Abstract
The sirtuins are NAD+-dependent, multifunctional lysine deacylases that play key roles in cellular homeostasis. They are increasingly being found to target a variety of substrates including acetyl-, butyryl-, malonyl-, and succinyl-lysines. Early assays for measuring sirtuin activity in vitro were criticized for their use of fluorophores on the peptide substrates used, which may alter the results obtained and not be representative of the in vivo situation. We describe a new protocol for the measurement of sirtuin activity by detecting the production of nicotinamide (NAM). The assay is amenable to any substrate and any modification removed by sirtuins. The assay may also be used to measure glycohydrolase (e.g., CD38) and ADP-ribosyltransferase activity (e.g., mARTs and PARPs).
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References
North BJ, Verdin E (2004) Sirtuins: Sir2-related NAD-dependent protein deacetylases. Genome Biol 5(5):224. doi:10.1186/gb-2004-5-5-224 gb-2004-5-5-224 [pii]
Gottlieb S, Esposito RE (1989) A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56(5):771–776. doi:0092-8674(89)90681-8 [pii]
Gotta M, Strahl-Bolsinger S, Renauld H, Laroche T, Kennedy BK, Grunstein M, Gasser SM (1997) Localization of Sir2p: the nucleolus as a compartment for silent information regulators. EMBO J 16(11):3243–3255. doi:10.1093/emboj/16.11.3243
Kaeberlein M, McVey M, Guarente L (1999) The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev 13(19):2570–2580
Das C, Lucia MS, Hansen KC, Tyler JK (2009) CBP/p300-mediated acetylation of histone H3 on lysine 56. Nature 459(7243):113–117. doi:nature07861 [pii] 10.1038/nature07861
Cohen HY, Miller C, Bitterman KJ, Wall NR, Hekking B, Kessler B, Howitz KT, Gorospe M, de Cabo R, Sinclair DA (2004) Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase. Science 305(5682):390–392. doi:10.1126/science.1099196 1099196
Rodgers JT, Lerin C, Gerhart-Hines Z, Puigserver P (2008) Metabolic adaptations through the PGC-1 alpha and SIRT1 pathways. FEBS Lett 582(1):46–53. doi:S0014-5793(07)01178-7 [pii] 10.1016/j.febslet.2007.11.034
Gerhart-Hines Z, Rodgers JT, Bare O, Lerin C, Kim SH, Mostoslavsky R, Alt FW, Wu Z, Puigserver P (2007) Metabolic control of muscle mitochondrial function and fatty acid oxidation through SIRT1/PGC-1alpha. EMBO J 26(7):1913–1923. doi:10.1038/sj.emboj.7601633
Bernier M, Paul RK, Martin-Montalvo A, Scheibye-Knudsen M, Song S, He HJ, Armour SM, Hubbard BP, Bohr VA, Wang L, Zong Y, Sinclair DA, de Cabo R (2011) Negative regulation of STAT3 protein-mediated cellular respiration by SIRT1 protein. J Biol Chem 286(22):19270–19279. doi:M110.200311 [pii] 10.1074/jbc.M110.200311
Dittenhafer-Reed KE, Feldman JL, Denu JM (2011) Catalysis and mechanistic insights into sirtuin activation. Chembiochem 12(2):281–289. doi:10.1002/cbic.201000434
Sauve AA, Celic I, Avalos J, Deng H, Boeke JD, Schramm VL (2001) Chemistry of gene silencing: the mechanism of NAD+−dependent deacetylation reactions. Biochemistry 40(51):15456–15463. doi:bi011858j [pii]
Smith BC, Denu JM (2006) Sir2 protein deacetylases: evidence for chemical intermediates and functions of a conserved histidine. Biochemistry 45(1):272–282. doi:10.1021/bi052014t
