SIRT3 mediates multi-tissue coupling for metabolic fuel switching

Cell Metabolism

Volumn 21, Issue 4, 2015, Pages 637-646

  Dittenhafer Reed, Kristin E ^a   Richards, Alicia L ^b   Fan, Jing ^a   Smallegan, Michael J ^a   Fotuhi Siahpirani, Alireza ^c   Kemmerer, Zachary A ^b   Prolla, Tomas A ^b   Roy, Sushmita ^a   Coon, Joshua J ^a,b   Denu, John M ^a  

^a UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; KETONE BODY; MITOCHONDRIAL PROTEIN; PROTEOME; SIRTUIN 3; SIRT3 PROTEIN, MOUSE;

ACETYLATION; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; BRAIN MITOCHONDRION; HEART MITOCHONDRION; HOMEOSTASIS; LIVER MITOCHONDRION; METABOLIC REGULATION; MOUSE; MUSCLE MITOCHONDRION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; ANIMAL; BIOLOGY; BRAIN; GENE EXPRESSION REGULATION; GENETICS; KIDNEY; KNOCKOUT MOUSE; LIVER; METABOLISM; MITOCHONDRION; PHYSIOLOGY;

MUS;

ACETYLATION; ANIMALS; BRAIN; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HOMEOSTASIS; KETONE BODIES; KIDNEY; LIVER; METABOLIC NETWORKS AND PATHWAYS; MICE; MICE, KNOCKOUT; MITOCHONDRIA; PROTEOMICS; SIRTUIN 3;

EID: 84928386194     PISSN: 15504131     EISSN: 19327420     Source Type: Journal    
DOI: 10.1016/j.cmet.2015.03.007     Document Type: Article

References (41)

