FNR Promotor

To let the bacteria sense low oxygen concentrations, a FNR promotor was used in this research. The promotor that was chosen is not a default one, since it is a so called tandem promotor. That is, it contains two FNR binding sites. The kinetics of this promotor are therefore different than the promotor previously described in the Decoy Sites model. Here the necessary adaptations of the Decoy Model to account for this special promotor will be described.

Promotor Design

The promotor that was used in this research was taken from research by Barnard et al.BusbyFNRAnne M.L. Barnard, Jeffrey Green, and Stephen J.W. Busby, Transcription regulation by tandem-bound FNR at Escherichia coli promoters. Journal of bacteriology 185.20, 5993-6004 (2003). The research showed the promotor (FF(-91.5)FF(-41.5)) expresses an 1.8 times higher activity than the most commonly used single binding site FNR promotor (FF(-41.5)). From hereon the tandem FF(-91.5)FF(-41.5) promotor will be referred to as the FNR-tandem promotor and default FF(-41.5) will be called FNR-single promotor. The global design of the FNR-single and FNR-tandem promotor are displayed below:

    -130      -120      -110      -100       -90       -80       -70       -60       -50       -40       -30       -20       -10        0
      |         |         |         |         |         |         |         |         |         |         |         |         |         |
(a)                                                   **********************************TTGAT****ATCAA**********************CATAAT*******
(b) **********************************TTGAT****ATCAA************************************TTGAT****ATCAA**********************CATAAT*******
(c)                                   ______________                                    ______________

The relative activity of the FNR-tandem promotor suggests that there is minimal hindrance between the two bound FNR proteins, but there also is no significant synergy.

References