Jackson MD, Schmidt MT, Oppenheimer NJ, Denu JM (2003) Mechanism of nicotinamide inhibition and transglycosidation by Sir2 histone/protein deacetylases. J Biol Chem 278(51):50985–50998. doi:10.1074/jbc.M306552200M306552200 [pii]
Smith BC, Denu JM (2007) Mechanism-based inhibition of Sir2 deacetylases by thioacetyl-lysine peptide. Biochemistry 46(50):14478–14486. doi:10.1021/bi7013294
Sauve AA, Wolberger C, Schramm VL, Boeke JD (2006) The biochemistry of sirtuins. Annu Rev Biochem 75:435–465. doi:10.1146/annurev.biochem.74.082803.133500
Jackson MD, Denu JM (2002) Structural identification of 2′- and 3′-O-acetyl-ADP-ribose as novel metabolites derived from the Sir2 family of beta -NAD+−dependent histone/protein deacetylases. J Biol Chem 277(21):18535–18544. doi:10.1074/jbc.M200671200 M200671200 [pii]
Borra MT, Langer MR, Slama JT, Denu JM (2004) Substrate specificity and kinetic mechanism of the Sir2 family of NAD+−dependent histone/protein deacetylases. Biochemistry 43(30):9877–9887. doi:10.1021/bi049592e
Smith BC, Denu JM (2007) Acetyl-lysine analog peptides as mechanistic probes of protein deacetylases. J Biol Chem 282(51):37256–37265. doi:M707878200 [pii] 10.1074/jbc.M707878200
Garrity J, Gardner JG, Hawse W, Wolberger C, Escalante-Semerena JC (2007) N-lysine propionylation controls the activity of propionyl-CoA synthetase. J Biol Chem 282(41):30239–30245. doi:M704409200 [pii] 10.1074/jbc.M704409200
Du J, Zhou Y, Su X, Yu JJ, Khan S, Jiang H, Kim J, Woo J, Kim JH, Choi BH, He B, Chen W, Zhang S, Cerione RA, Auwerx J, Hao Q, Lin H (2011) Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science 334(6057):806–809. doi:10.1126/science.1207861 334/6057/806 [pii]
Kowieski TM, Lee S, Denu JM (2008) Acetylation-dependent ADP-ribosylation by Trypanosoma brucei Sir2. J Biol Chem 283(9):5317–5326. doi:M707613200 [pii] 10.1074/jbc.M707613200
Hawse WF, Wolberger C (2009) Structure-based mechanism of ADP-ribosylation by sirtuins. J Biol Chem 284(48):33654–33661. doi:M109.024521 [pii] 10.1074/jbc.M109.024521
Kaeberlein M, McDonagh T, Heltweg B, Hixon J, Westman EA, Caldwell SD, Napper A, Curtis R, DiStefano PS, Fields S, Bedalov A, Kennedy BK (2005) Substrate-specific activation of sirtuins by resveratrol. J Biol Chem 280(17):17038–17045. doi:M500655200 [pii] 10.1074/jbc.M500655200
Howitz KT, Bitterman KJ, Cohen HY, Lamming DW, Lavu S, Wood JG, Zipkin RE, Chung P, Kisielewski A, Zhang LL, Scherer B, Sinclair DA (2003) Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature 425(6954):191–196. doi:10.1038/nature01960 nature01960 [pii]
Borra MT, Smith BC, Denu JM (2005) Mechanism of human SIRT1 activation by resveratrol. J Biol Chem 280(17):17187–17195. doi:M501250200 [pii] 10.1074/jbc.M501250200
Fan Y, Hense M, Ludewig R, Weisgerber C, Scriba GK (2011) Capillary electrophoresis-based sirtuin assay using non-peptide substrates. J Pharm Biomed Anal 54(4):772–778. doi:S0731-7085(10)00605-9 [pii] 10.1016/j.jpba.2010.10.010
Feng Y, Wu J, Chen L, Luo C, Shen X, Chen K, Jiang H, Liu D (2009) A fluorometric assay of SIRT1 deacetylation activity through quantification of nicotinamide adenine dinucleotide. Anal Biochem 395(2):205–210. doi:S0003-2697(09)00559-4 [pii] 10.1016/j.ab.2009.08.011
