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Quantitative Determination of MAR Hydrolase Residue Specificity In Vitro by Tandem Mass Spectrometry

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ADP-ribosylation and NAD+ Utilizing Enzymes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1813))

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Abstract

ADP-ribosylation is a posttranslational modification that involves the conjugation of monomers and polymers of the small molecule ADP-ribose onto amino acid side chains. A family of ADP-ribosyltransferases catalyzes the transfer of the ADP-ribose moiety of nicotinamide adenine dinucleotide (NAD+) onto a variety of amino acid side chains including aspartate, glutamate, lysine, arginine, cysteine, and serine. The monomeric form of the modification mono(ADP-ribosyl)ation (MARylation) is reversed by a number of enzymes including a family of MacroD-type macrodomain-containing mono(ADP-ribose) (MAR) hydrolases. Though it has been inferred from various chemical tests that these enzymes have specificity for MARylated aspartate and glutamate residues in vitro, the amino acid and site specificity of different family members are often not unambiguously defined. Here we describe a mass spectrometry-based assay to determine the site specificity of MAR hydrolases in vitro.

The original version of this chapter was revised. A correction to this chapter can be found at https://doi.org/10.1007/978-1-4939-8588-3_27

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Change history

  • 16 November 2018

    The funding information was omitted from the original Chapters 19 and 21. The below text has been added to these chapters respectively.

References

  1. Gupte R, Liu Z, Kraus WL (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev 31:101–126. https://doi.org/10.1101/gad.291518.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Vyas S, Matic I, Uchima L, Rood J, Zaja R, Hay RT et al (2014) Family-wide analysis of poly(ADP-ribose) polymerase activity. Nat Commun 5:4426. https://doi.org/10.1038/ncomms5426

    Article  CAS  PubMed  Google Scholar 

  3. Leidecker O, Bonfiglio JJ, Colby T, Zhang Q, Atanassov I, Zaja R et al (2016) Serine is a new target residue for endogenous ADP-ribosylation on histones. Nat Chem Biol 12(12):998–1000. https://doi.org/10.1038/nchembio.2180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hottiger MO, Hassa PO, Lüscher B, Schüler H, Koch-Nolte F (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem Sci 35:208–219. https://doi.org/10.1016/j.tibs.2009.12.003

    Article  CAS  PubMed  Google Scholar 

  5. Daniels CM, Ong S-E, Leung AKL (2015) The promise of proteomics for the study of ADP-ribosylation. Mol Cell 58:911–924. https://doi.org/10.1016/j.molcel.2015.06.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Denu JM (2005) The Sir2 family of protein deacetylases. Curr Opin Chem Biol 9:431–440. https://doi.org/10.1016/j.cbpa.2005.08.010

    Article  CAS  PubMed  Google Scholar 

  7. Houtkooper RH, Pirinen E, Auwerx J (2012) Sirtuins as regulators of metabolism and healthspan. Nat Rev Mol Cell Biol 13:225–238. https://doi.org/10.1038/nrm3293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Di Girolamo M, Dani N, Stilla A, Corda D (2005) Physiological relevance of the endogenous mono(ADP-ribosyl)ation of cellular proteins. FEBS J 272:4565–4575. https://doi.org/10.1111/j.1742-4658.2005.04876.x

    Article  CAS  PubMed  Google Scholar 

  9. Gregor J, Rack M, Perina D, Ahel I (2016) Macrodomains: structure, function, evolution, and catalytic activities. Ann Rev Biochem 85:431–454. https://doi.org/10.1146/annurev-biochem-060815-014935

    Article  CAS  Google Scholar 

  10. Palazzo L, Mikoč A, Ahel I (2017) ADP-RIBOSYLATION: new facets of an ancient modification. FEBS J 284(18):2932–2946. https://doi.org/10.1111/febs.14078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Jankevicius G, Hassler M, Golia B, Rybin V, Zacharias M, Timinszky G et al (2013) A family of macrodomain proteins reverses cellular mono-ADP-ribosylation. Nat Struct Mol Biol 20:508–514. https://doi.org/10.1038/nsmb.2523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Rosenthal F, Feijs KLH, Frugier E, Bonalli M, Forst AH, Imhof R et al (2013) Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat Struct Mol Biol 20:502–507. https://doi.org/10.1038/nsmb.2521

