Dynamic changes of the Escherichia coli transcriptome and proteome exerted by glucose repression

A system biology approach, including multi-omics analyses (i.e. time-resolved monitoring of mRNA and protein levels) with an advanced culturing method, was applied in order to identify posttranscriptionally regulated genes in E. coli under Carbon catabolite repression control. Approximately 800 proteins were quantified using ¹⁵N-metabolic labelling, in 3 parallel chemostat cultures. Of these, about 400 proteins were found to change significantly (p<0.05) in expression level, upon a glucose pulse, as compared to the reference conditions. Of almost half of the proteins that are significantly up- or down-regulated, the levels of mRNA and protein are not correspondingly altered. These genes are classified as potential post-transcriptionally regulated (PPTR) genes. Most of the PPTR genes are involved in transcription, nucleotide- and amino acid biosynthesis, membrane transporter expression, and central metabolism. Interestingly, only 30% of the PPTR genes has been reported to be regulated at the post-transcriptional level by small regulatory RNAs or by a riboswitch, while the regulator(s) and/or the mechanism of post-transcriptional regulation of the remaining PPTR genes (70%) is still unknown.