A Common Regulator for the Operons Encoding the Enzymes Involved in
            <scp>d</scp>
            -Galactarate,
            <scp>d</scp>
            -Glucarate, and
            <scp>d</scp>
            -Glycerate Utilization in
            <i>Escherichia coli</i>

Monterrubio, Rafael; Baldomà, Laura; Obradors, Nuria; Aguilar, Juan; Badı́a, Josefa

doi:10.1128/jb.182.9.2672-2674.2000

Cited by 45 publications

(42 citation statements)

References 18 publications

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“…The genes encoding glucarate permease (gudT), glucarate dehydrogenase (gudD), and tartronate semialdehyde reductase (garR) that are required for glucarate uptake and utilization in E. coli (46) are also significantly upregulated by H 2 in S. Typhimurium (Table 2). Furthermore, in E. coli, the operons that encode the enzymes of the D-glucarate, D-galactarate, and D-glycerate pathways are commonly regulated by an autogenous regulator, SdaR (43). S. Typhimurium also possesses protein CdaR (carbohydrate diacid transcriptional activator, encoded by cdaR) with a similar function and 97% homology with SdaR.…”

Section: Resultsmentioning

confidence: 99%

Hydrogen-Stimulated Carbon Acquisition and Conservation in Salmonella enterica Serovar Typhimurium

et al. 2011

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Salmonella enterica serovar Typhimurium can utilize molecular hydrogen for growth and amino acid transport during anaerobic growth. Via microarray we identified H 2 gas-affected gene expression changes in Salmonella. The addition of H 2 caused altered expression of 597 genes, of which 176 genes were upregulated and 421 were downregulated. The significantly H 2 -upregulated genes include those that encode proteins involved in the transport of iron, manganese, amino acids, nucleosides, and sugars. Genes encoding isocitrate lyase (aceA) and malate synthase (aceB), both involved in the carbon conserving glyoxylate pathway, and genes encoding the enzymes of the D-glucarate and D-glycerate pathways (gudT, gudD, garR, garL, garK) are significantly upregulated by H 2 . Cells grown with H 2 showed markedly increased AceA enzyme activity compared to cells without H 2 . Mutant strains with deletion of either aceA or aceB had reduced H 2 -dependent growth rates. Genes encoding the glutamine-specific transporters (glnH, glnP, glnQ) were upregulated by H 2 , and cells grown with H 2 showed increased [ 14 C]glutamine uptake. Similarly, the mannose uptake system genes (manX, manY) were upregulated by H 2, and cells grown with H 2 showed about 2.0-fold-increased [ 14 C]D-mannose uptake compared to the cells grown without H 2 . Hydrogen stimulates the expression of genes involved in nutrient and carbon acquisition and carbon-conserving pathways, linking carbon and energy metabolism to sustain H 2 -dependent growth.

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Section: Resultsmentioning

confidence: 99%

Hydrogen-Stimulated Carbon Acquisition and Conservation in Salmonella enterica Serovar Typhimurium

et al. 2011

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“…1). These genes are related to D-galactarate metabolism (18,35). BaeR increased the expression of three other clusters, one of which contains the amn and yeeN genes, one of which contains the gsp and yghU genes, and one of which contains the yieI and yieJ genes (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Analyses of Escherichia coli Gene Expression Responsive to the BaeSR Two-Component Regulatory System

