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PLoS One. 2014 Nov 6;9(11):e111962. doi: 10.1371/journal.pone.0111962. eCollection 2014.

Characterization of the YdeO regulon in Escherichia coli.

Author information

1
Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan.
2
Graduate School of Information Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
3
Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan; Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan.

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 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.

PMID:
25375160
PMCID:
PMC4222967
DOI:
10.1371/journal.pone.0111962
[Indexed for MEDLINE]
Free PMC Article

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