Promoter Strength

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The promoter site is a DNA sequence, where RNA polymerase (RNAP) binds to perform transcription. The strengh at which the promoter binds RNA polymerse determines how often a gene is transcribed and therefore, how many copies of mRNA exist. The strength with which the RNAP binds depends on two regions of the promoter that differ between procaryotes and eucaryotes.

Promotersites.png

The promoter sequences contain alterations of a sequence called consensus sequence. The consensus sequence posesses the highest affinity for the RNAP. Alterations of the consensus sequence lead to a decreased affinity for the RNAP. For example the consensus sequence

TTGACA
could be altered by replacing nucleotides at specific places

TTGACG
TAGACA
CTTACA
TTGACC
TTGAAA
TTGTCA

The procaryotic promoters include two consensus sequences. One 35 nucleotides upstream and another -10 letters upstream of the mRNA transcription start site (see picture above). The first letter read out by RNAP is denoted with the number one. In the procariotic gene of E. coli about 2000 promoters exist.

Similarly in eucaryotic promoters consensus sequences occur 75 and 25 nucleotides upstream of the mRNA transcription start site (see picture above).

The reason for the importance of this regions can be found in the sturcture of the RNA polymerase. The consensus sequences happen to bind the sigma-factor subunits $\sigma_4$ (TTGACA) and $\sigma_2$ (TATAAT) of the whole RNApolymerase complex also called holoenzyme. This amazing picture shows the structure of the promoter-RNAP complex, revealed by cristallographyic studies.

PromoterRNAPcomplex.png

Other important factors that influence RNAP binding and transcription initiation are UP elements, the operator sites that bind transcription factors. Sometimes promoters also contain TGn regions that bind the $\sigma_3$ region. For more details read the following article.



Further reading:

  • Douglas F. Browining and Sephen J. W. Busby - The regulation of bacterial transcription initiation (Nature Reviews 2004)