SIRT6 protein deacetylase interacts with MYH DNA glycosylase, APE1 endonuclease, and Rad9–Rad1–Hus1 checkpoint clamp

BMC Molecular Biology

A-Lien Lu³  Li Lan⁷  Satoshi Nakajima⁷  Michal Zalzman⁵  Xin Guan⁶  Austin Yan⁶  Amrita Madabushi¹  Guoli Shi⁴  Ying Gao²  Jin Jin⁶  Bor-Jang Hwang⁶ 

[1] Department of Natural and Physical Sciences, Life Sciences Institute, Baltimore City Community College, 801 West Baltimore Street, Baltimore 21201, MD, USA;School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China;Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, 108 North Greene Street, Baltimore 21201, MD, USA;University of Maryland School of Nursing, 655 West Lombard Street, Baltimore 21201, MD, USA;Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, 16 South Eutaw Street, Baltimore 21201, MD, USA;Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore 21201, MD, USA;Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh 15219, PA, USA

关键词: Protein–protein interaction;    Telomeres;    Rad9/Rad1/Hus1;    Checkpoint clamp;    APE1;    MutY homolog;    Sirtuin 6 (SIRT6);    DNA repair;   

Others  :  1211809
DOI  :  10.1186/s12867-015-0041-9

 received in 2015-01-05, accepted in 2015-05-29,  发布年份 2015

【 摘 要 】

Background

SIRT6, a member of the NAD⁺-dependent histone/protein deacetylase family, regulates genomic stability, metabolism, and lifespan. MYH glycosylase and APE1 are two base excision repair (BER) enzymes involved in mutation avoidance from oxidative DNA damage. Rad9–Rad1–Hus1 (9–1–1) checkpoint clamp promotes cell cycle checkpoint signaling and DNA repair. BER is coordinated with the checkpoint machinery and requires chromatin remodeling for efficient repair. SIRT6 is involved in DNA double-strand break repair and has been implicated in BER. Here we investigate the direct physical and functional interactions between SIRT6 and BER enzymes.

Results

We show that SIRT6 interacts with and stimulates MYH glycosylase and APE1. In addition, SIRT6 interacts with the 9-1-1 checkpoint clamp. These interactions are enhanced following oxidative stress. The interdomain connector of MYH is important for interactions with SIRT6, APE1, and 9–1–1. Mutagenesis studies indicate that SIRT6, APE1, and Hus1 bind overlapping but different sequence motifs on MYH. However, there is no competition of APE1, Hus1, or SIRT6 binding to MYH. Rather, one MYH partner enhances the association of the other two partners to MYH. Moreover, APE1 and Hus1 act together to stabilize the MYH/SIRT6 complex. Within human cells, MYH and SIRT6 are efficiently recruited to confined oxidative DNA damage sites within transcriptionally active chromatin, but not within repressive chromatin. In addition, Myh foci induced by oxidative stress and Sirt6 depletion are frequently localized on mouse telomeres.

Conclusions

Although SIRT6, APE1, and 9-1-1 bind to the interdomain connector of MYH, they do not compete for MYH association. Our findings indicate that SIRT6 forms a complex with MYH, APE1, and 9-1-1 to maintain genomic and telomeric integrity in mammalian cells.

