350
Views
13
CrossRef citations to date
0
Altmetric
Reviews

An integrated perspective and functional impact of the mitochondrial acetylome

, , , &

References

  • Warda M, Kim HK, Kim N, et al. A matter of life, death and diseases: mitochondria from a proteomic perspective. Expert Rev Proteomics 2013;10(1):97-111
  • Logan DC. The mitochondrial compartment. J Exp Bot 2006;57(6):1225-43
  • Meisinger C, Sickmann A, Pfanner N. The mitochondrial proteome: from inventory to function. Cell 2008;134(1):22-4
  • Newman JC, He W, Verdin E. Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 2012;287(51):42436-43
  • Padrao AI, Vitorino R, Duarte JA, et al. Unraveling the phosphoproteome dynamics in mammal mitochondria from a network perspective. J Proteome Res 2013;12(10):4257-67
  • Koc EC, Koc H. Regulation of mammalian mitochondrial translation by post-translational modifications. Biochim Biophys Acta 2012;1819(9-10):1055-66
  • Shao J, Xu D, Hu L, et al. Systematic analysis of human lysine acetylation proteins and accurate prediction of human lysine acetylation through bi-relative adapted binomial score Bayes feature representation. Mol Biosyst 2012;8(11):2964-73
  • Glozak MA, Sengupta N, Zhang X, Seto E. Acetylation and deacetylation of non-histone proteins. Gene 2005;363:15-23
  • Zhu Y, Park SH, Ozden O, et al. Exploring the electrostatic repulsion model in the role of Sirt3 in directing MnSOD acetylation status and enzymatic activity. Free Radic Biol Med 2012;53(4):828-33
  • Phillips DM. The presence of acetyl groups of histones. Biochem J 1963;87:258-63
  • Allfrey VG, Faulkner R, Mirsky AE. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA 1964;51:786-94
  • Rardin MJ, Newman JC, Held JM, et al. Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways. Proc Natl Acad Sci USA 2013;110(16):6601-6
  • Hebert AS, Dittenhafer-Reed KE, Yu W, et al. Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell 2013;49(1):186-99
  • Kouzarides T. Acetylation: a regulatory modification to rival phosphorylation? Embo J 2000;19(6):1176-9
  • Fritz KS, Galligan JJ, Hirschey MD, et al. Mitochondrial acetylome analysis in a mouse model of alcohol-induced liver injury utilizing SIRT3 knockout mice. J Proteome Res 2012;11(3):1633-43
  • Kim SC, Sprung R, Chen Y, et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol cell 2006;23(4):607-18
  • Anderson KA, Hirschey MD. Mitochondrial protein acetylation regulates metabolism. Essays Biochem 2012;52:23-35
  • Ghanta S, Grossmann RE, Brenner C. Mitochondrial protein acetylation as a cell-intrinsic, evolutionary driver of fat storage: chemical and metabolic logic of acetyl-lysine modifications. Crit Rev Biochem Mol Biol 2013;48(6):561-74
  • Guan KL, Xiong Y. Regulation of intermediary metabolism by protein acetylation. Trends Biochem Sci 2011;36(2):108-16
  • Close P, Creppe C, Gillard M, et al. The emerging role of lysine acetylation of non-nuclear proteins. Cell Mol Life Sci 2010;67(8):1255-64
  • Hirschey MD, Shimazu T, Jing E, et al. SIRT3 deficiency and mitochondrial protein hyperacetylation accelerate the development of the metabolic syndrome. Mol cell 2011;44(2):177-90
  • Sol EM, Wagner SA, Weinert BT, et al. Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3. PLoS One 2012;7(12):e50545
  • Schwer B, Eckersdorff M, Li Y, et al. Calorie restriction alters mitochondrial protein acetylation. Aging Cell 2009;8(5):604-6
  • Ahn B-H, Kim H-S, Song S, et al. A role for the mitochondrial deacetylase Sirt3 in regulating energy homeostasis. Proc Natl Acad Sci USA 2008;105(38):14447-52
  • Cimen H, Han M-J, Yang Y, et al. Regulation of Succinate Dehydrogenase Activity by SIRT3 in Mammalian Mitochondria. Biochemistry 2010;49(2):304-11
  • Zhang J, Lin A, Powers J, et al. Mitochondrial proteome design: from molecular identity to pathophysiological regulation. J Gen Physiol 2012;139(6):395-406
