title: Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.
abstract: 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 quantitative time-series analysis of both the transcriptome (using microarray analysis) and the proteome (through a combination of 15N-metabolic labeling and mass spectrometry). Changes in the transcriptome and corresponding proteome were analyzed using statistical procedures designed specifically for time-series data. By comparison of the two sets of data, a total of 96 genes were identified that are post-transcriptionally regulated. This gene list provides candidates for future in-depth investigation of the molecular mechanisms involved in post-transcriptional regulation during carbon catabolite repression in E. coli, like the involvement of small RNAs.
authors.affiliation: Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Orawan
authors.initials: O
authors.lastname: Borirak
authors.affiliation: Krebs Institute, Molecular Biology and Biotechnology, University of Sheffield, United Kingdom.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Rolfe
authors.affiliation: Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Leo J
authors.initials: LJ
authors.lastname: de Koning
authors.affiliation: Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Huub C J
authors.initials: HC
authors.lastname: Hoefsloot
authors.affiliation: Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Martijn
authors.initials: M
authors.lastname: Bekker
authors.affiliation: Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Henk L
authors.initials: HL
authors.lastname: Dekker
authors.affiliation: Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Winfried
authors.initials: W
authors.lastname: Roseboom
authors.affiliation: Krebs Institute, Molecular Biology and Biotechnology, University of Sheffield, United Kingdom.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Green
authors.affiliation: Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
authors.forename: Chris G
authors.initials: CG
authors.lastname: de Koster
authors.affiliation: Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands. Electronic address: K.J.Hellingwerf@uva.nl.
authors.forename: Klaas J
authors.initials: KJ
authors.lastname: Hellingwerf
mesh_terms: D019149:Bioreactors; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000172:deficiency*; D007553:Isotope Labeling; D046228:Microarray Analysis; D058977:Molecular Sequence Annotation; D009587:Nitrogen Isotopes; D020543:Proteome; D013997:Time Factors; D059467:Transcriptome
chemical_list: D029968:Escherichia coli Proteins; D009587:Nitrogen Isotopes; D020543:Proteome; D005947:Glucose
keywords: Carbon catabolite repression; Post-transcriptional control; Proteomics analysis; Small regulatory RNA; Time-series analysis; Transcriptomics analysis