Mitochondrial Metabolomics of Sym1-Depleted Yeast Cells Revealed Them to Be Lysine Auxotroph

• Published in: Cells (Basel, Switzerland) Vol. 12; no. 5; p. 692
• Main Authors: Lagies, Simon, Pan, Daqiang, Mohl, Daniel A, Plattner, Dietmar A, Gentle, Ian E, Kammerer, Bernd
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 22-02-2023; MDPI
• Subjects: Amino acids; Biosynthesis; compartment-specific metabolomics; Cytoplasm; Gas chromatography; High-performance liquid chromatography; Humans; Lysine; Lysine - metabolism; lysine auxotroph; Mass spectroscopy; Membrane proteins; Membrane Proteins - metabolism; Metabolism; Metabolites; Metabolomics; Metabolomics - methods; Mitochondria; Mitochondria - metabolism; Mitochondrial DNA; mitochondrial DNA depletion syndrome; Molecular weight; Orotic acid; Physiological aspects; Protein turnover; Proteins; Saccharomyces cerevisiae - metabolism; Statistical analysis; sym1; Yeast; Germany; United States > US; MDDS; compartment-specific metabolomics; mitochondrial DNA depletion syndrome; mitochondria; lysine auxotroph; sym1; yeast
• ISSN: 2073-4409; 2073-4409
• DOI: 10.3390/cells12050692

Metabolomics has expanded from cellular to subcellular level to elucidate subcellular compartmentalization. By applying isolated mitochondria to metabolome analysis, the hallmark of mitochondrial metabolites has been unraveled, showing compartment-specific distribution and regulation of metabolites. This method was employed in this work to study a mitochondrial inner membrane protein Sym1, whose human ortholog MPV17 is related to mitochondria DNA depletion syndrome. Gas chromatography-mass spectrometry-based metabolic profiling was combined with targeted liquid chromatography-mass spectrometry analysis to cover more metabolites. Furthermore, we applied a workflow employing ultra-high performance liquid chromatography-quadrupole time of flight mass spectrometry with a powerful chemometrics platform, focusing on only significantly changed metabolites. This workflow highly reduced the complexity of acquired data without losing metabolites of interest. Consequently, forty-one novel metabolites were identified in addition to the combined method, of which two metabolites, 4-guanidinobutanal and 4-guanidinobutanoate, were identified for the first time in
. With compartment-specific metabolomics, we identified
Δ cells as lysine auxotroph. The highly reduced carbamoyl-aspartate and orotic acid indicate a potential role of the mitochondrial inner membrane protein Sym1 in pyrimidine metabolism.