In Vitro Binding of the Pleiotropic Transcriptional Regulatory Protein, FruR, to the fru, pps, ace, pts and icd Operons of Escherichia coli and Salmonella typhimurium

Ramseier, Tom M.; Nègre, Didier; Cortay, Jean‐Claude; Scarabel, Marie; Cozzone, Alain J.; Saier, Milton H.

doi:10.1006/jmbi.1993.1561

Cited by 135 publications

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“…For example, the nmpC and tsx outer membrane porin-encoding genes fell into this category. Both exhibited only partial relief from catabolite repression in the crp mutant, but a crp-fruR double mutant (32,33) showed no glucose repression (unpublished results). The same behavior was observed for the dadA and dadX genes encoding D-amino acid dehydrogenase and alanine racemase, respectively, as well as the genes encoding the dicarboxylate transporters DctA and DcuA.…”

Section: Resultsmentioning

confidence: 89%

“…The genes that most clearly showed dual control of catabolite repression by Crp and Cra were gat, mgl, tre, and dsd (data not shown). These observations suggest that in several cases, catabolite repression depends on both Crp and Cra (32,33). The fact that many genes show residual glucose repression in the crp mutant is not surprising since multiple mechanisms of catabolite repression are recognized in E. coli (35).…”

Section: Resultsmentioning

confidence: 98%

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Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli

et al. 2004

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We report here the transcriptome analyses of highly expressed genes that are subject to catabolite repression or activation mediated by the cyclic AMP receptor protein (Crp). The results reveal that many operons encoding enzymes of central carbon metabolic pathways (e.g., Krebs cycle enzymes), as well as transporters and enzymes that initiate carbon metabolism, are subject to direct Crp-mediated catabolite repression. By contrast, few enzyme-encoding genes (direct regulation) but many ribosomal protein-and tRNA-encoding genes (indirect regulation) are subject to Crp-dependent glucose activation. Additionally, Crp mediates strong indirect catabolite repression of many cytoplasmic stress response proteins, including the major chaperone proteins, five ATP-dependent protease complexes, and several cold and heat shock proteins. These results were confirmed by (i) phenotypic analyses, (ii) real-time PCR studies, (iii) reporter gene fusion assays, and (iv) previously published reports about representative genes. The results serve to define and extend our appreciation of the Crp regulon.A dominant mechanism by which Escherichia coli and other related bacteria sense carbon sufficiency involves cyclic AMP and its receptor protein, Crp (15,35). The mechanisms by which Crp regulates gene expression in response to variable cytoplasmic levels of cyclic AMP have been extensively investigated with primary emphasis on E. coli and Salmonella strains (5,34,35,41). Dozens of operons have been shown to be subject to Crp-mediated control by using classical approaches (17). Transcriptome and proteome approaches have been used to study the control of various regulons, as well as to facilitate glucose flux analyses (10, 39). Indeed, the transcriptome approach has allowed investigators to challenge established paradigms, and the technology has enjoyed rapid adoption among researchers (7). However, no report has focused on genomewide analyses of Crp-mediated catabolite regulation in E. coli. In this study, we corrected this deficiency by conducting combined transcriptome, phenotypic, and bioinformatic analyses of the Crp-mediated responses of E. coli to exogenous glucose availability. We also tabulated comparative data derived from the classical literature and confirmed representative regulatory responses by using alternative approaches. We show here that a variety of stress-related genes, encoding chaperones (1, 4, 38), ATP-dependent proteases (9,11,20), and certain temperature shock proteins (12,31,40), are regulated in response to the presence of Crp, apparently by an indirect mechanism. MATERIALS AND METHODSBacterial strains and growth conditions. The strains used in this study were BW25113 and an isogenic crp mutant derivative, LJ3017, constructed as described by Zhang et al. (43). Strains were grown at 37°C with agitation at 250 rpm in Luria-Bertani (LB) broth containing 50 mM potassium phosphate, pH 7.4, and 0.2 mM L-cysteine with or without 0.4% glucose. Cells were grown in 25 ml of medium in 250-ml shake flasks starting at an opt...

