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Mitochondrial metabolomics reveals compartment-specific metabolic responses in yeast cells
1, 2 , 3 , 1, 4, 5 , 2 , 3, 6 , * 1, 6
1  Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
2  Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
3  Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
4  Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
5  Institute of Biology II, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
6  BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany


Mutations in mitochondrial membrane proteins could cause physiological and metabolic alterations in mitochondria as well as in cytosol. In order to address the origin of these alterations, mitochondria and cytosol of yeast wild-type BY4741 and two mutants, sdh2Δ and atp4Δ, were isolated from whole cells. These three compartments, namely mitochondria, cytosol and whole cell, were analyzed by gas chromatography-mass spectrometry based metabolic profiling, identifying seventy-three metabolites altogether, from which sixteen or ten were not detected either in mitochondria or cytosol. Compartment-specific distribution and regulation of metabolites were observed, showing the responses to the deletions of sdh2 and atp4. Based on the metabolic signature in mitochondrial matrix and cytosol, both mutants can be discriminated from wild-type by principal component analysis. De letions of electron chain transport components, sdh2 and atp4, altered not only citrate cycle related metabolites, but also diverse metabolites including amino acids, fatty acids, purine and pyrimidine intermediates and others. By applying metabolomics to isolated mitochondria and cytosol, compartment-specific metabolic regulation can be identified, which is helpful in understanding the molecular mechanism of mitochondrial homeostasis in response to genetic mutations.

Keywords: Mitochondria, budding yeast, metabolomics, compartmentalization, SDH2, ATP4
Comments on this paper
Anubhav Srivastava
Hi Daqiang,

Great presentation. Do you think with your mitochondria isolation procedure, some metabolites might be lost due to disruption of the outer membrane as the organelle might become leaky? What happens to the membrane potential of these isolated mitochondria?


Daqiang Pan
Hi Anubhav,

Thank you for your question. At first, the outer membrane was not disrupted as shown on page 6, the outer membrane protein tom40 and tom70 were not depleted until the protein K incubation. As we already know, a minimal activity of mitochondrial transporter might be there despite low temperature, we cannot exclude the possibility of any kind of leakage. However, our results showed the maintained compartmentalization (page 7) and compartment-specific metabolic alterations (page 8-10), which indicate no significant leakage. Since our focus was metabolomics, we have not compared the membrane potential yet. But it is interesting to get the information. So we may do it in our next preparation.