Effect of enzyme IIANtr on gene expression in Escherichia coli

Enzyme IIANtr (encoded by ptsN gene) is a component of the nitrogen phosphotransferase system (PTS). It has previously been shown that the dephosphorylated form of EIIANtr is required for the derepression of ilvBN encoding acetohydroxy acid synthase I (AHAS I) catalyzing the first step common to biosynthesis of branched-chain amino acids. Here we examine the effect of deletion of ptsN gene on global gene expression by microarray analysis. Most of the genes down-regulated in a ptsN mutant are controlled by sigma 70, while all the up-regulated genes are controlled by sigma S. As intracellular levels of sigma factors in the ptsN mutant were similar to those of the wild-type strain, this implied that the balance of sigma activities is modified by ptsN deletion. The E. coli K12 strain MG1655 and its isogenic ptsN mutant were used in all experiments. Overnight bacterial cultures were incubated in M9 minimal medium containing 0.5% glucose as carbon source. Cells from duplicate experiments were harvested in exponential growth phase when cultures reached an A600 of 0.4. RNA was extracted from each sample using a QIAGEN RNA extraction kit according to the manufacturer's instruction.