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

Orawan Borirak, Matthew D. Rolfe, Leo J. De Koning, Huub C.J. Hoefsloot, Martijn Bekker, Henk L. Dekker, Winfried Roseboom, Jeffrey Green, Chris G. De Koster, Klaas J. Hellingwerf*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


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 1 h, 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.

Original languageEnglish
Article number39611
Pages (from-to)1269-1279
Number of pages11
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Issue number10
Publication statusPublished - 18 Jul 2015
Externally publishedYes


  • Carbon catabolite repression
  • Post-transcriptional control
  • Proteomics analysis
  • Small regulatory RNA
  • Time-series analysis
  • Transcriptomics analysis


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