Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional response of steady-state Escherichia coli cultures to a glucose pulse, in order to elucidate the role of post-transcriptional regulation during carbon catabolite repression

ABSTRACT: Gene-expression measurements were made over a 60 minute time course as steady state E. coli cells were subjected to a pulse of glucose.

ORGANISM(S): Escherichia coli

SUBMITTER: Matthew Rolfe

PROVIDER: E-MTAB-2398 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

Borirak Orawan O Rolfe Matthew D MD de Koning Leo J LJ Hoefsloot Huub C J HC Bekker Martijn M Dekker Henk L HL Roseboom Winfried W Green Jeffrey J de Koster Chris G CG Hellingwerf Klaas J KJ

Biochimica et biophysica acta 20150604 10 Pt A

Time-series transcript- and protein-profiles were measured upon initiation of carbon catabolite repression in Escherichia coli, in order to investigate the extent of post-transcriptional control in this prototypical response. A glucose-limited chemostat culture was used as the CCR-free reference condition. Stopping the pump and simultaneously adding a pulse of glucose, that saturated the cells for at least 1h, was used to initiate the glucose response. Samples were collected and subjected to qua ...[more]

PMID: 26049081

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Project description:The Saccharomyces cerevisiae SFP1 is required for proper regulation of ribosome biogenesis and cell size in response to nutrients. A mutant deleted for SFP1 shows specific traits among which a slow growth phenotype, which is particularly evident during growth on glucose. To assess the effects of nutrients on the activity of Sfp1 independent by growth rate related feedback we grew an sfp1Î mutant and its isogenic reference strain in chemostat cultures, at the same specific growth rate, under glucose/ethanol-limitation. Our data show that Sfp1 is involved in the modulation of cell size and RiBi gene expression and that these two functions are differently influenced by nutrients. The continuous cultures were then pulsed with a glucose excess generating a situation of batch growth similar to shake flask cultures. The dynamic analysis of the metabolic and transcriptional response following the glucose addition suggested that Sfp1 plays a role at the crossroads of ribosome biogenesis and central carbon metabolism regulation. Finally, we show that the down-regulation of RP genes, which was observed in an sfp1Î strain during shake flask growth, cannot be directly ascribed to the absence of Sfp1 but is most probably a secondary effect due to the low growth potential of the mutant strain. Experiment Overall Design: After ten volume changes, few seconds after the samples for the steady state analysis were collected, the anaerobic glucose pulse experiments were started by sparging the medium reservoir and the fermenter with pure nitrogen gas (airflow of 0.5 L min-1, Hoek-Loos, Schiedam, <5 ppm O2). NorpreneTM tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic culture. Two minutes after nitrogen sparging and just before the addition of glucose, the medium and the effluent pumps were switched off. At this time point (which we will refer to as time T=0) the 200 mM glucose pulse was injected aseptically through a rubber septum. Experiment Overall Design: Sampling from chemostats, total RNA extraction, probe preparation and hybridization to Affymetrix GenechipÂ® microarrays were performed as previously described (1). Samples were collected at steady state and then at 5, 10, 30, 60 and 120 minutes after the pulse. The results relative to steady state samples were derived from three independent cultures, those relative to the time course analysis were derived from two independent cultures. Experiment Overall Design: 1) Cipollina C., van den Brink J., Daran-Lapujade P., Pronk J.T., Vai M. and de Winde J.H. (2007) Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: A chemostat study. Microbiology. In press.

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Dataset Information

Transcriptional response of steady-state Escherichia coli cultures to a glucose pulse, in order to elucidate the role of post-transcriptional regulation during carbon catabolite repression

Publications

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

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