TFIIB

The DNA part of each control module can be divided into three main regions, the core or basal promoter elements, the promoter proximal elements and the distal enhancer elements (Figure 9.1). The best characterized core promoter element is the TATA box, a DNA sequence that is rich in A-T base pairs and located 25 base pairs upstream of the transcription start site. The TATA box is recognized by one of the basal transcription factors, the TATA box-binding protein, TBP, which is part of a multisubunit complex called TFIID. This complex in combination with RNA polymerase 11 and other basal transcription factors such as TFIIA and TFIIB form a preinitiation complex for transcription. 

TFIIA and TFIIB are two basal transcription factors that are involved in the nucleation stages of the preinitiation complex by binding to the TBP-TATA box complex. Crystal structures of the ternary complex TFIIA-TBP-TATA box have been determined by the groups of Paul Sigler, Yale University, and Timothy Richmond, ETH, Zurich, and that of the TFIIB-TBP-TATA box by Stephen Burley and collaborators. The TBP-DNA interactions and the distortions of the DNA structure are essentially the same in these ternary complexes as in the binary TBP-TATA complex. 

TFIIB is arranged in two domains, both of which have the cyclin fold described in Chapter 6. Both domains bind to the TBP-TATA box complex at the C-terminal stirrup and helix of TBP. The phosphate and sugar moities of DNA form extensive non-sequence-specific contacts with TFIIB both upstream and downstream of the middle of the TATA box. 

TFIIA also has two domains, one of which is a four-helix bundle and the other an antiparallel p sandwich. The p sandwich interacts with the N-termi-nal half of TBP and thus positions TFIIA on the other side of the complex compared with TFIIB. This domain also interacts with phosphates and sugars of DNA upstream of the TATA box. Tbe four-helix bundle domain makes no contact with DNA or TBP and is far removed from the position of TFIIB. 

TFIIA and TFIIB bind to both TBP and DNA Flomeodomain proteins are involved in the development of many eucaryotic organisms Monomers of homeodomain proteins bind to DNA through a heltx-turn-helix motif In vivo specificity of homeodomain... 

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.

Figure 37-10. Two models for assembly of the active transcription complex and for how activators and coactivators might enhance transcription. Shown here as a small oval is TBP, which contains TFIID, a large oval that contains all the components of the basal transcription complex illustrated in Figure 37-9 (ie, RNAPII andTFIIA,TFIIB, TFIIE,TFIIF, and TFIIFI). Panel A The basal transcription complex is assembled on the promoter after the TBP subunit of TFIID is bound to the TATA box. Several TAFs (coactivators) are associated with TBP. In this example, a transcription activator, CTF, is shown bound to the CAAT box, forming a loop complex by interacting with a TAF bound to TBP. Panel B The recruitment model. The transcription activator CTF binds to the CAAT box and interacts with a coactivator (TAF in this case). This allows for an interaction with the preformed TBP-basal transcription complex. TBP can now bind to the TATA box, and the assembled complex is fully active.

CYCLIN Domain present in cyclins, TFIIB and retinoblastoma E(MFP)A 18(27) 22(27) 1AIS... 

In vitro interactions between HMG proteins and the basal transcription machinery have also been reported. Human HMGBl binds to the TATA-box binding protein (TBP) and interferes with the normal binding of TFIIB in the preinitiation complex [154,155], thereby inhibiting TBP function both HMGBl and TFIIB independently enhance binding of TBP to TATA-box DNA [154]. Similarly, Nhp6ap promotes the formation of a complex with TBP and TFIIA at the TATA... 

This consists of DNA-dependent RNA polymerase II and basal transcription factors (TFIIX, X = A - H). First, the basal factor TFIID binds to the promoter. TFIID, a large complex of numerous proteins, contains TATA boxbinding protein (TBP) and so-called TAFs (TBP-associated factors). The polymerase is attached to this core with the help of TFIIB. Before transcription starts, additional TFs have to bind, including TFIIH, which has heli-case activity and separates the two strands of DNA during elongation. In all, some 35 differ-... 

TBP I 38 sequence specific binding to TATA box, recruitment of TFIIB... 

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. 

TFllF is found in a pre-formed complex with RNA polymerase II and suppresses the non-specific binding of RNA polymerase to DNA. TFIIF supports the association of RNA polymerase with the promoter boimd complex of TFIIA, TFIIB and TFIID. 

General transcription initiation factors TFIIB, TFIIE, TFIIF and TFIIH have been identified as components of the RNA polymerase 11 holoenzyme of yeast. Various forms of the yeast holoenzyme contain further proteins, known as mediators or SRB proteins (SRB, suppressor of RNA polymerase B). The mediators fimction as coactivators (see 1.4.3.2). The holoenzyme is difficult to define structurally because the proteins accessory to the core enzyme (see table 1) may not be permanently associated with RNA polymerase II. 

An example of a negative cofactor is the NC2 complex, which can repress the basal transcription level. The NC2 complex consists of two subimits, both displaying homology to the histone proteins. The repressive fimction of NC2 is due to its competition with TFIIB and TFIIA for the promoter binding site, thus blocking formation of the pre-initiation complex. 

Direct inhibition of the formation of a pre-initiation complex complexation of basal transcription factors, such as TFIID or TFIIB, or competition with TFIIB for binding to the promoter. An example for this type of repression is the negative cofactor NC2 (see 1.4.3.2). Transcription repression can also result from phosphorylation of the basal transcription factors. By this token, the repression of transcription observed during mitosis is attributed to the hyperphosphorylation of TBP and TAFs. 

Roberts, S.G.E. and Green, M.R. Activator-indnced conformational change in general transcription factor TFIIB (1994) Nature 371, 717-720... 

TFIIF 2 30,000, 74,000 Binds tightly to Pol II binds to TFIIB and prevents... 

TATA-Binding Protein The first component to bind in the assembly of a preinitiation complex at the TATA box of a typical Pol II promoter is the TATA-binding protein (TBP). The complete complex includes the basal (or general) transcription factors TFIIB, TFIIE, TFIIF, TFIIH Pol II and perhaps TFIIA (not all of the factors are shown in Fig. 28-27). This minimal preinitiation complex, however, is often insufficient for the initiation of transcription and generally does not form at all if the promoter is obscured within chromatin. Positive regulation leading to transcription is imposed by the transactivators and coactivators. 

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