【 授权许可】

   
2015 Hwang et al.

【 图 表 】

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【 参考文献 】

• [1]Oikawa S, Kawanishi S. Site-specific DNA damage at GGG sequence by oxidative stress may accelerate telomere shortening. FEBS Lett. 1999; 453:365-368.
• [2]von Zglinicki T. Oxidative stress shortens telomeres. Trends Biochem Sci. 2002; 27:339-344.
• [3]Tchou J, Grollman AP. Repair of DNA containing the oxidatively-damaged base 8-hydroxyguanine. Mutat Res. 1993; 299:277-287.
• [4]Krokan HE, Nilsen H, Skorpen F, Otterlei M, Slupphaug G. Base excision repair of DNA in mammalian cells. FEBS Lett. 2000; 476:73-77.
• [5]Demple B, Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem. 1994; 63:915-948.
• [6]David SS, O’Shea VL, Kundu S. Base-excision repair of oxidative DNA damage. Nature. 2007; 447:941-950.
• [7]Lu A-L, Bai H, Shi G, Chang D-Y. MutY and MutY homologs (MYH) in genome maintenance. Front Biosci. 2006; 11:3062-3080.
• [8]Markkanen E, Dorn J, Hubscher U. MUTYH DNA glycosylase: the rationale for removing undamaged bases from the DNA. Front Genet. 2013; 4:18.
• [9]Al Tassan N, Chmiel NH, Maynard J, Fleming N, Livingston AL, Williams GT et al.. Inherited variants of MYH associated with somatic G:C to T:A mutations in colorectal tumors. Nat Genet. 2002; 30:227-232.
• [10]Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem. 2004; 73:39-85.
• [11]Luncsford PJ, Chang DY, Shi G, Bernstein J, Madabushi A, Patterson DN et al.. A structural hinge in eukaryotic MutY homologues mediates catalytic activity and Rad9-Rad1-Hus1 checkpoint complex interactions. J Mol Biol. 2010; 403:351-370.
• [12]Parker A, Gu Y, Mahoney W, Lee S-H, Singh KK, Lu A-L. Human homolog of the MutY protein (hMYH) physically interacts with protein involved in long-patch DNA base excision repair. J Biol Chem. 2001; 276:5547-5555.
• [13]Shi G, Chang D-Y, Cheng CC, Guan X, Venclovas C, Lu A-L. Physical and functional interactions between MutY homolog (MYH) and checkpoint proteins Rad9-Rad1-Hus1. Biochem J. 2006; 400:53-62.
• [14]Wilson DM, Thompson LH. Life without DNA repair. Proc Natl Acad Sci USA. 1997; 94:12754-12757.
• [15]Abbotts R, Madhusudan S. Human AP endonuclease 1 (APE1): from mechanistic insights to druggable target in cancer. Cancer Treat Rev. 2010; 36:425-435.
• [16]Demple B, Sung JS. Molecular and biological roles of Ape1 protein in mammalian base excision repair. DNA Repair (Amst). 2005; 4:1442-1449.
• [17]Madlener S, Strobel T, Vose S, Saydam O, Price BD, Demple B et al.. Essential role for mammalian apurinic/apyrimidinic (AP) endonuclease Ape1/Ref-1 in telomere maintenance. Proc Natl Acad Sci USA. 2013; 110:17844-17849.
• [18]Wilson SH, Kunkel TA. Passing the baton in base excision repair. Nat Struct Biol. 2000; 7:176-178.
• [19]Baldwin MR, O’Brien PJ. Human AP endonuclease 1 stimulates multiple-turnover base excision by alkyladenine DNA glycosylase. Biochemistry. 2009; 48:6022-6033.
• [20]Pope MA, Chmiel NH, David SS. Insight into the functional consequences of hMYH variants associated with colorectal cancer: distinct differences in the adenine glycosylase activity and the response to AP endonucleases of Y150C and G365D murine MYH. DNA Repair (Amst). 2005; 4:315-325.
• [21]Sidorenko VS, Nevinsky GA, Zharkov DO. Mechanism of interaction between human 8-oxoguanine-DNA glycosylase and AP endonuclease. DNA Repair (Amst). 2007; 6:317-328.
• [22]Xia L, Zheng L, Lee HW, Bates SE, Federico L, Shen B et al.. Human 3-methyladenine-DNA glycosylase: effect of sequence context on excision, association with PCNA, and stimulation by AP endonuclease. J Mol Biol. 2005; 346:1259-1274.
• [23]Yang H, Clendenin WM, Wong D, Demple B, Slupska MM, Chiang JH et al.. Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch. Nucleic Acids Res. 2001; 29:743-752.
• [24]Gembka A, Toueille M, Smirnova E, Poltz R, Ferrari E, Villani G et al.. The checkpoint clamp, Rad9-Rad1-Hus1 complex, preferentially stimulates the activity of apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta in long patch base excision repair. Nucleic Acids Res. 2007; 35:2596-2608.
• [25]Luncsford PJ, Manvilla BA, Patterson DN, Malik SS, Jin J, Hwang BJ et al.. Coordination of MYH DNA glycosylase and APE1 endonuclease activities via physical interactions. DNA Repair (Amst). 2013; 12:1043-1052.
• [26]Madabushi A, Lu A-L. The novel role of cell cycle checkpoint clamp Rad9-Hus1-Rad1 (the 9-1-1 complex) in DNA repair. In: Advances in Medicine and Biology. Berhardt LV, editor. Nova Publishers, Hauppauge; 2011: p.41-74.
• [27]Kugel S, Mostoslavsky R. Chromatin and beyond: the multitasking roles for SIRT6. Trends Biochem Sci. 2014; 39:72-81.
• [28]Jiang H, Khan S, Wang Y, Charron G, He B, Sebastian C et al.. SIRT6 regulates TNF-alpha secretion through hydrolysis of long-chain fatty acyl lysine. Nature. 2013; 496:110-113.
