Sauer Group, Oxidative Stress, Metabolomics, Kinetic Modelling

Tutors:

Andreas Kühne  ()

Dimitris Christodoulou ()

Duration: 3 months

Start: ASAP

Background

Reactive oxygen species (ROS) are highly reactive molecules that are byproducts of different metabolic processes. They are involved in cellular signaling, but at too high concentrations can lead to oxidative stress, a condition in which ROS damage cells by oxidizing small molecules, proteins and DNA. Therefore, cells protect themselves with various antioxidant systems. On the long-term, cells induce gene expression programs for continuous ROS detoxification and DNA-damage repair, mainly regulated by the transcription factors SoxRS, OxyR (E.coli) Nrf2 and p53.

However, a short term response of metabolism after induction of oxidative stress is necessary to reduce ROS induced damage by neutralizing ROS or reducing oxidized macromolecules, e.g. using the glutathione or the thioredoxin system, respectively. Reduced nicotinamide adenine dinucleotide phosphate (NAPDH), which is mainly produced in the pentose phosphate pathway, is essential to keep those systems running. Therefore cells have an acute demand of NADPH upon oxidative stress. In yeast, oxidative stress immediately induces a rerouting of metabolic flux from glycolysis into the pentose phosphate pathway by oxidation mediated inhibition of the glycolytic enzyme GAPDH. However, in our lab we collected evidence that other regulations independent of GAPDH inhibition are involved in the activation of pentose phosphate pathway flux for increased NADPH generation upon oxidative stress in E. coli and human cells.

Your project

This project is planned to be 20% experimental work and 80% computational analysis and uses state of the art approaches in both parts. The goals of this project entail i) investigation of existing metabolomics data of the immediate metabolic responses of E.coli, Yeast and skin fibroblasts to oxidative stress, ii) integration of the data into dynamic metabolic models to identify allosteric mechanisms involved in the responses and iii) investigation of whether the mechanisms are conserved across species or not. This project is part of an effort ongoing in this lab to mechanistically understand the immediate metabolic response to oxidative stress.

To this end, you will perform physiology and metabolomics experiments in different organisms upon oxidative stress. However, primarily you will use existing targeted and non-target mass spectrometry dynamic metabolomics data and learn how to handle quantitative and dynamic datasets in combination with kinetic models, in order to extract novel biological insights. You will develop and use kinetic models of glycolysis and pentose phosphate pathway to better understand the regulations underlying this complex phenomenon and generate relevant testable hypotheses.