Characterization of the YdeO regulon in Escherichia coli

• Published in: PloS one 2014-11, Vol.9 (11), p.e111962-e111962
• Main Authors: Yamanaka, Yuki, Oshima, Taku, Ishihama, Akira, Yamamoto, Kaneyoshi
• Format: Article
• Language: English
• Subjects: Acid resistance; Anaerobic conditions; Anaerobic respiration; Anaerobiosis; Bile salts; Binding Sites; Biology and life sciences; Chemical properties; Chromosomes; Deoxyribonuclease; Deoxyribonucleic acid; DNA; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - physiology; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Footprinting; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genomes; Genomics; Glutamate; Glutamate decarboxylase; Glutamic Acid - metabolism; Glycerol; Intestine; Kinases; Na+/H+-exchanging ATPase; Operon; Operons; Plasmids; Proteins; Research and Analysis Methods; Salts; Signal transduction; Sodium; Stomach; Stress, Physiological; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0111962

Enterobacteria are able to survive under stressful conditions within animals, such as acidic conditions in the stomach, bile salts during transfer to the intestine and anaerobic conditions within the intestine. The glutamate-dependent (GAD) system plays a major role in acid resistance in Escherichia coli, and expression of the GAD system is controlled by the regulatory cascade consisting of EvgAS > YdeO > GadE. To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites. All of the seven operons identified by ChIP-chip as being potentially regulated by YdeO were confirmed as being under the direct control of YdeO using RT-qPCR, EMSA, DNaseI-footprinting and reporter assays. Within this YdeO regulon, we identified four stress-response transcription factors, DctR, NhaR, GadE, and GadW and enzymes for anaerobic respiration. Both GadE and GadW are involved in regulation of the GAD system and NhaR is an activator for the sodium/proton antiporter gene. In conjunction with co-transcribed Slp, DctR is involved in protection against metabolic endoproducts under acidic conditions. Taken all together, we suggest that YdeO is a key regulator of E. coli survival in both acidic and anaerobic conditions.