2005

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Bacteria have developed signaling systems for eliciting a variety of adaptive responses to their environments. These adaptive responses are often mediated by two-component regulatory systems. A typical two-component regulatory system is composed of a histidine kinase sensor residing in the inner membrane and a cognate response regulator in the cytoplasm. Similar systems control the expression of genes for nutrient acquisition, virulence, antibiotic resistance, and numerous other pathways in diverse bacteria (2,17,47,48). There are also analogous signaling systems in cells of eukaryotes, including fungi, amoebae, and plants (19,31,59,60,62). In Escherichia coli, 29 histidine kinase sensors, 32 response regulators, and one HPt (histidine-containing phosphotransmitter) domain protein have been found during analyses of the E. coli K-12 genome (34). Each sensor responds to specific environmental changes to cope with the numerous conditions that E. coli faces. The functions of many of these systems remain undetermined.In a previous study, it was found that the BaeSR two-component system modulates the drug resistance of E. coli by regulating the expression of drug transporter genes (5, 36). The response regulator BaeR modulates the expression of mdtABC and acrD, which encode multidurug exporter systems (15,16,36). Overproduction of BaeR, in the background of a deficiency of the E. coli major multidrug exporter AcrB, confers resistance against ␤-lactams, novobiocin, sodium dodecyl sulfate, and bile salts. However, the physiological role of the BaeSR system has remained unknown.We hypothesized that the BaeSR system controls the expression of a wide range of genes. E. coli microarrays have been successfully used to quantify the entire complement of individual mRNA transcripts (40,46). Therefore, to reveal the whole picture of the BaeSR-controlled genes, a microarray analysis of genes affected by BaeR overproduction was performed in this study. The expression levels of all of the BaeR-affected genes were also investigated by quantitative real-time reverse transcription-PCR (qRT-PCR) analysis. Also, we investigated the effect of baeSR deletion on the levels of expression of genes by qRT-PCR analysis. In order to understand the response of the BaeSR system to signals, we examined the effect of addition of indole on gene expression levels. Combination of these expression data sets revealed a BaeR-binding site sequence motif. Furthermore, we examined the effects of deletion of phoBR or creBC on the levels of expression of the BaeR-induced genes to elucidate the genetic network of the BaeSR system.

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“…The GAF domains were often found in multiple copies per chemoreceptor ( Table 1). The Diacid_rec domain is found in several proteins characterized as carbohydrate diacid regulators (54). It is always located N terminal to the MA domain (Table 1).…”

Section: Ligand Binding Domains Found In Cytoplasmic Chemoreceptorsmentioning

confidence: 99%

Internal Sense of Direction: Sensing and Signaling from Cytoplasmic Chemoreceptors

Collins

Lacal

Ottemann

2014

Microbiol Mol Biol Rev

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SUMMARY Chemoreceptors sense environmental signals and drive chemotactic responses in Bacteria and Archaea . There are two main classes of chemoreceptors: integral inner membrane and soluble cytoplasmic proteins. The latter were identified more recently than integral membrane chemoreceptors and have been studied much less thoroughly. These cytoplasmic chemoreceptors are the subject of this review. Our analysis determined that 14% of bacterial and 43% of archaeal chemoreceptors are cytoplasmic, based on currently sequenced genomes. Cytoplasmic chemoreceptors appear to share the same key structural features as integral membrane chemoreceptors, including the formations of homodimers, trimers of dimers, and 12-nm hexagonal arrays within the cell. Cytoplasmic chemoreceptors exhibit varied subcellular locations, with some localizing to the poles and others appearing both cytoplasmic and polar. Some cytoplasmic chemoreceptors adopt more exotic locations, including the formations of exclusively internal clusters or moving dynamic clusters that coalesce at points of contact with other cells. Cytoplasmic chemoreceptors presumably sense signals within the cytoplasm and bear diverse signal input domains that are mostly N terminal to the domain that defines chemoreceptors, the so-called MA domain. Similar to the case for transmembrane receptors, our analysis suggests that the most common signal input domain is the PAS (Per-Arnt-Sim) domain, but a variety of other N-terminal domains exist. It is also common, however, for cytoplasmic chemoreceptors to have C-terminal domains that may function for signal input. The most common of these is the recently identified chemoreceptor zinc binding (CZB) domain, found in 8% of all cytoplasmic chemoreceptors. The widespread nature and diverse signal input domains suggest that these chemoreceptors can monitor a variety of cytoplasmically based signals, most of which remain to be determined.

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A Common Regulator for the Operons Encoding the Enzymes Involved in d -Galactarate, d -Glucarate, and d -Glycerate Utilization in Escherichia coli

Cited by 45 publications

References 18 publications

Hydrogen-Stimulated Carbon Acquisition and Conservation in Salmonella enterica Serovar Typhimurium

Hydrogen-Stimulated Carbon Acquisition and Conservation in Salmonella enterica Serovar Typhimurium

Genome-Wide Analyses of Escherichia coli Gene Expression Responsive to the BaeSR Two-Component Regulatory System

Internal Sense of Direction: Sensing and Signaling from Cytoplasmic Chemoreceptors

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