Overview of Transcription Initiation in Procaryotes

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- 

The RNA polymerase of E. coli possesses with its subimit construction (a2PP o) a simple structure in comparison to eucaryotic RNA polymerases. The sigma factor is only required for the recognition of the promoter and the subsequent formation of a tight complex. After the incorporation of the first 8-10 nucleotides into the transcript, the sigma factor dissociates from the holoenzyme, and the remaining core enzyme carries out the rest of the elongation. 

There are several sigma factors in E. coli (o , o , which can associate with 

In a first approximation, the formation of a transcription-competent complex can be described according to a two-step mechanism (Fig. 1.17). The initial binding of the RNA polymerase to the promotor leads to the formation of a closed complex in which the RNA polymerase is only weaWy bound. Isomerization of the closed complex transforms it intoa transcription-competent open state. In the open complex, the RNA polymerase is tightly bound, and the DNA is partially unwound at the transcription start site. 

Key elements of r70-dependent promotors are the TATA box, with the consensus sequence TATAAT 10 bp upstream from the transcription initiation site (pos. -10), and the sequence TTGACA at the position -35 (Fig. 1.18). Both sequences are necessary for the recognition of the promotor by a70. Structural analysis of the Thermus aquaticus RNA polymerase holoenzyme bound to DNA shows that all sequence-specific contacts with the core promotor are mediated by the sigma subunit (Murakami et al. 2002). This archaeal RNA polymerase has a subunit structure (a ji/i oxr) similar to that of the eubacterial enzyme. The intervening sequences, as well as other upstream sequences, can also influence the efficiency of transcription initiation. It is not possible to define consensus sequences at these positions. An optimal r70-dependent promotor can be defined as a sequence with the - 35 hexamer as well as the -10 hexamer 17 bp away. The latter lies 7 bp upstream from the transcription initiation site. 

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