data indicate an octamer-like structure, whereas others support two tetramers.

TFIIB interacts with the C-terminal stirrup of TBP and the DNA both upstream and downstream of the TATA box, whereas TBIIA interacts with the N-terminal stirrup and the DNA upstream of the TATA box on the opposite face of the double helix from TFIIB (Nikolov and Burley, 1997). Therefore, both TFIIA and TFIIB can bind to the TBP-DNA complex simultaneously and synergistically stabilize the complex. Furthermore, TFIIB binding also contributes to the directionality of transcription and forms a bridge between TBP and Pol II and specifies the transcription start site. It will be interesting to see how these interactions fit into the structure of the TFIID complex. 

The ability of the histone-like TAFs to form an octamer-like structure raises the possibility that the TAF octamer may wrap promoter DNA in a manner similar to the nucleosome (Hoffmann et al., 1997 Oelgeschlager et al., 1996). This hypothesis is supported by the resemblance of DNase I footprinting patterns of TFIID on the Adenovirus Major Late (AdML) promoter to those of nucleosomal DNA. However, the arginine side chains in histones that form primary contacts with DNA are not conserved in TAFs (Luger et al., 1997). Therefore, the histone fold domain interaction may be used only for the formation of a compact structure and is not necessarily involved in DNA wrapping. 

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