An impaired respiratory electron chain triggers retrograde response and de-ubiquitination of solute carrier amino acid transporters

ABSTRACT: Hundreds of genes have been associated with respiratory chain disease so far. Elimination of the respiratory electron chain by depleting the entire mitochondrial DNA (mtDNA, ��0 cells) has therefore one of the most severe impacts on the energy metabolism in eukaryotic cells. Here, we integrated proteomic data sets including the post transcriptional modifications (PTM���s) phosphorylation and ubiquitination, with metabolomic data sets and selected enzyme activities in the osteosarcoma cell line 143B.TK-. We applied a shotgun based SILAC LC-MS proteomics and a targeted metabolomics approach to elucidate the consequences of the ��0 state. Pathway analysis revealed a non-uniform down-regulation of the respiratory electron chain, the tricarboxylic acid (TCA) cycle and the pyruvate metabolism in ��0 cells. Surprisingly, some metabolites of the TCA cycle were dramatically reduced in ��0 cells, like citric acid (100-fold) and aconitic acid (6-fold), others instead increased, like succinic and fumaric acid (5-fold). Enzyme activities were xy. Exceptionally, the mitochondrial retrograde response, a pathway of communication from mitochondria to the nucleus, was up-regulated in ��0 cells, like signalling by GPCR, EGFR, G12/13 alpha cAMP and RhoGTPase. We observed a striking de-ubiquitination of 80S ribosomal proteins (3-fold) and SLC amino acid transporters (7-fold) in ��0 cells, the later might cause the observed significant increase of amino acids levels in ��0 cells. We conclude that mtDNA depletion not only leads to an uneven down-regulation of mitochondrial energy pathways, but also to a strong retrograde response. The partly collapsed TCA cycle and de-ubiquitination of SLC transporters lead to an altered amino acid metabolism.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Bone Marrow

DISEASE(S): Osteosarcoma

SUBMITTER: Ina Gielisch  

LAB HEAD: David Meierhofer

PROVIDER: PXD002270 | Pride | 2022-02-22

REPOSITORIES: Pride