The hierarchic network of metal-response transcription factors in <i>Escherichia coli</i>

Yamamoto, Kaneyoshi

doi:10.1080/09168451.2014.915731

Cited by 11 publications

(13 citation statements)

References 124 publications

(127 reference statements)

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“…E. coli responds to temporary low pH using the glutamate-dependent acid resistant system, which involves two complex regulatory systems: EvgAS > YdeO > GadE; and Crp> RpoS > GadX > GadW [9], [12]. In this study, we showed that YdeO directly regulates the expression of three transcription factor genes, nhaR , gadE, and gadW (see Fig.…”

Section: Discussionmentioning

confidence: 63%

“…Knowledge about the regulatory functions of YdeO is limited except that it is known that YdeO activates transcription of the gad system components, gadE , gadA and gadBC [7], [8], [9]. The expression of ydeO is activated by the two-component system EvgSA [9], [10], [11], forming a regulatory cascade, EvgA > YdeO > GadE [9], [12]. In this study, we performed a comprehensive interrogation of YdeO-binding sites in vivo on the E. coli genome using ChIP-chip analysis, and identified a set of YdeO-regulated genes, including four stress-response transcription factors, DctR, NhaR, GadE, and GadW, and several genes involved in respiration.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of the YdeO Regulon in Escherichia coli

2014

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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.

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Section: Discussionmentioning

confidence: 63%

Section: Introductionmentioning

confidence: 99%

Characterization of the YdeO Regulon in Escherichia coli

2014

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“…In E. coli , the promoter selectivity of RNA polymerase is determined after interaction with seven species of the sigma subunit with the promoter recognition activity (Ishihama , ). The promoter selectivity of each holoenzyme is further modulated after interaction with a total of approximately 300 species of transcription factor (TF) (Ishihama , ; Yamamoto ), of which approximately 10% are organized into the two‐component system (TCS) (Mizuno ; Yamamoto et al . ).…”

Section: Introductionmentioning

confidence: 99%

Cross talk in promoter recognition between six NarL‐family response regulators of Escherichia coli two‐component system

Yoshida

Ishihama

2015

Genes to Cells

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Bacterial two‐component system (TCS) is composed of the sensor kinase (SK) and the response regulator (RR). After monitoring an environmental signal or condition, SK activates RR through phosphorylation, ultimately leading to the signal‐dependent regulation of genome transcription. In Escherichia coli, a total of more than 30 SK‐RR pairs exist, each forming a cognate signal transduction system. Cross talk of the signal transduction takes place at three stages: signal recognition by SK (stage 1); RR phosphorylation by SK (stage 2); and target recognition by RR (stage 3). Previously, we analyzed the stage 2 cross talk between the whole set of E. coli SK‐RR pairs and found that the cross talk takes place for certain combinations. As an initial attempt to identify the stage 3 cross talk at the step of target promoter recognition by RR, we analyzed in this study the cross‐recognition of target promoters by six NarL‐family RRs, EvgA, NarL, NarP, RcsB, UhpA, and UvrY. Results of both in vivo and in vitro studies indicated that the stage 3 cross talk takes place for limited combinations, in particular, including a multifactor‐regulated ydeP promoter.

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“…In bacteria, the selection of genes for expression is mainly determined at the transcription step, by controlling the distribution of the limited number of RNA polymerase (RNAP) molecules on the genome (Ishihama, 2000(Ishihama, , 2010Yamamoto, 2014). The promoter selectivity of RNAP is determined by association with one of seven species of the sigma subunit and a total of about 300 species of transcription factor (TF) (Ishihama, 2010(Ishihama, , 2012Keseler et al, 2013;Riley et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli

Nakano

Ishihama

2015

Microbiology

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Sulfur makes up 1 % of the dry mass of bacteria, and it is an abundant element (0.1 %) on earth. Sulfur in the environment is, however, mostly in oxidized forms and inaccessible to living organisms. At present, the entire assimilation pathway of external sulfur to sulfur-containing biomolecules and its regulation in Escherichia coli remain poorly understood, except for the metabolic pathway of cysteine synthesis, the first-step metabolite of sulfur assembly. During the search for regulation targets of uncharacterized transcription factors by Genomic SELEX screening, we found that the hitherto uncharacterized YdcN regulates a set of genes involved in the utilization of sulfur, including the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. Taking these findings together, we propose renaming YdcN as SutR (regulator of sulfur utilization).

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The hierarchic network of metal-response transcription factors in Escherichia coli

Abstract: To cite this article: Kaneyoshi Yamamoto (2014) The hierarchic network of metal-response transcription factors in Escherichiacoli, Bioscience, Biotechnology, and Biochemistry, 78:5,[737][738][739][740][741][742][743][744][745][746][747]

Cited by 11 publications

References 124 publications

Characterization of the YdeO Regulon in Escherichia coli

Characterization of the YdeO Regulon in Escherichia coli

Cross talk in promoter recognition between six NarL‐family response regulators of Escherichia coli two‐component system

Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli

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