Computational prediction of DtxR regulon-A Dissection of physiological process controlled by DtxR in Corynebacterium species

We developed a user friendly software tool to identify the potential binding sites of any regulatory protein based on Shannon relative entropy method. Known DtxR binding sites of Corynebacterium diphtheriae (C. diphtheriae) were used to generate a position specific reference profile for DtxR which was used to identify the potential DNA binding sites within the upstream sequences of Corynebacterium glutamicum (C. glutamicum) genes. In addition, DtxR regulated operons were also identified taking into account the predicted DtxR regulatory sites and Rhoindependent transcription termination sites. The analysis predicted the binding sites upstream to a number of genes/operons which code for proteins involved in hemolysis and haemin transport. The analysis also predicts the binding sites upstream to genes that are involved in iron storage and oxidative stress defense including ferritin, starvation inducible DNA binding protein (Dps) and a homologue of endonuclease VIII (Nei). Both Dps and Nei homologue could be involved in controlling ferrous iron induced DNA damage. Where b refers to each of the possible base (A, T, G, C), fb,i is observed frequency of each base at the position i and qi is frequency of base b in the genome sequence. The contribution of each base to the positional Shannon relative entropy was calculated by multiplying each base frequency with positional Shannon relative entropy.