Analysis of gene expression in Escherichia coli in response to oxygen, nitrate and global regulators of transcription

Gene regulation in Escherichia coli in response to certain environmental signals involves hierarchical patterns of control. E. coli contains two known global regulators of transcription in response to oxygen level, ArcA and Fnr, that regulate genes involved in energy generation and other cellular processes. In the presence of nitrate, E. coli regulates genes involved in anaerobic respiration and fermentation, among others. Many genes respond differentially to the presence of multiple stimuli such as nitrate and oxygen. HNS regulates transcription of a large number of genes, many of which are also modulated by additional transcription factors.; Microarray studies have been performed to determine the response of the E. coli genome to nitrate, oxygen, ArcA, and Fnr. A comparison was made of microarray results using cells grown in batch culture and cells grown using a chemostat. Theses studies have implications for microarray experiments done in other systems. It was found that cells grown in a chemostat were reduced in the rate of false positives. Results from microarray experiments led to the characterization of the yjiH operon. We propose that this operon functions in scavenging of aspartate from peptides, for conversion to fumarate for use as a respiratory substrate.; The global regulator ArcA is part of a two-component sensor/transmitter and response regulator system. It becomes activated by phosphorylation at its N-terminal domain under anaerobic conditions, then transduces a signal to its C-terminal region. This conformational change results in DNA binding and regulation of transcription of dozens of operons. ArcA was studied to understand further the mechanism by which it regulates transcription. It was found that direct upregulation of many genes in E. coli by ArcA results from anti-repression of HNS. In a separate study, we found that mutations in ArcA that might be expected to prevent regulation, actually in some cases improved it.