Promoters recognition sequences

At low Trp concentration the Trp repressor is mainly in the unbound, inactive form. The free form of the Trp repressor binds with a ca. lO -fold lower affinity to the recognition sequence than the Trp-bound form. The promoter remains free under these conditions and transcription of the genes for Trp biosynthesis can occur. The shutting on and off of the Trp operon is based on the disparate DNA affinities of the free and Trp-boimd repressor. ... 

The recognition sequences of regulatory proteins may overlap not only the promotor site, but can also be found in the immediate vicinity of the a promoter. The sequence elements are relatively simple and often include only one binding site for regulatory proteins. 

The p53 protein controls the expression of the CDK inhibitor p21 and two copies of the p53 recognition sequence are found in its promoter region. Activation of p53 leads to increased formation of the p21 inhibitor, which brings about a halt in the cell cycle in G1 phase. The p53 protein has a negative control function according to this mechanism. Inactivation of p53 means loss of an important control element of the cell cycle. 

The fact that GBF-1 bound to the cab-E G-box-like sequence, but bound only weakly to the USF recognition sequence and the G-box-like elements of the A. majus chalcone synthase promoter, contrasted with results reported for the plant nuclear factor CG-1 (Staiger et al., 1989). This latter factor was shown to interact with both the USF recognition sequence and one of the G-box-like elements of the A. majus chalcone synthase promoter it did not interact with the cab-E motif. These cumulative DNA-binding studies indicate that GBF-1 and CG-1 have different DNA-binding properties. 

A couple of important points exist about the consensus. First, not all bases in the consensus are conserved to the same amount. The bases marked with bold type and underlined are more conserved than the others, and the -10 region is more conserved overall than is the -35 region. Secondly, the promoter sequence is asymmetrical that is, it reads differently in one direction than in the other. (Compare this to the recognition sequence for the restriction enzyme BamHI, GGATCC.) This asymmetry means that RNA polymerase gets directional information from the promoter in addition to information about the starting point for transcription. 

The desensitization motifs in the dopamine Di receptor, as an example, may be at least partly located in the proximal carboxyl tail of the receptor [137], It is likely that this region interacts with portions of the third intracellular loop in order to promote desensitization. These structures may also be involved in recycling and trafficking of inactivated receptors [162, 163], A portion of the proximal carboxyl tail of the dopamine Di receptor may contain some of the residues necessary, but not sufficient on their own, for GRK2 mediated desensitization. A motif consisting of a serine or threonine preceded by an acidic amino acid may define the GRK2 recognition sequence [163],... 

The recognition quality of the program was tested on 200 promoters, which were not included in the learning set. We provide the accuracy values for different levels of correctly predicted promoters in Table 3.8. The data demonstrate a poor quality of TATA— promoter recognition on long sequences and show that their recognition function can provide relatively... 

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