Transcription polymerase complexes

ACTIVATION OF TRANSCRIPTION by soluble hormones. The hormone is carried to its site of action by a carrier protein in the blood. The hormone crosses the membrane (by itself) and binds to a soluble receptor. A conformation change induced by hormone binding causes the receptor to expose its DNA binding site. This site binds to a specific sequence in the DNA upstream of genes that are to be activated for transcription. The transcription activation occurs through another domain of the protein that binds to components of the RNA polymerase complex. 

Enzyme-stabilized single-stranded DNA (known as the open complex) is the first intermediate formed in transcription initiation of RNA polymerases its formation is the rate-limiting step. Designing molecules which bind specifically to the open complex is a strategy for generating potent transcription inhibitors. The redox-stable complex of Cu(I) with 1,2-dimethyl- 1,10-phenanthroline is an example of such a strategy (405). The Cu(I) complex binds specifically to the single-stranded DNA of transcriptional open complexes and is an effective inhibitor of eukaryotic and prokaryotic transcription. 

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. 

A transcription-competent complex must be present at the initiation site, with partial melting of the DNA, for the RNA polymerase to be able to add ribonucleotides complementary to the DNA template. 

The formation of a transcription-competent complex can be described according to a two step mechanism (fig 1.27). The initial binding of the RNA polymerase to the pro-... 

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.

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... 

Figure 7.15. Functions of cold-shock proteins (Csp s) as RNA chaperones. The model shows how Csp s assist in coupling transcription to translation. Cold-shock proteins bind relatively weakly to nascent mRNA extending from the RNA polymerase complex (RNAP) and maintain the mRNA in a linear form that can be bound to ribosomes and translated into protein. Under nonstressful conditions, the weakly binding Csp s are present at adequate concentrations to perform this chaperoning function. However, during cold stress, the propensity for RNA to form secondary structures that block translation becomes greater. This necessitates that a higher level of Csp s be present in the cell, to ensure that chaperoning of mRNA is effective. (Figure modified after Graumann and Marahiel, 1998.)...

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