BW25113 glucose to acetate transition
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli
PROVIDER: GSE3250 | GEO | 2005/09/14
SECONDARY ACCESSION(S): PRJNA92897
REPOSITORIES: GEO
Similar Datasets
Project description:In bacterial adaptation to the dynamic environment, metabolic genes are typically thought to be the executors, whereas global transcription regulators are regarded as the decision makers. Although the feedback from metabolic consequence is believed to be important, much less is understood. This work demonstrates that the gluconeogenic genes in Escherichia coli, ppsA, sfcA, and maeB, provide a feedback loop to the global regulator, CRP, in carbon source transition. Disruption of one of the gluconeogenic pathways has no phenotype in balanced growth, but causes a significant delay in the diauxic transition from glucose to acetate. To investigate the underlying mechanism, we measured the transcriptome profiles during the transition using DNA microarray, and Network Component Analysis was employed to obtain the transcription factor activities. Results showed that one of the global regulators, CRP, was insufficiently activated during the transition in the ppsA deletion mutant. Indeed, addition of cAMP partially rescued the delay in transition. These results suggest that the gluconeogenic flux to phosphoenolpyruvate is important for full activation of adenylate cyclase through phosphorylated enzyme IIAglu of the phosphotransferase system. Reduction of this flux causes insufficient activation of CRP and a global metabolic deficiency, which exemplifies a significant feedback interaction from metabolism to the global regulatory system. Keywords: Time course Cells were grown up in M9 glucose media until mid log phase, then harvested and transitioned into M9 acetate media. Samples were taken immediately prior to transition to acetate (reference sample) and at 5, 15, 30, 60, 120, 180, 240, 300, and 360 minutes after transition.
2005-09-14 | E-GEOD-3250 | biostudies-arrayexpress
Project description:Escherichia coli exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native crp gene with a catabolite repression mutant (referred to as crp*) alleviates diauxic effects in E. coli and enables co-utilization of glucose and other sugars. While previous studies have examined the effects of expressing CRP* mutants on the expression of specific catabolic genes, little is known about the global transcriptional effects of CRP* expression. In this study, we compare the transcriptome of E. coli W3110 (expressing wild-type CRP) to that of mutant strain PC05 (expressing CRP*) in the presence and absence of glucose.
2009-08-12 | GSE17584 | GEO
Project description:Escherichia coli exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native crp gene with a catabolite repression mutant (referred to as crp*) alleviates diauxic effects in E. coli and enables co-utilization of glucose and other sugars. While previous studies have examined the effects of expressing CRP* mutants on the expression of specific catabolic genes, little is known about the global transcriptional effects of CRP* expression. In this study, we compare the transcriptome of E. coli W3110 (expressing wild-type CRP) to that of mutant strain PC05 (expressing CRP*) in the presence and absence of glucose. Experiment Overall Design: Four different conditions were tested in this study: W3110 in LB medium (WT), W3110 in LB+glucose medium (WT G), PC05 in LB medium (CRP*), and PC05 in LB+glucose medium (CRP* G).
2009-08-21 | E-GEOD-17584 | biostudies-arrayexpress
Project description:Strand-specific RNA sequencing was performed on wild type yeast in log phase, after diauxic shift, and after entry into quiescence with incorporation of external ERCC RNA spike-in controls to account for global changes in RNA abundance. We find that RNA profiles undergo at least two transitions: 1) From log-to-diauxic shift where stress response genes are induced and translational machinery is massively repressed. 2) From diauxic shift-to-quiescence, where global transcript abundance is repressed 15-fold. The transition from diauxic shift to quiescence was found to require Rpd3, as deletion of Rpd3 prevented the global repression of the transcriptome after the diauxic shift.
2015-08-20 | GSE67149 | GEO
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a (ccpN-yqfL) double mutant. Abstract of the associated publication (article accepted): The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes. Two-condition experiment: wt vs. (ccpN-yqfL) double mutant. 2 totally independent comparisons were performed different days with 2 independent RNA preparations and 2 sets of macroarrays.
