Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator

Song, Sukgil; Park, Chankyo

doi:10.1128/jb.179.22.7025-7032.1997

Cited by 145 publications

(152 citation statements)

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“…These regulatory proteins have been assigned to families based on sequence homology; however, different proteins in the same families may have different DNA and substratebinding specificities (17). Also, proteins placed in different families may share the same name because of their regulon composition, as in the case of the Escherichia coli and Bacillus subtilis xylR protein (18,19). Of the 69 transcription/ transduction genes on the array, six share similarity with the …”

Section: Resultsmentioning

confidence: 99%

“…TM0949 displays 30% identity with E. coli XylR, the positive regulator of the xylFGH ABC transporter operon, and showed a particularly strong induction on xylose. ABC transporters located downstream of TM0949 show similarity to xylFGH, and it remains to be seen whether these genes, annotated as ribose ABC transporters, are induced during growth on xylose as observed in E. coli (18,48). The CRP-like transcriptional regulator TM1171 was up-regulated primarily on xylose but to a lesser extent on CMC.…”

Section: Regulation Of T Maritima Glycoside Hydrolasesmentioning

confidence: 99%

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Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Chhabra¹,

Shockley²,

Conners³

et al. 2003

Journal of Biological Chemistry

121

126

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The hyperthermophilic bacterium Thermotoga maritima MSB8 was grown on a variety of carbohydrates to determine the influence of carbon and energy source on differential gene expression. Despite the fact that T. maritima has been phylogenetically characterized as a primitive microorganism from an evolutionary perspective, results here suggest that it has versatile and discriminating mechanisms for regulating and effecting complex carbohydrate utilization. Growth of T. maritima on monosaccharides was found to be slower than growth on polysaccharides, although growth to cell densities of 10 8 to 10 9 cells/ml was observed on all carbohydrates tested. Differential expression of genes encoding carbohydrate-active proteins encoded in the T. maritima genome was followed using a targeted cDNA microarray in conjunction with mixed model statistical analysis. Coordinated regulation of genes responding to specific carbohydrates was noted. Although glucose generally repressed expression of all glycoside hydrolase genes, other sugars induced or repressed these genes to varying extents. Expression profiles of most endo-acting glycoside hydrolase genes correlated well with their reported biochemical properties, although exo-acting glycoside hydrolase genes displayed less specific expression patterns. Genes encoding selected putative ABC sugar transporters were found to respond to specific carbohydrates, and in some cases putative oligopeptide transporter genes were also found to respond to specific sugar substrates. Several genes encoding putative transcriptional regulators were expressed during growth on specific sugars, thus suggesting functional assignments. The transcriptional response of T. maritima to specific carbohydrate growth substrates indicated that sugar backbone-and linkage-specific regulatory networks are operational in this organism during the uptake and utilization of carbohydrate substrates. Furthermore, the wide ranging collection of such networks in T. maritima suggests that this organism is capable of adapting to a variety of growth environments containing carbohydrate growth substrates.

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Section: Resultsmentioning

confidence: 99%

Section: Regulation Of T Maritima Glycoside Hydrolasesmentioning

confidence: 99%

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Chhabra¹,

Shockley²,

Conners³

et al. 2003

Journal of Biological Chemistry

121

126

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“…If xylose is present, CRP activated by cAMP and the xylose-specific activator XylR (activated when bound by xylose) together coactivate the xylose catabolic operons, xylAB and xylFGH (Fig. 1A) (11). After xylose is imported by XylFGH, a xylosespecific ATP-binding cassette transporter protein, xylose is converted to xylulose through a reversible one-step reaction catalyzed by xylose isomerase, XylA.…”

mentioning

confidence: 99%

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Sievert

Nieves

Panyon

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Microbial production of fuels and chemicals from lignocellulosic biomass provides promising biorenewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. Although industrial Escherichia coli strains efficiently use glucose, their ability to use xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94% of a glucose–xylose mixture (50 g⋅L−1 each) was used in mineral salt media that led to a 50% increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild type, suggesting its potential wide application in industrial E. coli biocatalysts.

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“…The feaR gene is under catabolic repression, and is highly expressed in the presence of succinate. XylR is a transcription factor involved in D-xylose degradation and utilization (Song & Park, 1997). PuuR is a transcription repressor that regulates transcription of several genes involved in putrescine utilization and transport (Kurihara et al, 2005).…”

Section: Expression Levels Of Tfs Under Aerobic Conditionsmentioning

confidence: 99%

Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families

Watanabe

Ishihama

2014

Microbiology

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The expression pattern of the genome in Escherichia coli is controlled by regulating the utilization of a limited number of RNA polymerases between a total of 4600 genes on its genome. The distribution pattern of RNA polymerase on the genome changes after two steps of protein-protein interaction with seven sigma subunits and about 300 transcription factors (TFs). Based on a systematic search for the regulation target promoters recognized by each TF, we propose two novel concepts: each TF regulates a number of target promoters; and each promoter is regulated by many TFs. In parallel, attempts have been made to determine the intracellular concentrations of all TFs using two systems: quantitative immunoblot analysis using TF-specific antibodies; and reporter assay of TF promoter activities. The direct measurement of TF protein level has so far been published for a set of 60 regulators with known functions. This study describes the determination of growth phase-dependent expression levels of 90 TFs using the reporter assay system. The translational fusion vector was constructed from the TF promoter sequence including an N-terminal proximal TF segment and the reporter GFP. At the beginning of cell growth, highlevel expression was observed only for a small number of TFs. In the exponential phase, approximately 80 % TFs are expressed, but the expressed TF species change upon transfer to the stationary phase. Significant changes in the pattern of TF expression were observed between aerobic and anaerobic conditions. The list of intracellular levels of TFs provides further understanding to the transcription regulation of the E. coli genome under various stressful conditions. INTRODUCTIONSingle-cell bacteria are directly exposed to frequently changing environments in nature and thus carry sophisticated genetic systems for adaptation to environmental changes (Ishihama, 2010(Ishihama, , 2012Yamamoto, 2014). On the basis of the complete genome sequence of several model Escherichia coli strains, the whole set of about 4600 genes has been predicted to exist in E. coli K-12 (Hayashi et al., 2006;Riley et al., 2006). In growing E. coli cells under laboratory culture conditions, only one-quarter to one-third of the genes on its genome are expressed, the others remaining silent. The majority of these uncharacterized silent genes must be expressed and utilized for adaptation and survival of E. coli under stressful conditions. Thus, even for this well-characterized model organism, the gene functions remain unidentified or unpredicted for approximately one-quarter because expression conditions of these silent genes have not yet been established.As the total number of RNA polymerases (RNAPs) in E. coli K-12 is less than the total number of genes on its genome (Ishihama, 2000), we proposed a model in which the change in genome transcription pattern takes place mainly through controlling the utilization of this limited number of transcription apparatuses between 4600 genes on the genome (Ishihama, 2010(Ishihama, , 2012. Two groups of reg...

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Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator

Cited by 145 publications

References 50 publications

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Carbohydrate-induced Differential Gene Expression Patterns in the Hyperthermophilic Bacterium Thermotoga maritima

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families

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