Limits...
Characterization of the YdeO regulon in Escherichia coli.

Yamanaka Y, Oshima T, Ishihama A, Yamamoto K - PLoS ONE (2014)

Bottom Line: To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Bioscience, 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.

Show MeSH

Related in: MedlinePlus

The characterization and location of YdeO-box on target promoters.We examined the conservation of the inverted repeat across seven YdeO-binding regions detected in vivo by ChIP-chip analysis, 131-bp on nhaR promoter, 216-bp on hyaA promoter, 139-bp on appC promoter, 217-bp on yiiS promoter, 181-bp on gadW promoter, 241-bp on gadE promoter, and 145-bp on slp promoter. [A] The panel shows the DNA sequence, containing the identified hexa-mer repeat (YdeO-box). The YdeO-box identified in all of promoters located on seven binding sites of YdeO. The number indicates the distance from each transcription start site (RegulonDB [http://regulondb.ccg.unam.mx]). [B] Organization of the promoters controlled by YdeO is shown. The locations of a hexamer of YdeO-binding sites (triangle) at relative positions from the transcription initiation site (solid arrow) are shown for the promoters. The filled bars represent open reading frames of the target genes.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4222967&req=5

pone-0111962-g004: The characterization and location of YdeO-box on target promoters.We examined the conservation of the inverted repeat across seven YdeO-binding regions detected in vivo by ChIP-chip analysis, 131-bp on nhaR promoter, 216-bp on hyaA promoter, 139-bp on appC promoter, 217-bp on yiiS promoter, 181-bp on gadW promoter, 241-bp on gadE promoter, and 145-bp on slp promoter. [A] The panel shows the DNA sequence, containing the identified hexa-mer repeat (YdeO-box). The YdeO-box identified in all of promoters located on seven binding sites of YdeO. The number indicates the distance from each transcription start site (RegulonDB [http://regulondb.ccg.unam.mx]). [B] Organization of the promoters controlled by YdeO is shown. The locations of a hexamer of YdeO-binding sites (triangle) at relative positions from the transcription initiation site (solid arrow) are shown for the promoters. The filled bars represent open reading frames of the target genes.

Mentions: To identify the YdeO-binding sequence, we performed DNase I footprinting of the gadW promoter with increasing concentrations of YdeO. At low protein levels, YdeO protected the region from –53 to +8 of the gadW promoter (Fig. 2B, lanes 2–4). In the presence of 15-fold molar excess of YdeO, the protected region by YdeO expanded from –53 to +84 of the gadW promoter possibly due to protein-protein interaction (Fig. 2B, lane 5) in agreement with the smeared band formation observed by EMSA (see above). Within the core YdeO-binding region, the inverted repeat of hexa-nucleotides, 5′-ATTTCA-3′, was identified (see Figs. 2C and 4A).


Characterization of the YdeO regulon in Escherichia coli.

Yamanaka Y, Oshima T, Ishihama A, Yamamoto K - PLoS ONE (2014)

The characterization and location of YdeO-box on target promoters.We examined the conservation of the inverted repeat across seven YdeO-binding regions detected in vivo by ChIP-chip analysis, 131-bp on nhaR promoter, 216-bp on hyaA promoter, 139-bp on appC promoter, 217-bp on yiiS promoter, 181-bp on gadW promoter, 241-bp on gadE promoter, and 145-bp on slp promoter. [A] The panel shows the DNA sequence, containing the identified hexa-mer repeat (YdeO-box). The YdeO-box identified in all of promoters located on seven binding sites of YdeO. The number indicates the distance from each transcription start site (RegulonDB [http://regulondb.ccg.unam.mx]). [B] Organization of the promoters controlled by YdeO is shown. The locations of a hexamer of YdeO-binding sites (triangle) at relative positions from the transcription initiation site (solid arrow) are shown for the promoters. The filled bars represent open reading frames of the target genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222967&req=5

pone-0111962-g004: The characterization and location of YdeO-box on target promoters.We examined the conservation of the inverted repeat across seven YdeO-binding regions detected in vivo by ChIP-chip analysis, 131-bp on nhaR promoter, 216-bp on hyaA promoter, 139-bp on appC promoter, 217-bp on yiiS promoter, 181-bp on gadW promoter, 241-bp on gadE promoter, and 145-bp on slp promoter. [A] The panel shows the DNA sequence, containing the identified hexa-mer repeat (YdeO-box). The YdeO-box identified in all of promoters located on seven binding sites of YdeO. The number indicates the distance from each transcription start site (RegulonDB [http://regulondb.ccg.unam.mx]). [B] Organization of the promoters controlled by YdeO is shown. The locations of a hexamer of YdeO-binding sites (triangle) at relative positions from the transcription initiation site (solid arrow) are shown for the promoters. The filled bars represent open reading frames of the target genes.
Mentions: To identify the YdeO-binding sequence, we performed DNase I footprinting of the gadW promoter with increasing concentrations of YdeO. At low protein levels, YdeO protected the region from –53 to +8 of the gadW promoter (Fig. 2B, lanes 2–4). In the presence of 15-fold molar excess of YdeO, the protected region by YdeO expanded from –53 to +84 of the gadW promoter possibly due to protein-protein interaction (Fig. 2B, lane 5) in agreement with the smeared band formation observed by EMSA (see above). Within the core YdeO-binding region, the inverted repeat of hexa-nucleotides, 5′-ATTTCA-3′, was identified (see Figs. 2C and 4A).

Bottom Line: To understand the YdeO regulon in vivo, we used ChIP-chip to interrogate the E. coli genome for candidate YdeO binding sites.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Bioscience, 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.

Show MeSH
Related in: MedlinePlus