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

• Published in: Biochimica et biophysica acta Vol. 1854; no. 10; pp. 1269 - 1279
• Main Authors: Borirak, Orawan, Rolfe, Matthew D., de Koning, Leo J., Hoefsloot, Huub C.J., Bekker, Martijn, Dekker, Henk L., Roseboom, Winfried, Green, Jeffrey, de Koster, Chris G., Hellingwerf, Klaas J.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2015
• Subjects: Bioreactors; carbon; Carbon catabolite repression; data collection; Escherichia coli; Escherichia coli - genetics; Escherichia coli - growth & development; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; genes; glucose; Glucose - deficiency; Isotope Labeling; mass spectrometry; Microarray Analysis; microarray technology; Molecular Sequence Annotation; Nitrogen Isotopes; Post-transcriptional control; Proteome; Proteomics analysis; RNA; Small regulatory RNA; Time Factors; Time-series analysis; Transcriptome; transcriptomics; Transcriptomics analysis; Transcriptomics analysis; Post-transcriptional control; Carbon catabolite repression; PTS; AUC; STEM; Small regulatory RNA; CCR; FDR; SLP; Time-series analysis; MudPIT; Proteomics analysis; SCXC; ED
• ISSN: 1570-9639; 0006-3002; 1878-1454
• DOI: 10.1016/j.bbapap.2015.05.017

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. •Post-transcriptional regulation was analyzed in E. coli upon glucose repression.•For this, glucose limited chemostat-grown cells were pulsed with excess glucose.•Quantitative time-series analyses of proteome and transcriptome were performed.•Developed statistical procedures were applied specifically for time-series data.•We identified 96 genes that are subject to post-transcriptional regulation (p<0.05).