• [29]Michishita E, McCord RA, Berber E, Kioi M, Padilla-Nash H, Damian M et al.. SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin. Nature. 2008; 452:492-496.
• [30]Michishita E, McCord RA, Boxer LD, Barber MF, Hong T, Gozani O et al.. Cell cycle-dependent deacetylation of telomeric histone H3 lysine K56 by human SIRT6. Cell Cycle. 2009; 8:2664-2666.
• [31]Van Meter M, Kashyap M, Rezazadeh S, Geneva AJ, Morello TD, Seluanov A et al.. SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age. Nat Commun. 2014; 5:5011.
• [32]Mostoslavsky R, Chua KF, Lombard DB, Pang WW, Fischer MR, Gellon L et al.. Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell. 2006; 124:315-329.
• [33]Mao Z, Hine C, Tian X, Van Meter M, Au M, Vaidya A et al.. SIRT6 promotes DNA repair under stress by activating PARP1. Science. 2011; 332:1443-1446.
• [34]Polyakova O, Borman S, Grimley R, Vamathevan J, Hayes B, Solari R. Identification of novel interacting partners of Sirtuin6. PLoS One. 2012; 7:e51555.
• [35]Xu Z, Zhang L, Zhang W, Meng D, Zhang H, Jiang Y et al.. SIRT6 rescues the age related decline in base excision repair in a PARP1-dependent manner. Cell Cycle. 2015; 14:269-276.
• [36]Liszt G, Ford E, Kurtev M, Guarente L. Mouse Sir2 homolog SIRT6 is a nuclear ADP-ribosyltransferase. J Biol Chem. 2005; 280:21313-21320.
• [37]Suh D, Wilson DM, Povirk LF. 3′-phosphodiesterase activity of human apurinic/apyrimidinic endonuclease at DNA double-strand break ends. Nucleic Acids Res. 1997; 25:2495-2500.
• [38]Toiber D, Erdel F, Bouazoune K, Silberman DM, Zhong L, Mulligan P et al.. SIRT6 recruits SNF2H to DNA break sites, preventing genomic instability through chromatin remodeling. Mol Cell. 2013; 51:454-468.
• [39]Turco E, Ventura I, Minoprio A, Russo MT, Torreri P, Degan P et al.. Understanding the role of the Q338H MUTYH variant in oxidative damage repair. Nucleic Acids Res. 2013; 41:4093-4103.
• [40]McCord RA, Michishita E, Hong T, Berber E, Boxer LD, Kusumoto R et al.. SIRT6 stabilizes DNA-dependent protein kinase at chromatin for DNA double-strand break repair. Aging (Albany NY). 2009; 1:109-121.
• [41]Lan L, Nakajima S, Wei L, Sun L, Hsieh CL, Sobol RW et al.. Novel method for site-specific induction of oxidative DNA damage reveals differences in recruitment of repair proteins to heterochromatin and euchromatin. Nucleic Acids Res. 2014; 42:2330-2345.
• [42]Muftuoglu M, Wong HK, Imam SZ, Wilson DM, Bohr VA, Opresko PL. Telomere repeat binding factor 2 interacts with base excision repair proteins and stimulates DNA synthesis by DNA polymerase beta. Cancer Res. 2006; 66:113-124.
• [43]Rhee DB, Ghosh A, Lu J, Bohr VA, Liu Y. Factors that influence telomeric oxidative base damage and repair by DNA glycosylase OGG1. DNA Repair (Amst). 2011; 10:34-44.
• [44]Wang Z, Rhee DB, Lu J, Bohr CT, Zhou F, Vallabhaneni H et al.. Characterization of oxidative Guanine damage and repair in mammalian telomeres. PLoS Genet. 2010; 6:e1000951.
• [45]Francia S, Weiss RS, Hande MP, Freire R, d’Adda DF. Telomere and telomerase modulation by the mammalian Rad9/Rad1/Hus1 DNA-damage-checkpoint complex. Curr Biol. 2006; 16:1551-1558.
• [46]Chang DY, Shi G, Durand-Dubief M, Ekwall K, Lu AL. The role of MutY homolog (Myh1) in controlling the histone deacetylase Hst4 in the fission yeast Schizosaccharomyces pombe. J Mol Biol. 2011; 405:653-665.
• [47]Kaidi A, Weinert BT, Choudhary C, Jackson SP. Human SIRT6 promotes DNA end resection through CtIP deacetylation. Science. 2010; 329:1348-1353.
• [48]Benetti R, Garcia-Cao M, Blasco MA. Telomere length regulates the epigenetic status of mammalian telomeres and subtelomeres. Nat Genet. 2007; 39:243-250.
• [49]Madabushi A, Hwang BJ, Jin J, Lu AL. Histone deacetylase SIRT1 modulates and deacetylates DNA base excision repair enzyme thymine DNA glycosylase. Biochem J. 2013; 456:89-98.
• [50]Hirano S, Tominaga Y, Ichinoe A, Ushijima Y, Tsuchimoto D, Honda-Ohnishi Y et al.. Mutator phenotype of MUTYH-null mouse embryonic stem cells. J Biol Chem. 2003; 278:38121-38124.
• [51]Fitzgerald ME, Drohat AC. Coordinating the initial steps of base excision repair. Apurinic/apyrimidinic endonuclease 1 actively stimulates thymine DNA glycosylase by disrupting the product complex. J Biol Chem. 2008; 283:32680-32690.
• [52]Hwang BJ, Shi G, Lu AL. Mammalian MutY homolog (MYH or MUTYH) protects cells from oxidative DNA damage. DNA Repair (Amst). 2013; 13:10-21.
• [53]Gu Y, Lu A-L. Differential DNA recognition and glycosylase activity of the native human MutY homolog (hMYH) and recombinant hMYH expressed in bacteria. Nucl Acids Res. 2001; 29:2666-2674.
• [54]McGoldrick JP, Yeh Y-C, Solomon M, Essigmann JM, Lu A-L. Characterization of a mammalian homolog of the Escherichia coli MutY mismatch repair protein. Mol Cell Biol. 1995; 15:989-996.