Transcription, procaryotic

Eucaryotes have many more genes and a broader range of specific transcription factors than procaryotes and gene expression is regulated by using sets of these factors in a combinatorial way. Eucaryotes have found several different solutions to the problem of producing a three-dimensional scaffold that allows a protein to interact specifically with DNA. In the next chapter we shall discuss some of the solutions that have no counterpart in procaryotes. However, the procaryotic helix-turn-helix solution to this problem (see Chapter 8) is also exploited in eucaryotes, in homeodomain proteins and some other families of transcription factors. 

Bacteria, being procaryotic, do not show compartmentation of the biosynthetic processes. The genome of a bacterium relates directly to the cytoplasm of the cell. Transcription into mRNA can lead directly to translation, and the processes of transcription and translation are not carried out in separate organelles. Animal cells, being eucaryotic, show compartmentation of the transcription and translation processes. Transcription of the genome into mRNA occurs in the nucleus, whereas translation occurs in the cytoplasm. The messenger RNA in the eucaryote is usually modified by adding to it... 

A single tyrosine is in the C-terminal portion of the transcription factor 1 (TF1), a type II procaryotic DNA binding protein encoded by Bacillus subtilis phage SPOl. Time-resolved fluorescence decay measurements yielded... 

Using the unique characteristics of the procaryotic polymerases, a number of investigators have attempted to define what happens to the histones during transcription. In the mid 1980s two different laboratories did a set of important experiments. Lorch et al. [84] observed that during transcription with SP6 RNA polymerase of a DNA that contained an SP6 promoter, flanked by DNA sufficient... 

Procaryotes and eucaryotes differ decisively in the structure of the transcription start site and the complexity of the transcription appartus. For a better understanding we want to briefly summarize procaryotic transcription and then contrast it to eucaryotic transcription (review Eick and Heumarm, 1994). 

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. 

Fig. 1.27. Two-step mechanism of transcription initiation. The binding of a procaryotic RNA polymerase to its promoter can be subdivided into two steps. In the first step the RNA polymerase binds to the closed promoter with low affinity. The closed complex isomerizes in a second step to an open complex in which the promoter is partially unwound. Detailed consideration reveals that further steps can be distinguished. These are not shown here for simplicity reasons.

A detailed, structural based description of the mechanism of transcription stimulation in procaryotes is currently not possible since such data is not yet available. 

Fig. 1.29. Mechanism of promoter activation of (/ -dependent genes in procaryotes. The formation of an open, initiation-competent transcription complex for (/ -dependent genes requires the assistance of transcription activators, which bind to their cognate UAS element. Upon loop formation of the intervening DNA sequences, the transcription activator interacts with the (/ -con-taing RNA polymerase bound to the promoter. The activation is accompanied by ATP hydrolysis and leads to the formation of an open complex.

As in procaryotes, the elementary steps of initiation, elongation and termination can be distinguished in eucaryotic transcription. Aside from the specific RNA polymerases, transcription in eucaryotes requires the action of numerous other proteins which are collectively known as transcription factors. Transcription factors are required at the level of initiation, elongation, and termination and are accordingly known as initiation factors, elongation factors and termination factors of transcription. 

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. 

The general transcription initiation factors can be assigned the role fulfilled by a single protein in procaryotes-namely the o-factor. This role includes the correct positioning of the RNA polymerase on the promoter and the preparation for the incorporation of the first nucleotide. 

As in procaryotes, there are transcription activating proteins, the transcriptional activators, as well as proteins which inhibit transcription, the transcriptional repressors. Of the two classes, the activators are the most extensively studied and characterized. The mechanism of eucaryotic repressors has only been clarified in a few cases. 

The principle means by which the activity of sequence-specific DNA-binding proteins is controlled have aheady been presented in section 1.2. The importance of these mechanisms for regulation in eucaryotes will be discussed below. Altogether, the demands on eucaryotic organisms with regard to the regulation of transcription activity are much more complex than for procaryotes. This tenet holds for the structure of the transcription apparatus as well as for the mechanism of transcription regulation. 

In contrast to the procaryotes, where the er70-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 oftranscription. Together with RNA polymerase... 

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