    Article  CAS  PubMed  Google Scholar 

  13. Li C, Debing Y, Jankevicius G, Neyts J, Ahel I, Coutard B et al (2016) Viral macro domains reverse protein ADP-ribosylation. J Virol 90(19):8478–8486. https://doi.org/10.1128/JVI.00705-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Fehr AR, Channappanavar R, Jankevicius G, Fett C, Zhao J, Athmer J (2016) The conserved coronavirus macrodomain promotes virulence and suppresses the innate immune response during severe acute. 7:1–12. https://doi.org/10.1128/mBio.01721-16.Editor

  15. McPherson RL, Abraham R, Sreekumar E, Ong S-E, Cheng S-J, Baxter VK et al (2017) ADP-ribosylhydrolase activity of Chikungunya virus macrodomain is critical for virus replication and virulence. Proc Natl Acad Sci 114(7):1666–1671. https://doi.org/10.1073/PNAS.1621485114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Eckei L, Krieg S, Bütepage M, Lehmann A, Gross A, Lippok B et al (2017) The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases. Sci Rep 7:41746. https://doi.org/10.1038/srep41746

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Haikarainen T, Lehtiö L (2016) Proximal ADP-ribose hydrolysis in trypanosomatids is catalyzed by a macrodomain. Sci Rep 6:24213. https://doi.org/10.1038/srep24213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Zapata-Pérez R, Gil-Ortiz F, Martínez-Moñino AB, García-Saura AG, Juanhuix J, Sánchez-Ferrer Á (2017) Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis. Open Biol 7:160327. https://doi.org/10.1098/rsob.160327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Marjanovic MP, Palazzo L, Perina D, Sabljic I, Roko Z, Colby T et al (2016) Disruption of macrodomain protein SCO6735 increases antibiotic production in streptomyces coelicolor*. J Biol Chem 291:23175–23187. https://doi.org/10.1074/jbc.M116.721894

    Article  CAS  Google Scholar 

  20. Rack JGM, Morra R, Barkauskaite E, Kraehenbuehl R, Ariza A, Qu Y et al (2015) Identification of a class of protein ADP-ribosylating sirtuins in microbial pathogens. Mol Cell 59:309–320. https://doi.org/10.1016/j.molcel.2015.06.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Feijs KLH, Forst AH, Verheugd P, Lüscher B (2013) Macrodomain-containing proteins: regulating new intracellular functions of mono(ADP-ribosyl)ation. Nat Rev Mol Cell Biol 14:443–451. https://doi.org/10.1038/nrm3601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Barkauskaite E, Jankevicius G, Ladurner AG, Ahel I, Timinszky G (2013) The recognition and removal of cellular poly(ADP-ribose) signals. FEBS J 280:3491–3507. https://doi.org/10.1111/febs.12358

    Article  CAS  PubMed  Google Scholar 

  23. Zhang Y, Wang J, Ding M, Yu Y (2013) Site-specific characterization of the Asp- and Glu-ADP-ribosylated proteome. Nat Methods 10:981–984. https://doi.org/10.1038/nmeth.2603

    Article  CAS  PubMed  Google Scholar 

  24. Martello R, Leutert M, Jungmichel S, Bilan V, Larsen SC, Young C et al (2016) ADP-ribosylome of mammalian cells and tissue. Nat Commun 7:1–13. https://doi.org/10.1038/ncomms12917

    Article  CAS  Google Scholar 

  25. Daniels CM, Ong SE, Leung AKL (2014) Phosphoproteomic approach to characterize protein mono- and poly(ADP-ribosyl)ation sites from cells. J Proteome Res 13:3510–3522. https://doi.org/10.1021/pr401032q

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Palazzo L, Thomas B, Jemth A-S, Colby T, Leidecker O, Feijs KLH et al (2015) Processing of protein ADP-ribosylation by Nudix hydrolases. Biochem J 468:293–301. https://doi.org/10.1042/BJ20141554

