Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation

• Published in: Molecular cell Vol. 82; no. 2; pp. 447 - 462.e6
• Main Authors: Trefely, Sophie, Huber, Katharina, Liu, Joyce, Noji, Michael, Stransky, Stephanie, Singh, Jay, Doan, Mary T., Lovell, Claudia D., von Krusenstiern, Eliana, Jiang, Helen, Bostwick, Anna, Pepper, Hannah L., Izzo, Luke, Zhao, Steven, Xu, Jimmy P., Bedi, Kenneth C., Rame, J. Eduardo, Bogner-Strauss, Juliane G., Mesaros, Clementina, Sidoli, Simone, Wellen, Kathryn E., Snyder, Nathaniel W.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 20.01.2022
• Subjects: acyl coenzyme A; Acyl Coenzyme A - metabolism; acyl-CoA; Animals; branched chain amino acids; Cell Compartmentation; Cell Differentiation; Cell Nucleus - metabolism; Chromatography, Liquid; cytosol; Cytosol - metabolism; Energy Metabolism; Epigenesis, Genetic; epigenome; fractionation; Hep G2 Cells; histone; histones; Histones - metabolism; Humans; internal standard; Isoleucine; isotope labeling; liquid chromatography; mass spectrometry; matrix effects; metabolism; metabolites; Metabolome; Metabolomics; Mice; mitochondria; Mitochondria - metabolism; nucleus; nutrient availability; oxygen; Oxygen - metabolism; propionylation; Protein Processing, Post-Translational; Spectrometry, Mass, Electrospray Ionization; stable isotopes; subcellular; thioesters; propionylation; acyl-CoA; internal standard; metabolomics; mitochondria; subcellular; matrix effects; nucleus; branched chain amino acids; histone; isoleucine
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2021.11.006

Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome. [Display omitted] •SILEC-SF allows metabolite quantitation in the subcellular compartments by LC-MS•Acyl-coenzyme A thioesters from mitochondria, cytosol, and nucleus were measured•Nuclear profile was distinct from other compartments and enriched in propionyl-CoA•Isoleucine is a major source of nuclear propionyl-CoA and histone propionylation Trefely et al., developed and applied a technique termed SILEC-SF to measure acyl-coenzyme A thioesters in subcellular compartments by liquid chromatography-mass spectrometry. SILEC-SF was applied to different cell and tissue types to examine the compartmentalized responses across the cytosol, mitochondria, and nucleus to oxygen tension, cellular differentiation, and nutrient availability.