SIRT3 mediates multi-tissue coupling for metabolic fuel switching.

SIRT3 is a member of the Sirtuin family of NAD(+)-dependent deacylases and plays a critical role in metabolic regulation. Organism-wide SIRT3 loss manifests in metabolic alterations; however, the coordinating role of SIRT3 among metabolically distinct tissues is unknown. Using multi-tissue quantitative proteomics comparing fasted wild-type mice to mice lacking SIRT3, innovative bioinformatic analysis, and biochemical validation, we provide a comprehensive view of mitochondrial acetylation and SIRT3 function. We find SIRT3 regulates the acetyl-proteome in core mitochondrial processes common to brain, heart, kidney, liver, and skeletal muscle, but differentially regulates metabolic pathways in fuel-producing and fuel-utilizing tissues. We propose an additional maintenance function for SIRT3 in liver and kidney where SIRT3 expression is elevated to reduce the acetate load on mitochondrial proteins. We provide evidence that SIRT3 impacts ketone body utilization in the brain and reveal a pivotal role for SIRT3 in the coordination between tissues required for metabolic homeostasis.

[1]  Rich Caruana,et al.  Consensus Clusterings , 2007, Seventh IEEE International Conference on Data Mining (ICDM 2007).

[2]  Eric Verdin,et al.  Mammalian Sir2 Homolog SIRT3 Regulates Global Mitochondrial Lysine Acetylation , 2007, Molecular and Cellular Biology.

[3]  Q. Tong,et al.  SIRT3, a Mitochondrial Sirtuin Deacetylase, Regulates Mitochondrial Function and Thermogenesis in Brown Adipocytes* , 2005, Journal of Biological Chemistry.

[4]  J. B. Allred,et al.  Determination of coenzyme A and acetyl CoA in tissue extracts. , 1969, Analytical biochemistry.

[5]  S. Carr,et al.  A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology , 2008, Cell.

[6]  Derek J. Bailey,et al.  COMPASS: A suite of pre‐ and post‐search proteomics software tools for OMSSA , 2011, Proteomics.

[7]  Sean D. Mooney,et al.  Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways , 2013, Proceedings of the National Academy of Sciences.

[8]  R. Harris,et al.  A molecular model of human branched-chain amino acid metabolism. , 1998, The American journal of clinical nutrition.

[9]  E. Verdin,et al.  Mitochondrial Protein Acylation and Intermediary Metabolism: Regulation by Sirtuins and Implications for Metabolic Disease* , 2012, The Journal of Biological Chemistry.

[10]  J. Denu,et al.  Kinetic Mechanism of the Histone Acetyltransferase GCN5 from Yeast* , 2000, The Journal of Biological Chemistry.

[11]  Daniel Amador-Noguez,et al.  Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. , 2010, Analytical chemistry.

[12]  Hubert Schorle,et al.  Starvation response in mouse liver shows strong correlation with life-span-prolonging processes. , 2004, Physiological genomics.

[13]  Derek J. Bailey,et al.  Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* , 2012, Molecular & Cellular Proteomics.

[14]  Lloyd M. Smith,et al.  Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. , 2011, Molecular cell.

[15]  I. Scott,et al.  GCN5-like Protein 1 (GCN5L1) Controls Mitochondrial Content through Coordinated Regulation of Mitochondrial Biogenesis and Mitophagy* , 2013, The Journal of Biological Chemistry.

[16]  Robert V Farese,et al.  SIRT 3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation , 2010 .

[17]  M. Westphall,et al.  Quantification of Mitochondrial Acetylation Dynamics Highlights Prominent Sites of Metabolic Regulation* , 2013, The Journal of Biological Chemistry.

[18]  M. Caudill,et al.  Comprar Biochemical, Physiological, and Molecular Aspects of Human Nutrition, 3rd Edition | Marie A. Caudill | 9781437709599 | Saunders , 2012 .

[19]  Matthew J. Rardin,et al.  Sirt3 Regulates Metabolic Flexibility of Skeletal Muscle Through Reversible Enzymatic Deacetylation , 2013, Diabetes.

[20]  D. Constantin-Teodosiu,et al.  Radioisotopic assays of CoASH and carnitine and their acetylated forms in human skeletal muscle. , 1990, Analytical biochemistry.

[21]  Dorte B. Bekker-Jensen,et al.  Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns , 2012, Cell reports.

[22]  Gary D Bader,et al.  Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation , 2010, PloS one.

[23]  P. Garland,et al.  Steady-state concentrations of coenzyme A, acetyl-coenzyme A and long-chain fatty acyl-coenzyme A in rat-liver mitochondria oxidizing palmitate. , 1965, The Biochemical journal.

[24]  Wei Yu,et al.  Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. , 2013, Molecular cell.

[25]  N. Grishin,et al.  Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. , 2006, Molecular cell.

[26]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[27]  F. Alt,et al.  SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. , 2010, Cell metabolism.

[28]  R. Eisenstein.  Biochemical, Physiological, and Molecular Aspects of Human Nutrition, 2nd Edition , 2006 .

[29]  D. Reinberg,et al.  SIRT3 Functions in the Nucleus in the Control of Stress-Related Gene Expression , 2012, Molecular and Cellular Biology.

[30]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[31]  H. W. Lee,et al.  Nonenzymatic acetylation of histones with acetyl-CoA. , 1970, Biochimica et biophysica acta.

[32]  Satoru Miyano,et al.  Open source clustering software , 2004 .

[33]  Eric Verdin,et al.  Mitochondrial sirtuins: regulators of protein acylation and metabolism , 2012, Trends in Endocrinology & Metabolism.

[34]  Bing Li,et al.  Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. , 2011, Molecular cell.

[35]  Wei Yu,et al.  Sirt3 Mediates Reduction of Oxidative Damage and Prevention of Age-Related Hearing Loss under Caloric Restriction , 2010, Cell.

[36]  J. Chin,et al.  A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histones Defines the Effects of H3 K56 Acetylation , 2009, Molecular cell.

[37]  Robert Tibshirani,et al.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd Edition , 2001, Springer Series in Statistics.

[38]  M. Mann,et al.  Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions , 2009, Science.

[39]  Rafael A Irizarry,et al.  Gene set enrichment analysis made simple , 2009, Statistical methods in medical research.

[40]  Klaus Nordhausen,et al.  The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition by Trevor Hastie, Robert Tibshirani, Jerome Friedman , 2009 .

[41]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[42]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[43]  C. Stanley,et al.  Measurement of tissue acyl-CoAs using flow-injection tandem mass spectrometry: acyl-CoA profiles in short-chain fatty acid oxidation defects. , 2012, Molecular genetics and metabolism.