1. J.B. Allred, and D.G. Guy Determination of coenzyme A and acetyl CoA in tissue extracts Anal. Biochem. 29 1969 293 299
2. M. Bauer, A.C. Hamm, M. Bonaus, A. Jacob, J. Jaekel, H. Schorle, M.J. Pankratz, and J.D. Katzenberger Starvation response in mouse liver shows strong correlation with life-span-prolonging processes Physiol. Genomics 17 2004 230 244
3. L. Cai, B.M. Sutter, B. Li, and B.P. Tu Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes Mol. Cell 42 2011 426 437
4. G. Cederblad, J.I. Carlin, D. Constantin-Teodosiu, P. Harper, and E. Hultman Radioisotopic assays of CoASH and carnitine and their acetylated forms in human skeletal muscle Anal. Biochem. 185 1990 274 278
5. C. Choudhary, C. Kumar, F. Gnad, M.L. Nielsen, M. Rehman, T.C. Walther, J.V. Olsen, and M. Mann Lysine acetylation targets protein complexes and co-regulates major cellular functions Science 325 2009 834 840
6. M.J. de Hoon, S. Imoto, J. Nolan, and S. Miyano Open source clustering software Bioinformatics 20 2004 1453 1454
7. P.B. Garland, D. Shepherd, and D.W. Yates Steady-state concentrations of coenzyme A, acetyl-coenzyme A and long-chain fatty acyl-coenzyme A in rat-liver mitochondria oxidizing palmitate Biochem. J. 97 1965 587 594
8. W.C. Hallows, W. Yu, B.C. Smith, M.K. Devries, J.J. Ellinger, S. Someya, M.R. Shortreed, T. Prolla, J.L. Markley, and L.M. Smith Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction Mol. Cell 41 2011 139 149
9. T. Hastie, R. Tibshirani, and J.H. Friedman The Elements of Statistical Learning: Data Mining, Inference, and Prediction Second Edition 2009 Springer
10. W. He, J.C. Newman, M.Z. Wang, L. Ho, and E. Verdin Mitochondrial sirtuins: regulators of protein acylation and metabolism Trends Endocrinol. Metab. 23 2012 467 476
11. A.S. Hebert, K.E. Dittenhafer-Reed, W. Yu, D.J. Bailey, E.S. Selen, M.D. Boersma, J.J. Carson, M. Tonelli, A.J. Balloon, and A.J. Higbee Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome Mol. Cell 49 2013 186 199
12. M.D. Hirschey, T. Shimazu, E. Goetzman, E. Jing, B. Schwer, D.B. Lombard, C.A. Grueter, C. Harris, S. Biddinger, and O.R. Ilkayeva SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation Nature 464 2010 121 125
13. W. Huang, B.T. Sherman, and R.A. Lempicki Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Nucleic Acids Res. 37 2009 1 13
14. W. Huang, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 4 2009 44 57
15. R.A. Irizarry, C. Wang, Y. Zhou, and T.P. Speed Gene set enrichment analysis made simple Stat. Methods Med. Res. 18 2009 565 575
16. T. Iwahara, R. Bonasio, V. Narendra, and D. Reinberg SIRT3 functions in the nucleus in the control of stress-related gene expression Mol. Cell. Biol. 32 2012 5022 5034
17. E. Jing, B.T. O'Neill, M.J. Rardin, A. Kleinridders, O.R. Ilkeyeva, S. Ussar, J.R. Bain, K.Y. Lee, E.M. Verdin, and C.B. Newgard Sirt3 regulates metabolic flexibility of skeletal muscle through reversible enzymatic deacetylation Diabetes 62 2013 3404 3417
18. M. Kanehisa, and S. Goto KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28 2000 27 30
19. S.C. Kim, R. Sprung, Y. Chen, Y. Xu, H. Ball, J. Pei, T. Cheng, Y. Kho, H. Xiao, and L. Xiao Substrate and functional diversity of lysine acetylation revealed by a proteomics survey Mol. Cell 23 2006 607 618
20. D.B. Lombard, F.W. Alt, H.L. Cheng, J. Bunkenborg, R.S. Streeper, R. Mostoslavsky, J. Kim, G. Yancopoulos, D. Valenzuela, and A. Murphy Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation Mol. Cell. Biol. 27 2007 8807 8814
21. W. Lu, M.F. Clasquin, E. Melamud, D. Amador-Noguez, A.A. Caudy, and J.D. Rabinowitz Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer Anal. Chem. 82 2010 3212 3221
22. A. Lundby, K. Lage, B.T. Weinert, D.B. Bekker-Jensen, A. Secher, T. Skovgaard, C.D. Kelstrup, A. Dmytriyev, C. Choudhary, C. Lundby, and J.V. Olsen Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns Cell Rep. 2 2012 419 431
23. D. Merico, R. Isserlin, O. Stueker, A. Emili, and G.D. Bader Enrichment map: a network-based method for gene-set enrichment visualization and interpretation PLoS ONE 5 2010 e13984
24. H. Neumann, S.M. Hancock, R. Buning, A. Routh, L. Chapman, J. Somers, T. Owen-Hughes, J. van Noort, D. Rhodes, and J.W. Chin A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation Mol. Cell 36 2009 153 163
25. J.C. Newman, W. He, and E. Verdin Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease J. Biol. Chem. 287 2012 42436 42443
26. Nguyen, N.; and Caruana, R. (2007). Consensus Clusterings. Seventh IEEE International Conference on Data Mining (ICDM '07).
27. D.J. Pagliarini, S.E. Calvo, B. Chang, S.A. Sheth, S.B. Vafai, S.E. Ong, G.A. Walford, C. Sugiana, A. Boneh, and W.K. Chen A mitochondrial protein compendium elucidates complex I disease biology Cell 134 2008 112 123
28. W.K. Paik, D. Pearson, H.W. Lee, and S. Kim Nonenzymatic acetylation of histones with acetyl-CoA Biochim. Biophys. Acta 213 1970 513 522
29. A.A. Palladino, J. Chen, S. Kallish, C.A. Stanley, and M.J. Bennett Measurement of tissue acyl-CoAs using flow-injection tandem mass spectrometry: acyl-CoA profiles in short-chain fatty acid oxidation defects Mol. Genet. Metab. 107 2012 679 683
30. A.C. Peterson, J.D. Russell, D.J. Bailey, M.S. Westphall, and J.J. Coon Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics Mol. Cell. Proteomics 11 2012 1475 1488
31. M.J. Rardin, J.C. Newman, J.M. Held, M.P. Cusack, D.J. Sorensen, B. Li, B. Schilling, S.D. Mooney, C.R. Kahn, E. Verdin, and B.W. Gibson Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways Proc. Natl. Acad. Sci. USA 110 2013 6601 6606
32. A.J. Saldanha Java Treeview - extensible visualization of microarray data Bioinformatics 20 2004 3246 3248
33. I. Scott, B.R. Webster, C.K. Chan, J.U. Okonkwo, K. Han, and M.N. Sack GCN5-like protein 1 (GCN5L1) controls mitochondrial content through coordinated regulation of mitochondrial biogenesis and mitophagy J. Biol. Chem. 289 2014 2864 2872
34. T. Shi, F. Wang, E. Stieren, and Q. Tong SIRT3, a mitochondrial sirtuin deacetylase, regulates mitochondrial function and thermogenesis in brown adipocytes J. Biol. Chem. 280 2005 13560 13567
35. T. Shimazu, M.D. Hirschey, L. Hua, K.E. Dittenhafer-Reed, B. Schwer, D.B. Lombard, Y. Li, J. Bunkenborg, F.W. Alt, and J.M. Denu SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production Cell Metab. 12 2010 654 661
36. S. Someya, W. Yu, W.C. Hallows, J. Xu, J.M. Vann, C. Leeuwenburgh, M. Tanokura, J.M. Denu, and T.A. Prolla Sirt3 mediates reduction of oxidative damage and prevention of age-related hearing loss under caloric restriction Cell 143 2010 802 812
37. A.J. Still, B.J. Floyd, A.S. Hebert, C.A. Bingman, J.J. Carson, D.R. Gunderson, B.K. Dolan, P.A. Grimsrud, K.E. Dittenhafer-Reed, and D.S. Stapleton Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation J. Biol. Chem. 288 2013 26209 26219
38. M.H. Stipanuk, and M.A. Caudill Biochemical, Physiological, and Molecular Aspects of Human Nutrition Third Edition 2013 Elsevier/Saunders
39. A. Suryawan, J.W. Hawes, R.A. Harris, Y. Shimomura, A.E. Jenkins, and S.M. Hutson A molecular model of human branched-chain amino acid metabolism Am. J. Clin. Nutr. 68 1998 72 81
40. K.G. Tanner, M.R. Langer, Y. Kim, and J.M. Denu Kinetic mechanism of the histone acetyltransferase GCN5 from yeast J. Biol. Chem. 275 2000 22048 22055
41. C.D. Wenger, D.H. Phanstiel, M.V. Lee, D.J. Bailey, and J.J. Coon COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA Proteomics 11 2011 1064 1074