Transcription factor preinitiation complex

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. 

The promoter proximal elements are usually 100 to 200 base pairs long and relatively close to the site of initiation of transcription. Within each of these elements there are DNA sequences specifically recognized by several different transcription factors which either interact directly with the preinitiation complex or indirectly through other proteins. 

Figure 9.2 Schematic model for transcriptional activation. The TATA box-binding protein, which bends the DNA upon binding to the TATA box, binds to RNA polymerase and a number of associated proteins to form the preinitiation complex. This complex interacts with different specific transcription factors that bind to promoter proximal elements and enhancer elements.

The general transcription factor TFllD is believed to be the key link between specific transcription factors and the general preinitiation complex. However, the purification and molecular characterization of TFllD from higher eucaryotes have been hampered by its instability and heterogeneity. All preparations of TFllD contain the TATA box-binding protein in combination with a variety of different proteins called TBP-associated factors, TAFs. When the preinitiation complex has been assembled, strand separation of the DNA duplex occurs at the transcription start site, and RNA polymerase II is released from the promoter to initiate transcription. However, TFIID can remain bound to the core promoter and support rapid reinitiation of transcription by recruiting another molecule of RNA polymerase. 

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. 

DNA binding by TBP is strongly dependent on the presence of T-A base pairs in the TATA box. Bending allows remote sites on the DNA, with their bound cognate specific transcription factors, to come close together such that the proteins can interact to form the transcriptional preinitiation complex. 

Figure 37-7. Transcription elements and binding factors in the herpes simplex virus thymidine kinase ffW gene. DNA-dependent RNA polymerase II binds to the region of the TATA box (which is bound by transcription factor TEND) to form a multicomponent preinitiation complex capable of initiating transcription at a single nucleotide (+1).The frequency of this event is increased by the presence of upstream c/s-acting elements (the GC and CAAT boxes). These elements bind frans-acting transcription factors, in this example Spl and CTF (also called C/EBP, NF1, NFY). These cis elements can function independently of orientation (arrows).

RNA polymerases interact with unique cw-active regions of genes, termed promoters, in order to form preinitiation complexes (PICs) capable of initiation. In eukaryotes the process of PIC formation is facilitated by multiple general transcription factors (GTFs), TFIIA, B, D, E, F, and H. 

Through these examples, I wanted to illustrate the fact that the expression molecular description can have at least three different meanings. These three levels of representation are not independent. For instance, the atoms and bonds that make up the jaws of RNA polymerase II can be described, as well as RNA polymerase II can be integrated, with transcription factors and DNA, in the general picture of the preinitiation transcription complex. However, in order to answer a specific question, one particular level of description is always more significant, better adapted than others, with a greater explanatory value. 

These may enhance or obstruct the assembly of the preinitiation complex of RNA polymerase and relevant transcription factors [9]. Physiological isoform expression varies with cell type and maturity. In rat heart, the predominant form shifts from neonatal a3 to adult a2. 

Kosa, P. E, Ghosh, G., DeDecker, B. S. and Sigler, P. B. (1997). The 2.1-A crystal structure of an archaeal preinitiation complex TATA-box-binding protein/transcription factor (II)B core/TATA-box. Proc. Nat. Acad. Sci. USA 94, 6042-6047. 

Regulation of RNA Polymerase II Activity Regulation of transcription at Pol II promoters is quite elaborate. It involves the interaction of a wide variety of other proteins with the preinitiation complex. Some of these regulatory proteins interact with transcription factors, others with Pol II itself. Many interact through TFIID, a complex of about 12 proteins, including TBP and certain... 

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. 

The basal transcription complex described in Chapter 29 initiates transcription at a low frequency. Recall that several general transcription factors (the preinitiation complex) join with KNA polymerase II to form the transcription complex. Additional transcription factors must bind to other sites for a gene to achieve a high rate of mRNA synthesis. In contrast with the regulators of prokaryotic transcription, few eukaryotic transcription factors have any effect on transcription on their own. Instead, each factor recruits other proteins to build up large complexes that interact with the... 

Detailed biochemical studies revealed how the Pol II preinitiation complex, comprising a Pol II molecule and general transcription factors bound to a promoter region of DNA, is assembled. In these studies DNase I footprinting and electrophoretic mobility shift assays were used to determine the order in which Pol II and general transcription factors bound to TATA-box promoters. Because the complete, multisubunit TFIID is difficult to purify, researchers used only the isolated TBP component of this general transcription factor in these experiments. Pol II can initiate transcription in vitro in the absence of the other TFIID subunits. 

Eukaryotic transcription activators and repressors exert their effects largely by binding to multisubunit co-activators or co-repressors that influence assembly of Pol II transcription preinitiation complexes either by modulating chromatin structure (indirect effect) or by interacting with Pol II and general transcription factors (direct effect). 

The first step in translation is the assembly of the initiation complex. In bacteria, this is done in a three-step process that involves the initiation factors IF-1, IF-2, and IF-3, the 30S and 50S ribosomal subunits, and the hydrolysis of GTP. As shown in Figure 26.10, the first step is the formation of a preinitiation complex consisting of IF-1, IF-3, and the 30S ribosomal subunit. This preinitiation complex binds with high affinity to a translational start site on the mRNA transcript which is close to the 50 end and includes the first codon of the open-reading frame. This codon is called the initiation codon and it is usually AUG, which specifies the amino-acid methionine in the genetic code (Fig. 26.6). 

The zinc-ribbon motif is found in a diverse group of proteins with limited sequence similarity and includes proteins involved in transcription (e.g. Transcription Factor IIB ) and translation (the G domain of the y-subunit of the heterotrimeric translation initiation factor elFZ). In TFIIB, the surface of the ribbon domain is conserved and is essential for the recruitment of RNA polymerase II (Pol II) to the Preinitiation Complex (PIC). The GCM (glia cell missing) transcriptional regulators make novel use of a ribbon-like zinc complex to bind to DNA in an unusual way. Here, one edge of a live-stranded antiparallel /3-sheet inserts into the major groove. The middle three antiparallel /3-strands of the live-stranded... 

Transcription initiation begins by the formation of a preinitiation complex, and most of the control of transcription occurs at this step. This complex normally contains RNA polymerase II and six general transcription factors (GTFs)—TTHA, TFIIB, TTIID, TFIIE, TFIIF, and TFIIH. 

The general transcription factors are required for all promoters. Much work is still going on to determine the structure and function of each of the parts of the preinitiation complex. Each GTF has a specific function, and each is added to the complex in a defined order. Table 11.3 is a summary of the components of the preinitiation complex. 

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