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Title: Characterization of the YdeO regulon in Escherichia coli
Authors: Yamanaka Y. 
Oshima T.
Ishihama A.
Yamamoto K.
Keywords: antiporter
bacterial protein
transcription factor
transcription factor DctR
transcription factor GadE
transcription factor GadW
transcription factor NhaR
unclassified drug
Escherichia coli protein
glutamic acid
transcription factor
YdeO protein, E coli
anaerobic respiration
bacterial gene
bacterial genome
bacterial metabolism
binding site
cellular stress response
chromatin immunoprecipitation
DNA footprinting
Escherichia coli
gel mobility shift assay
gene function
gene identification
genetic regulation
in vivo study
luciferase assay
metabolic regulation
quantitative analysis
reverse transcription polymerase chain reaction
YdeO gene
anaerobic growth
Escherichia coli
gene expression profiling
gene expression regulation
physiological stress
Escherichia coli
Binding Sites
Escherichia coli
Escherichia coli Proteins
Gene Expression Profiling
Gene Expression Regulation, Bacterial
Glutamic Acid
Stress, Physiological
Transcription Factors
Issue Date: 2014
Citation: Yamanaka Y., Oshima T., Ishihama A., Yamamoto K. (2014). Characterization of the YdeO regulon in Escherichia coli. PLoS ONE 9 (11) : e111962. ScholarBank@NUS Repository.
Abstract: 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 EvAS > 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. © 2014 Yamanaka et al.
Source Title: PLoS ONE
ISSN: 19326203
DOI: 10.1371/journal.pone.0111962
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