Milne JC, Lambert PD, Schenk S, Carney DP, Smith JJ, Gagne DJ, Jin L, Boss O, Perni RB, Vu CB, Bemis JE, Xie R, Disch JS, Ng PY, Nunes JJ, Lynch AV, Yang H, Galonek H, Israelian K, Choy W, Iffland A, Lavu S, Medvedik O, Sinclair DA, Olefsky JM, Jirousek MR, Elliott PJ, Westphal CH (2007) Small molecule activators of SIRT1 as therapeutics for the treatment of type 2 diabetes. Nature 450(7170):712–716. doi:nature06261 [pii] 10.1038/nature06261
Hubbard BP, Gomes AP, Dai H, Li J, Case AW, Considine T, Riera TV, Lee JE, E SY, Lamming DW, Pentelute BL, Schuman ER, Stevens LA, Ling AJ, Armour SM, Michan S, Zhao H, Jiang Y, Sweitzer SM, Blum CA, Disch JS, Ng PY, Howitz KT, Rolo AP, Hamuro Y, Moss J, Perni RB, Ellis JL, Vlasuk GP, Sinclair DA (2013) Evidence for a common mechanism of SIRT1 regulation by allosteric activators. Science 339(6124):1216–1219. doi:10.1126/science.1231097 339/6124/1216 [pii]
Smith BC, Hallows WC, Denu JM (2009) A continuous microplate assay for sirtuins and nicotinamide-producing enzymes. Anal Biochem 394(1):101–109. doi:S0003-2697(09)00493-X [pii] 10.1016/j.ab.2009.07.019
Ghislain M, Talla E, Francois JM (2002) Identification and functional analysis of the Saccharomyces cerevisiae nicotinamidase gene, PNC1. Yeast 19(3):215–224. doi:10.1002/yea.810 [pii] 10.1002/yea.810
Mondzac A, Ehrlich GE, Seegmiller JE (1965) An enzymatic determination of ammonia in biological fluids. J Lab Clin Med 66(3):526–531
Sugawara K, Oyama F (1981) Fluorogenic reaction and specific microdetermination of ammonia. J Biochem 89(3):771–774
Nishina H, Inageda K, Takahashi K, Hoshino S, Ikeda K, Katada T (1994) Cell surface antigen CD38 identified as ecto-enzyme of NAD glycohydrolase has hyaluronate-binding activity. Biochem Biophys Res Commun 203(2):1318–1323. doi:S0006-291X(84)72326-6 [pii] 10.1006/bbrc.1994.2326
Burkle A (2005) Poly(ADP-ribose). The most elaborate metabolite of NAD+. FEBS J 272(18):4576–4589. doi:EJB4864 [pii] 10.1111/j.1742-4658.2005.04864.x
Schneider B, Xu YW, Janin J, Veron M, Deville-Bonne D (1998) 3′-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity. J Biol Chem 273(44):28773–28778
Wood JG, Rogina B, Lavu S, Howitz K, Helfand SL, Tatar M, Sinclair D (2004) Sirtuin activators mimic caloric restriction and delay ageing in metazoans. Nature 430(7000):686–689. doi:10.1038/nature02789nature02789 [pii]
Acknowledgements
This work was supported by an NSERC PGS-D Fellowship to B.P.H., the Paul F. Glenn Foundation for Medical Research, the United Mitochondrial Disease Foundation, The Juvenile Diabetes Research Foundation, and NIA/NIH grants to D.A.S. B.P.H. and D.A.S. are inventors on a patent licensed to Millipore. D.A.S. is a consultant to GlaxoSmithKline.
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Hubbard, B.P., Sinclair, D.A. (2013). Measurement of Sirtuin Enzyme Activity Using a Substrate-Agnostic Fluorometric Nicotinamide Assay. In: Hirschey, M. (eds) Sirtuins. Methods in Molecular Biology, vol 1077. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-637-5_11
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DOI: https://doi.org/10.1007/978-1-62703-637-5_11
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