Figure 4.

Regulation of pykA, hexR and enzymes of the ED pathway in MR1 and overlay of the regulatory information with the experimental data. The figure indicates that enzymes of the ED pathway (SO2486_ SO2489) as well as pykA are significantly upregulated in the Crp(−) mutant, but hexR and the intergenic region between hexR and pykA are downregulated. The regulatory information provided in the first track of the browser (TractorDB) gives an explanation for the observed changes in the gene expressions. It indicates that the genes, hexR and pykA and the operon with the enzymes of the ED pathway have binding sites in their promoters predicted by TractorDB. Thus, both genes and the operon are likely regulated by Crp. In the wild-type strain of MR1, the ED pathway is not active because of upregulation of hexR by Crp during the transition from aerobic to anaerobic conditions. The Crp(−) mutant strain does not produce Crp; therefore, the transcriptional repressor HexR is absent in the mutant, and enzymes of the ED pathway, which were suppressed by HexR in the wild-type strain, are upregulated in the Crp(−) strain.