Transcription promoter complex

TBP binds to the TATA box in the minor groove of DNA (most transcription factors bind in the major groove) and causes an approximately 100-degree bend or kink of the DNA helix. This bending is thought to facilitate the interaction of TBP-associated factors with other components of the transcription initiation complex and possibly with factors bound to upstream elements. Although defined as a component of class II gene promoters, TBP, by virtue of its association with... 

The mechanism by which transcription factors increase (or decrease) the rate of transcription is unclear. It is likely that, bound to the enhancer or promoter DNA sequences, they interact with other proteins to stimulate on inhibit formation of the transcription-initiator complex. 

Once integrated into the host chromosome, the assembly of new viral particles necessitates the prodnction of viral RNA transcripts and proteins. Initiation of viral transcription is also an RNA independent process where host transcription promoters and enhancer elements such as NF-kB bind to the 5 -LTR. The host transcriptional complex is then recrnited and transcription commences.Once transcription has been initiated, RNA and RNA-RNA interactions play a critical role in mediating the production of viral transcripts. The multiprotein transcription complex has a recognition factor for nonhost DNA and quickly releases from viral DNA, creating short, abortive transcripts. Processing and nuclear export of these transcripts leads to the translation of the HIV Tat protein, a small early-phase viral protein (Figure 10.4) that plays a key role in the ultimate formation of fnll-length viral RNA transcripts. 

The complex that RNA polymerase forms at the promoter site just prior to initiation. Some bacterial promoters require high NTP concentrations to initiate efficient transcription, because this represents a status report on the stores of ATP, UTP, GTP, and CTP needed for RNA synthesis. Nature has evolved a kinetic control device high initiating ATP and GTP concentrations must be present to stabilize an otherwise short-lived polymerase-promoter complex. The reader may also recall that bacterial translation is also tightly controlled, and amino acid starvation leads to ppGpp synthesis, the so-called stringent-response agent that also potently inhibits RNA polymerase. Such kinetic control ensures that NTP and amino acid concentrations are adequate before transcription and translation occur. 

Activation of the biosynthetic genes is dependent on direct interaction between the MYB and bHLH TFs within the transcriptional activation complex. The complex binds DNA through discrete cA-elements in the target gene promoters, one that is recognized specifically by the MYB member and one (the ARE) that is recognized by an as yet unidentified protein. The bHLH member functions in part through the ARE, and may be the protein that binds directly to it, or alternatively, interacts with a different protein that binds to it. ... 

Transcription initiation in procaryotes is controlled via promoters and regulatory DNA sequences located near the promoter. The role of the promoter is to provide a defined association site for the RNA polymerase and to correctly orient it. The binding of the RNA polymerase to its promoter is controlled by the sigma factor, a component of the RNA polymerase holoenzyme. The sigma factor selects which genes are to be transcribed by specifically recognizing the promoter sequence and structure and by allowing the RNA polymerase to form a transcription-competent complex at the transcription start site. 

In contrast to the procaryotes, where the o -holoenzyme of the RNA polymerase can initiate transcription without the aid of accessory factors, the eucaryotic RNA polymerase requires the help of numerous proteins to begin transcription. These proteins are termed basal or general initiation factors of transcription. Together with RNA polymerase II, they participate in the basal transcription apparatus. The various components must associate in a defined order for the formation of a transcription-competent complex, from which a low level of transcription is possible. An increase in the basal transcriptional level requires the effect of specific transcriptional activators, which bind cognate DNA sequences at a variable distance from the promoter. The transcriptional activators themselves require the aid of further protein factors, known as coactivators (see 1.4.3.2), in order to attain full stimulatory activity. 

Fig. 1.40. Model of repression and activation of transcription. The figure illustrates various mechanisms of repression of transcription, a) genes are in a generally repressed states in inactive chromatin. In a first phase of activation the chromatin is restrnctured. b) The promoter is now accessible for the binding of the basal transcription factors and for RNA polymerase II. c) An initiation complex is formed that contains the central components of the transcription apparatns, bnt which enables transcription only at a low rate, d) the binding of repressors to the transcription initiation complex can prevent fnrther activation of transcription at this step, e) the binding of transcription activators to their DNA elements leads to activation of transcription, f) an active repression is affected by proteins that bind seqnence specifically to DNA elements and in their DNA-bound form inhibit the transcritption preventing interactions with the transcription apparatus.

Structure of chromatin which promotes transcription. A large protein complex takes part in this remodeling. Some of the proteins in the complex, like the CBP/p300 protein (see also 1.4.6), possess histone acetylase activity. The activated, DNA-boimd receptor possibly recruits a histone acetylase to the chromatin. It can thus create the conditions necessary for the formation of a transcription initiation complex by this histone modification. 

DNA bending can cause an enhancer element that is far from the promoter in the linear DNA molecule, to interact with the transcription-initiation complex. 

A satisfactory mathematical model for initiation of transcription supposes that the polymerase and DNA bind reversibly to form a complex with formation constant Kf. This initial specific polymerase-promoter complex is referred to as a closed complex because it is thought that the bases in the DNA chain are all still paired. It is postulated that in a rate-determining step the closed complex is converted into an open complex, which is ready to initiate mRNA synthesis (Eq. 28-1).26 67 In the open complex the hydrogen bonds... 

The rate of initiation of transcription can be regulated in several ways, most of which influence the rate of formation of the RNA polymerase-DNA promoter complex. The primary sequence of nucleotides in the promoter region is the first factor to be considered. The closer this sequence is to the consensus sequence, the greater the affinity of the polymerase for the promoter (fig. 30.1). 

Schematic diagram of the repressor control of trp operon expression. The trp promoter (P) and trp operator (O) regions overlap. The trp aporepressor is encoded by a distantly located trpR gene. L-Tryptophan binding converts the aporepressor to the repressor that binds at the operator locus. This complex prevents the formation of the polymerase-promoter complex and transcription of the operon that begins in the leader region (trpL). Only a fraction of the transcripts extends beyond the attenuator locus in the leader region. The regulation of this fraction is discussed in the text.

Those protein-coding genes that have an initiator element instead of a TATA box (see above) appear to need another protein(s) that binds to the initiator element and facilitates the binding of TBP. The other transcription factors then bind to form the transcription initiation complex in a similar manner to that described above for genes possessing a TATA box promoter. 

Typically each protein-coding gene in a eukaryotic cell has several control elements in its promoter (Fig. 1) and hence is under the control of several transcription factors which interact with each other and with the transcription initiation complex by protein protein interaction to determine the rate of transcription of that gene. 

The rRNA promoter consists of a core element which straddles the transcriptional start site (designated as position +1) from residues -31 to +6 plus an upstream control element (UCE) about 50-80 bp in size and located about 100 bp upstream from the start site (i.e. at position -100 Fig. 4b). A transcription factor called upstream binding factor (UBF) binds both to the UCE as well as to a region next to and overlapping with the core element. Interestingly, TATA box binding protein (TBP see Topic G6), also binds to the rRNA promoter (in fact, TBP is required for initiation by all three eukaryotic RNA polymerases). The UBF and TBP transcription factors interact with each other and with RNA Pol I to form a transcription initiation complex. The RNA Pol I then transcribes... 

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