  • Hirschey MD, Shimazu T, Huang JY, Verdin E. Acetylation of mitochondrial proteins. In: Allison WS, Murphy AN, editors. Mitochondrial function, part B: mitochondrial protein kinases, protein phosphatases and mitochondrial diseases. Elsevier; UK: 2009. p. 137-47
  • Silva AMN, Vitorino R, Domingues MRM, et al. Post-translational Modifications and Mass Spectrometry Detection. Free Radic Biol Med 2013;65:925-41
  • Hirschey MD, Shimazu T, Goetzman E, et al. SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation. Nature 2010;464(7285):121-U137
  • Grillon JM, Johnson KR, Kotlo K, Danziger RS. Non-histone lysine acetylated proteins in heart failure. Biochim Biophys Acta 2012;1822(4):607-14
  • Lundby A, Lage K, Weinert BT, et al. Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Rep 2012;2(2):419-31
  • Wasinger VC, Zeng M, Yau Y. Current status and advances in quantitative proteomic mass spectrometry. Int J Proteomics 2013;2013:180605
  • Schilling B, Rardin MJ, MacLean BX, et al. Platform-independent and Label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation. Mol Cell Proteomics 2012;11(5):202-14
  • Still AJ, Floyd BJ, Hebert AS, et al. Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. J Biol Chem 2013;288(36):26209-19
  • Jiao X, Sherman BT, Huang da W, et al. DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics 2012;28(13):1805-6
  • Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucl Acids Res 2013;41(Database issue):D377-86
  • Croft D, O’Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucl Acids Res 2011;39(Database issue):D691-7
  • Chou MF, Schwartz D. Biological sequence motif discovery using motif-x. In: Baxevanis AD, et al. Current protocols in bioinformatics/editoral board, Chapter 13, Unit 13. John Wiley & Sons; NY, USA: 2011. p. 15-24
  • Wang L, Du Y, Lu M, Li T. ASEB: a web server for KAT-specific acetylation site prediction. Nucl acids Res 2012;40(Web Server issue):W376-9
  • Xue Y, Ren J, Gao X, et al. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Mol Cell Proteomics 2008;7(9):1598-608
  • Sigrist CJA, Cerutti L, de Castro E, et al. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 2010;38:D161-6
  • Kincaid B, Bossy-Wetzel E. Forever young: SIRT3 a shield against mitochondrial meltdown, aging, and neurodegeneration. Front Aging Neurosci 2013;5:48
  • Masri S, Patel VR, Eckel-Mahan KL, et al. Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci USA 2013;110(9):3339-44
  • Jiang Y, Wang X. Comparative mitochondrial proteomics: perspective in human diseases. J Hematol Oncol 2012;5:11
  • Smith AC, Blackshaw JA, Robinson AJ. MitoMiner: a data warehouse for mitochondrial proteomics data. Nucl Acids Res 2012;40(Database issue):D1160-7
  • Elstner M, Andreoli C, Ahting U, et al. MitoP2: an integrative tool for the analysis of the mitochondrial proteome. Mol Biotechnol 2008;40(3):306-15
  • Pagliarini DJ, Calvo SE, Chang B, et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008;134(1):112-23
  • McDonald TG, Van Eyk JE. Mitochondrial proteomics. Undercover in the lipid bilayer. Basic Res Cardiol 2003;98(4):219-27
  • Deng N, Zhang J, Zong C, et al. Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria. Mol Cell Proteomics 2011;10(2):M110.000117
  • Pfam. Available from: http://pfam.sanger.ac.uk
  • Choudhary C, Kumar C, Gnad F, et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009;325(5942):834-40
  • Kendrick AA, Choudhury M, Rahman SM, et al. Fatty liver is associated with reduced SIRT3 activity and mitochondrial protein hyperacetylation. Biochem J 2011;433(3):505-14
  • Vadvalkar SS, Baily CN, Matsuzaki S, et al. Metabolic inflexibility and protein lysine acetylation in heart mitochondria of a chronic model of type 1 diabetes. Biochem J 2013;449(1):253-61
  • Yuan H, Marmorstein R. Histone acetyltransferases: rising ancient counterparts to protein kinases. Biopolymers 2013;99(2):98-111