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 98%

Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli

et al. 2004

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“…3). We identified a sequence 123 bp upstream of the potential transcriptional start site that is highly homologous to the FruR consensus binding site (49,55,56), indicating that the expression of glk is regulated by this global regulator of carbon metabolism.…”

Section: Resultsmentioning

confidence: 99%

Molecular characterization of glucokinase from Escherichia coli K-12

et al. 1997

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glk, the structural gene for glucokinase of Escherichia coli, was cloned and sequenced. Overexpression of glk resulted in the synthesis of a cytoplasmic protein with a molecular weight of 35,000. The enzyme was purified, and its kinetic parameters were determined. Its K m values for glucose and ATP were 0.78 and 3.76 mM, respectively. Its V max was 158 U/mg of protein. A chromosomal glk-lacZ fusion was constructed and used to monitor glk expression. Under all conditions tested, only growth on glucose reduced the expression of glk by about 50%. A fruR mutation slightly increased the expression of glk-lacZ, whereas the overexpression of plasmid-encoded fruR ؉ weakly decreased expression. A FruR consensus binding motif was found 123 bp upstream of the potential transcriptional start site of glk. Overexpression of glk interfered with the expression of the maltose system. Repression was strongest in strains that exhibited constitutive mal gene expression due to endogenous induction and, in the absence of a functional MalK protein, the ATP-hydrolyzing subunit of the maltose transport system. It was least effective in wild-type strains growing on maltose or in strains constitutive for the maltose system due to a mutation in malT rendering the mal gene expression independent of inducer. This demonstrates that free internal glucose plays an essential role in the formation of the endogenous inducer of the maltose system.In Escherichia coli and most other bacteria, glucose is transported by the phosphoenolpyruvate:sugar phosphotransferase system (PTS) as glucose-6-phosphate (53), thus eliminating the need for glucokinase in the utilization of glucose. In contrast, the utilization of glucose-containing disaccharides such as lactose, maltose, or trehalose involves the formation of glucose inside the cell and requires its phosphorylation for the effective utilization of the disaccharides. Surprisingly, the presence of a glk mutation (22) does not appear to be a disadvantage in the utilization of these disaccharides. Severe reduction in growth is observed only when, in addition to having the glk mutation, the strain also lacks the ability to phosphorylate glucose via the PTS pathway (14, 59). Two different findings might be relevant for this phenomenon. In the first, glucose and galactose, the products of intracellular ␤-galactosidase action, have been found in large amounts outside the cell after the uptake of lactose, implying that growth on lactose is mediated via the uptake of the secreted products (PTS-mediated phosphorylation in the case of glucose) (35). In the second, internal phosphorylation of glucose by the PTS has been evoked (14). The findings indicate that the enzyme II Glc is also responsible for the utilization of internal glucose.As a consequence, the interest in E. coli glucokinase has been low. Glucokinase activity in E. coli was measured as early as 1953 (21), and MM6, an E. coli mutant defective in the utilization of glucose, was shown to contain normal amounts of glucokinase (4). In that study, the K m of...

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“…Other gluconeogenic enzymes and reversible glycolytic enzymes drive the PEP toward glucose-6-phosphate. Note that Cra also activates genes that encode gluconeogenesis enzymes (319,366,367,389).…”

Section: Acetate Activation Pathwaysmentioning

confidence: 99%

The Acetate Switch

Wolfe

2005

Microbiol Mol Biol Rev

1,068

1,274

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To succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. One such change in life-style, the “acetate switch,” occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. This review explains why, when, and how cells excrete or dissimilate acetate. The central components of the “switch” (phosphotransacetylase [PTA], acetate kinase [ACK], and AMP-forming acetyl coenzyme A synthetase [AMP-ACS]) and the behavior of cells that lack these components are introduced. Acetyl phosphate (acetyl∼P), the high-energy intermediate of acetate dissimilation, is discussed, and conditions that influence its intracellular concentration are described. Evidence is provided that acetyl∼P influences cellular processes from organelle biogenesis to cell cycle regulation and from biofilm development to pathogenesis. The merits of each mechanism proposed to explain the interaction of acetyl∼P with two-component signal transduction pathways are addressed. A short list of enzymes that generate acetyl∼P by PTA-ACKA-independent mechanisms is introduced and discussed briefly. Attention is then directed to the mechanisms used by cells to “flip the switch,” the induction and activation of the acetate-scavenging AMP-ACS. First, evidence is presented that nucleoid proteins orchestrate a progression of distinct nucleoprotein complexes to ensure proper transcription of its gene. Next, the way in which cells regulate AMP-ACS activity through reversible acetylation is described. Finally, the “acetate switch” as it exists in selected eubacteria, archaea, and eukaryotes, including humans, is described

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In Vitro Binding of the Pleiotropic Transcriptional Regulatory Protein, FruR, to the fru, pps, ace, pts and icd Operons of Escherichia coli and Salmonella typhimurium

Cited by 135 publications

References 0 publications

Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli

Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli

Molecular characterization of glucokinase from Escherichia coli K-12

The Acetate Switch

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