Geodesic
Mechanisms regulating \emph{Escherichia coli dps} gene expression under stress: reconstruction on kinetic data
Matematičeskaâ biologiâ i bioinformatika, Tome 10 (2015) no. 1, pp. 1-14.

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Mechanisms governing the expression of the dps gene with the presence of cadmium ions have been reconstructed from the dynamics of the fluorescence of a genosensor construct with the dps promoter of Escherichia coli and the gfp reporter gene. Mathematical modeling and bioinformational analysis have been invoked. Estimation of the consistence of various hypotheses on genetic mechanisms governing dps expression shows that the regulation of the activity of the gene in response to cadmium is most probably regulated by interaction of three transcription factors. Two of them are activators of the gene, and the third is a repressor. They differ in cadmium sensitivity. According to the model, noncompetitive relationships among the transcription factors are the most likely. Analysis of the regulatory dps region indicates that, with regard to the ability of cadmium to induce oxidative stress, binding sites for transcription factors OxyR, H-NS, and Rob (or IscR) meets these conditions. Of them, OxyR and Rob (or IscR) can be the expression activators, and H-MS, the repressor. Overlapping candidate binding sites for Rob and IscR have been detected in the dps promoter by the SITECON method and tested in gel shift experiments with recombinant E. coli Rob and IscR proteins. 
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     title = {Mechanisms regulating {\emph{Escherichia} coli dps} gene expression under stress: reconstruction on kinetic data},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
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T. M. Khlebodarova; T. Yu. Stepanova; D. Yu. Oshchepkov; N. V. Tikunova; I. V. Babkin; V. A. Likhoshvai. Mechanisms regulating \emph{Escherichia coli dps} gene expression under stress: reconstruction on kinetic data. Matematičeskaâ biologiâ i bioinformatika, Tome 10 (2015) no. 1, pp. 1-14. http://geodesic.mathdoc.fr/item/MBB_2015_10_1_a4/

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