  • Wagner GR, Payne RM. Widespread and enzyme-independent Nepsilon-acetylation and Nepsilon-succinylation of proteins in the chemical conditions of the mitochondrial matrix. J Biol Chem 2013;288(40):29036-45
  • Scott I, Webster BR, Li JH, Sack MN. Identification of a molecular component of the mitochondrial acetyltransferase programme: a novel role for GCN5L1. Biochem J 2012;443(3):655-61
  • Lombard DB, Alt FW, Cheng HL, et al. Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation. Mol cell Biol 2007;27(24):8807-14
  • Laurent G, German NJ, Saha AK, et al. SIRT4 coordinates the balance between lipid synthesis and catabolism by repressing malonyl CoA decarboxylase. Mol cell 2013;50(5):686-98
  • Nakagawa T, Lomb DJ, Haigis MC, Guarente L. SIRT5 Deacetylates carbamoyl phosphate synthetase 1 and regulates the urea cycle. Cell 2009;137(3):560-70
  • Nakagawa T, Guarente L. Urea cycle regulation by mitochondrial sirtuin, SIRT5. Aging (Albany NY) 2009;1(6):578-81
  • Hallows WC, Lee S, Denu JM. Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases. Proc Natl Acad Sci USA 2006;103(27):10230-5
  • Fujino T, Kondo J, Ishikawa M, et al. Acetyl-CoA synthetase 2, a mitochondrial matrix enzyme involved in the oxidation of acetate. J Biol Chem 2001;276(14):11420-6
  • Hallows WC, Yu W, Smith BC, et al. Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Mol Cell 2011;41(2):139-49
  • Bharathi SS, Zhang Y, Mohsen AW, et al. Sirtuin 3 (SIRT3) protein regulates long-chain acyl-CoA dehydrogenase by deacetylating conserved lysines near the active site. J Biol Chem 2013;288(47):33837-47
  • Shulga N, Wilson-Smith R, Pastorino JG. Sirtuin-3 deacetylation of cyclophilin D induces dissociation of hexokinase II from the mitochondria. J Cell Sci 2010;123(6):894-902
  • Qiu X, Brown K, Hirschey MD, et al. Calorie restriction reduces oxidative stress by SIRT3-mediated SOD2 activation. Cell Metab 2010;12(6):662-7
  • Chen Y, Zhang J, Lin Y, et al. Tumour suppressor SIRT3 deacetylates and activates manganese superoxide dismutase to scavenge ROS. EMBO Rep 2011;12(6):534-41
  • Tao R, Coleman MC, Pennington JD, et al. Sirt3-mediated deacetylation of evolutionarily conserved lysine 122 regulates MnSOD activity in response to stress. Mol cell 2010;40(6):893-904
  • Sundaresan NR, Gupta M, Kim G, et al. Sirt3 blocks the cardiac hypertrophic response by augmenting Foxo3a-dependent antioxidant defense mechanisms in mice. J Clin Investig 2009;119(9):2758-71
  • Jing EX, Emanuelli B, Hirschey MD, et al. Sirtuin-3 (Sirt3) regulates skeletal muscle metabolism and insulin signaling via altered mitochondrial oxidation and reactive oxygen species production. Proc Natl Acad Sci USA 2011;108(35):14608-13
  • Bao J, Scott I, Lu Z, et al. SIRT3 is regulated by nutrient excess and modulates hepatic susceptibility to lipotoxicity. Free Radic Biol Med 2010;49(7):1230-7
  • Wagner GR, Payne RM. Mitochondrial acetylation and diseases of aging. J Aging Res 2011;2011:234875
  • Tao R, Vassilopoulos A, Parisiadou L, et al. Regulation of MnSOD Enzymatic activity by Sirt3 connects the mitochondrial acetylome signaling networks to aging and carcinogenesis. Antioxid Redox Signal 2013. [Epub ahead of print]
  • Karamanlidis G, Lee CF, Garcia-Menendez L, et al. Mitochondrial complex I deficiency increases protein acetylation and accelerates heart failure. Cell Metab 2013;18(2):239-50
  • Benigni A, Corna D, Zoja C, et al. Disruption of the Ang II type 1 receptor promotes longevity in mice. J Clin Investig 2009;119(3):524-30
  • Lombard DB, Zwaans BM. SIRT3: as simple as it seems. Gerontology 2014;60(1):56-64
  • Bindea G, Galon J, Mlecnik B. CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics 2013;29(5):661-3
  • Franceschini A, Szklarczyk D, Frankild S, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucl Acids Res 2013;41(Database issue):D808-15

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.