Promoter recognition specificity

When isolated from bacteria, prokaryotic RNA polymerase has two forms The core enzyme and the holoenzyme. The core enzyme is a tetramer whose composition is given as 0C2PP (two alpha subunits, one beta subunit, and one beta-prime subunit). Core RNA polymerase is capable of faithfully copying DNA into RNA but does not initiate at the correct site in a gene. That is, it does not recognize the promoter specifically. Correct promoter recognition is the function of the holoenzyme form of RNA polymerase. 

The tasks of transcriptional and translational signal recognition involve the prediction of promoters and sites that function in the initiation and termination of transcription and translation. Bacterial promoter sites, specifically the Escherichia coli RNA polymerase promoter site, are now very well characterized. The main problem is that the two conserved regions of the bacterial promoter, the -10 and -35 regions, are separated from each other by 15 to 21 bases, making the detection of the entire promoter as a single pattern difficult. Eukaryotic promoters are less well characterized than their bacterial equivalents. The major elements are the CCAAT box, GC box, TATA box and cap site. 

Promoter recognition by a specific pollutant followed by gene expression, enzyme synthesis and catalytic activity. 

The initiation reaction. A promoter not only locates the site of initiation but also determines the direction of transcription and, therefore, the strand of the DNA duplex that is to serve as the template. The requirement for two specific recognition sequences ensures this directionality. The RNA polymerase may bind randomly to DNA, then move rapidly along the double helix imtil it locates a strong binding site where it binds to the recognition sequences of the promoter through specific interactions in the major groove of the DNA helix (see Fig. 5-3). 

How does RNA polymerase know where to begin transcription In prokaryotic transcription, RNA polymerase is directed to the gene to be transcribed by the interactions between the polymerase s O-subunit and sequences of DNA near the start site called promoters. Gonsensus sequences have been established for prokaryotic promoters, and the key elements are sequences at —35 and —10, the latter called the Pribnow box. In eukaryotic transcription, RNA polymerase binds to promoters as well, but there is no O-subunit, although there is a specific subunit, RBP4, that is involved in promoter recognition. 

There are a large number of transcription factors. Some are called general transcription factors, and they are involved in transcription initiation. They aid in promoter recognition and binding. They have a specific order and location of binding. Other transcription factors bind to enhancers or response elements and increase the rate of transcription above basal levels. 

As described above, studies of deletion and point mutations suggest that an extensive set of sequences is important in promoter recognition. Each component in these sequences that influences the activity of a promoter in vivo must be recognized by one or more transcription factors. In addition to sequence recognition factors, other components might be required to interact with pol II to permit initiation. Obviously, modulation of activity of these factors could either enhance or suppress the rate of transcription. The specificity of such regulatory signals would depend on whether a factor was specific for only a subset of promoters. 

In prokaryotic RNA polymerases, the ct-factor is required for promoter recognition and binding. It is loosely bound to the core complex and released after the nascent RNA chain becomes 8-9 nucleotides long. The core polymerase with <7 -factor has a high affinity for nonspecific DNA. The <7-factor alters the conformation of theholoenzymeso that its affinity for nonspecific DNA is reduced and the specific binding affinity for the promoter is significantly enhanced. 

A sequence stretch 300 base pairs upstream of the transcriptional start site suffices for most of the transcriptional regulation of the IL-6 gene (Fig. 1). Within this sequence stretch several transcription factors find their specific recognition sites. In 5 to 3 direction, AP-1, CREB, C/EBP 3/NF-IL6, SP-1 and NF-kB can bind to the promoter followed by TATA and its TATA binding protein TBP. Most enhancer factors become active in response to one or several different stimuli and the active factors can trigger transcription individually or in concert. For example, AP-1 is active upon cellular stress, or upon stimuli that tell cells to proliferate CREB becomes also active if cells experience growth signals, but also upon elevation of intracellular levels of cyclic adenosine monophosphate (cAMP), which occurs upon stimulation if so called hormone-activated G protein-coupled receptors. 

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