Project Idea: Post transcriptional regulation in metabolic transition in E.coli, Manon Morin, Sepideh Dolatshahi [Albert]

Question: What is the role of the post transcriptional regulation by the CSR system during the glucose/acetate switch?

We are interested in specifics of how csrA regulates both Glycolysis and Gluconeogenesis and the transition between those two states. (Literature has some examples of specific inhibition targets, we want a more complete dynamic picture)

Data: 

  • Enzymatic assays which show us how enzyme activities change from WT to knockout (proteomics)
  • Time series of metabolite concentrations (metabolomics)
  • Time series of gene expression data (genomics)

Modeling approach: 

We start with a manageable piece of the whole picture which spreads along metabolomics, proteomics, and transcriptomics levels.

After long discussions, we chose to initially focus on one reaction (enzyme) at a time, and build a model incorporating the three levels of regulation.

So far we have data for the wild type strain. We are planning to do parameter estimation to fit the related experimental data. And the behavior in the  strain could be predicted by removing the CsrA protein from the model. The predictive results could be tested using the data from  (will be collected in Sep-Oct).

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