    Article  CAS  PubMed  Google Scholar 

  27. Palazzo L, Daniels CM, Nettleship JE, Rahman N, McPherson RL, Ong S-E et al (2016) ENPP1 processes protein ADP-ribosylation in vitro. FEBS J 283(18):3371–3388. https://doi.org/10.1111/febs.13811

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Rosenthal F, Nanni P, Barkow-Oesterreicher S, Hottiger MO (2015) Optimization of LTQ-Orbitrap mass spectrometer parameters for the identification of ADP-ribosylation sites. J Proteome Res 14(9):4072–4079. https://doi.org/10.1021/acs.jproteome.5b00432

    Article  CAS  PubMed  Google Scholar 

  29. Bilan V, Leutert M, Nanni P, Panse C, Hottiger MO (2017) Combining higher-energy collision dissociation and electron-transfer/higher-energy collision dissociation fragmentation in a product-dependent manner confidently assigns proteome wide ADP-ribose acceptor sites. Anal Chem. https://doi.org/10.1021/acs.analchem.6b03365

    Article  CAS  PubMed  Google Scholar 

  30. Daniels CM, Thirawatananond P, Ong S-E, Gabelli SB, Leung AKL (2015) Nudix hydrolases degrade protein-conjugated ADP-ribose. Sci Rep 5:18271. https://doi.org/10.1038/srep18271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Bonfiglio JJ, Fontana P, Zhang Q, Colby T, Gibbs-Seymour I, Atanassov I et al (2017) Serine ADP-ribosylation depends on HPF1. Mol Cell 65(5):932–940.e6. https://doi.org/10.1016/j.molcel.2017.01.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Chapman JD, Gagné JP, Poirier GG, Goodlett DR (2013) Mapping PARP-1 auto-ADP-ribosylation sites by liquid chromatography-tandem mass spectrometry. J Proteome Res 12:1868–1880. https://doi.org/10.1021/pr301219h

    Article  CAS  PubMed  Google Scholar 

  33. Mashimo M, Kato J, Moss J (2014) Structure and function of the ARH family of ADP-ribosyl-acceptor hydrolases. DNA Repair (Amst) 23:88–94. https://doi.org/10.1016/j.dnarep.2014.03.005

    Article  CAS  Google Scholar 

  34. Peterson FC, Chen D, Lytle BL, Rossi MN, Ahel I, Denu JM et al (2011) Orphan macrodomain protein (human C6orf130) is an O-acyl-ADP-ribose deacylase: solution structure and catalytic properties. J Biol Chem 286:35955–35965. https://doi.org/10.1074/jbc.M111.276238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Proto 2(8):1896–1906. https://doi.org/10.1038/nprot.2007.261

    Article  CAS  Google Scholar 

  36. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10:1794–1805. https://doi.org/10.1021/pr101065j

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by a Johns Hopkins Catalyst Award (AKLL) and research grants from the Johns Hopkins University School of Medicine Sherrilyn and Ken Fisher Center for Environmental Infectious Disease (AKLL). The proteomics work was also in part supported by R01GM104135S1 (AKLL and RLM), S10OD021502 (SEO), and T32CA009110 (RLM) from the U.S. National Institutes of Health, and the American Cancer Society Research Scholar Award 129539-RSG-16-062-01-RMC (AKLL).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA

    Robert Lyle McPherson & Anthony K. L. Leung

  2. Department of Pharmacology, University of Washington, Seattle, WA, USA

    Shao-En Ong

  3. Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA

    Anthony K. L. Leung

  4. Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA

    Anthony K. L. Leung

Authors
  1. Robert Lyle McPherson
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  2. Shao-En Ong
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  3. Anthony K. L. Leung
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Correspondence to Anthony K. L. Leung .

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Editors and Affiliations

  1. Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA

    Paul Chang

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McPherson, R.L., Ong, SE., Leung, A.K.L. (2018). Quantitative Determination of MAR Hydrolase Residue Specificity In Vitro by Tandem Mass Spectrometry. In: Chang, P. (eds) ADP-ribosylation and NAD+ Utilizing Enzymes. Methods in Molecular Biology, vol 1813. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-8588-3_19

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  • DOI: https://doi.org/10.1007/978-1-4939-8588-3_19

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-8587-6

  • Online ISBN: 978-1-4939-8588-3

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