2008-07-01 | E-GEOD-11876 | biostudies-arrayexpress
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN (yqzB) non polar mutant. Abstract of associated publication (article accepted): The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes. Two-condition experiment, wt vs. ccpN mutant. 4 experiments were performed different days with 3 independent RNA preparations (from separate cultures) and 3 independent sets of macroarrays: Experiment 1 (samples wt1 and ccpN1): total RNA extract1 / membranes set A Expereince 2 (samples wt2 and ccpN2): total RNA extract 2 / membranes set A Experiment 3 (samples wt2 and ccpN2): total RNA extract 3 / membranes set B Experiment 4 (samples wt2 and ccpN2): total RNA extract 3 / membranes set C
2008-06-26 | E-GEOD-11873 | biostudies-arrayexpress
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a (ccpN-yqfL) double mutant. Abstract of the associated publication (article accepted): The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes.
2008-07-01 | GSE11876 | GEO
Project description:Global transcriptional profiling of Bacillus subtilis cells comparing wild-type to a ccpN (yqzB) non polar mutant. Abstract of associated publication (article accepted): The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA, and of a small non-coding regulatory RNA, sr1, involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1, the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes.
2008-06-26 | GSE11873 | GEO
Project description:In this study, we identify the regulatory mechanisms that coordinate catabolism and anabolism in the bacterium Escherichia coli. Integrating protein, metabolite, and metabolic flux changes in genetically implemented gradual catabolic or anabolic limitations, we show that a combination of global and local mechanisms coordinates the response to metabolic limitations. To allocate proteomic resources between catabolism and anabolism, E. coli uses a simple global gene regulatory program. Surprisingly, this program is largely implemented by a single transcription factor Crp, which not only directly activates the expression of catabolic enzymes, but also indirectly reduces the expression of anabolic enzymes by passively sequestering cellular resources needed for their synthesis. However, this regulatory program rarely controls metabolic fluxes alone; instead, fluxes are further adjusted locally through passive changes in metabolite concentrations. Together, these mechanisms constitute a limited but effective global regulatory program that coarsely partitions resources between different parts of metabolism while ensuring the robust coordination of individual metabolic reactions.
2021-03-03 | MSV000086992 | MassIVE
Project description:This is the model described in: Bacterial adaptation through distributed sensing of metabolic fluxes
Oliver Kotte, Judith B Zaugg and Matthias Heinemann;Mol Sys Biol2010;6:355. doi:10.1038/msb.2010.10;
Abstract:
The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli's central metabolism and its regulation, fundamental aspects of the employed sensing and regulatory adjustment mechanisms remain unclear. In this paper, using a differential equation model that couples enzymatic and transcriptional regulation of E. coli's central metabolism, we show that the interplay of known interactions explains in molecular-level detail the system-wide adjustments of metabolic operation between glycolytic and gluconeogenic carbon sources. We show that these adaptations are enabled by an indirect recognition of carbon sources through a mechanism we termed distributed sensing of intracellular metabolic fluxes. This mechanism uses two general motifs to establish flux-signaling metabolites, whose bindings to transcription factors form flux sensors. As these sensors are embedded in global feedback loop architectures, closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously (not requiring upstream sensing and signaling) to fluctuating carbon sources.
In its current form this SBML model is parametrized for the glucose to acetate transition and to simulate the extended diauxic shift as shown in figure 3 and scenario 6 of the attached matlab file. In this scenario the cells first are grown from an OD600 (BM) of 0.03 with a starting glucose concentration of 0.5 g/l for 8.15 h (29340 sec). Then a medium containing 5 g/l acetate is inoculated with these cells to an OD600 of 0.03 and grown for another 19.7 hours (70920 sec). Finally the cells are shifted to a medium containing both glucose and acetate at a concentration of 3 g/l with a starting OD600 of 0.0005.
The shifts where implemented using events triggering at the times determined by the parameters shift1 and shift2 (in hours). To simulate other scenarios the initial conditions need to be changed as described in the supplemental materials (supplement 1)
The original SBML model and the MATLAB file used for the calculations can be down loaded as supplementary materials of the publication from the MSB website. (supplement 2).
The units of the external metabolites are in [g/l], those of the biomass in optical density,OD600, taken as dimensionless, and [micromole/(gramm dry weight)] for all intracellular metabolites. As the latter cannot be implemented in SBML, it was chosen to be micromole only and the units of the parameters are left mostly undefined.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.For more information see the terms of use.To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2010-03-14 | BIOMD0000000244 | BioModels