Nitrogen regulatory protein C-controlled genes of Escherichia coli: Scavenging as a defense against nitrogen limitation

Nitrogen regulatory protein C (NtrC) of enteric bacteria activates transcri ption of genes/operons whose products minimize the slowing of growth under nitrogen-limiting conditions. To reveal slowing of growth under nitrogen-li miting conditions. To reveal the NtrC regulon of Escherichia coli we compar ed mRNA levels in a mutant strain that overexpresses NtrC-activated genes [ glnL(Up)] to those in a strain with an ntrC (glnG) null allele by using DNA microarrays. Both strains could be grown under conditions of nitrogen exce ss. Thus, we could avoid differences in gene expression caused by slow grow th or nitrogen limitation per se. Rearranging the spot images from microarr ays in genome order allowed us to detect all of the operons known to be und er NtrC control and facilitated detection of a number of new ones. Many of these operons encode transport systems for nitrogen-containing compounds, i ncluding compounds recycled during cell-wall synthesis, and hence scavengin g appears to be a primary response to nitrogen limitation. In all, approxim ate to2% of the E. coli genome appears to be under NtrC control, although t ranscription of some operons depends on the nitrogen assimilation control p rotein, which serves as an adapter between NtrC and sigma (70)-dependent pr omoters.