Affinity-Based Assays for the Identification and Quantitative Evaluation of Noncovalent Poly(ADP-Ribose)-Binding Proteins

Methods in Molecular Biology

Volumn 780, Issue , 2011, Pages 93-115

  Gagné, Jean Philippe ^a   Haince, Jean François ^a   Pic, Émilie ^a   Poirier, Guy G ^a  

^a LAVAL UNIVERSITY   (Canada)

Author keywords

Consensus motif prediction; Electrophoretic mobility shift assay; EMSA; Immunoprecipitation; Mass spectrometry; Noncovalent binding; pADPr; PARG; PARP; Poly(ADP ribose); Polymer blot; siRNA; SPR; Surface plasmon resonance

Indexed keywords

CARRIER PROTEIN; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE; POLY(ADENOSINE DIPHOSPHATE RIBOSE);

ARTICLE; GEL MOBILITY SHIFT ASSAY; GENETICS; IMMUNOPRECIPITATION; MASS SPECTROMETRY; METABOLISM; SURFACE PLASMON RESONANCE;

CARRIER PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; IMMUNOPRECIPITATION; MASS SPECTROMETRY; POLY ADENOSINE DIPHOSPHATE RIBOSE; POLY(ADP-RIBOSE) POLYMERASES; SURFACE PLASMON RESONANCE;

EID: 80054756419     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-270-0_7     Document Type: Chapter

References (60)

1. Hassa PO, Haenni SS, Elser M, Hottiger MO (2006) Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev 70:789–829
2. Schreiber V, Dantzer F, Ame JC, de Murcia G (2006) Poly(ADP-ribose): novel functions for an old molecule. Nat Rev Mol Cell Biol 7:517–528
3. Malanga M, Althaus F (2006) DNA damage signaling through poly(ADP-Ribose). In: Burkle A (ed) Poly(ADP-Ribosyl)ation. Landes Bioscience and Springer Science + Business Media, New York, NY, pp 41–50
4. Haince JF, McDonald D, Rodrigue A, Dery U, Masson JY, Hendzel MJ, Poirier GG (2008) PARP1-dependent kinetics of recruitment of MRE11 and NBS1 proteins to multiple DNA damage sites. J Biol Chem 283:1197–1208
5. Gottschalk AJ, Timinszky G, Kong SE, Jin J, Cai Y, Swanson SK, Washburn MP, Florens L, Ladurner AG, Conaway JW, Conaway RC (2009) Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci USA 106:13770–13774
6. Beneke S, Burkle A (2007) Poly(ADP-ribosyl) ation in mammalian ageing. Nucleic Acids Res 35:7456–7465
7. Chang P, Jacobson MK, Mitchison TJ (2004) Poly(ADP-ribose) is required for spindle assembly and structure. Nature 432:645–649
8. d’Adda di Fagagna F, Hande MP, Tong WM, Lansdorp PM, Wang ZQ, Jackson SP (1999) Functions of poly(ADP-ribose) polymerase in controlling telomere length and chromosomal stability. Nat Genet 23:76–80
9. Kraus WL (2008) Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr Opin Cell Biol 20:294–302
10. Hassa PO (2009) The molecular “Jekyll and Hyde” duality of PARP1 in cell death and cell survival. Front Biosci 14:72–111
11. Andrabi SA, Kim NS, Yu SW, Wang H, Koh DW, Sasaki M, Klaus JA, Otsuka T, Zhang Z, Koehler RC, Hurn PD, Poirier GG, Dawson VL, Dawson TM (2006) Poly(ADP-ribose) (PAR) polymer is a death signal. Proc Natl Acad Sci USA 103:18308–18313
12. D’Amours D, Desnoyers S, D’Silva I, Poirier GG (1999) Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions. Biochem J 342(Pt 2):249–268
13. Minaga T, Kun E (1983) Probable helical conformation of poly(ADP-ribose). The effect of cations on spectral properties. J Biol Chem 258:5726–5730
14. Minaga T, Kun E (1983) Spectral analysis of the conformation of polyadenosine diphosphoribose. Evidence indicating secondary structure. J Biol Chem 258:725–730
15. Kleine H, Poreba E, Lesniewicz K, Hassa PO, Hottiger MO, Litchfield DW, Shilton BH, Luscher B (2008) Substrate-assisted catalysis by PARP10 limits its activity to mono-ADP-ribo-sylation. Mol Cell 32:57–69
16. Chang P, Coughlin M, Mitchison TJ (2005) Tankyrase-1 polymerization of poly(ADP-ribose) is required for spindle structure and function. Nat Cell Biol 7:1133–1139
17. Rippmann JF, Damm K, Schnapp A (2002) Functional characterization of the poly(ADP-ribose) polymerase activity of tankyrase 1, a potential regulator of telomere length. J Mol Biol 323:217–224
18. Loseva O, Jemth AS, Bryant HE, Schuler H, Lehtio L, Karlberg T, Helleday T (2010) PARP-3 is a mono-ADP-ribosylase that activates PARP-1 in the absence of DNA. J Biol Chem 285:8054–8060
19. Gagné JP, Hendzel MJ, Droit A, Poirier GG (2006) The expanding role of poly(ADP-ribose) metabolism: current challenges and new perspectives. Curr Opin Cell Biol 18:145–151
20. Andrabi SA, Dawson TM, Dawson VL (2008) Mitochondrial and nuclear cross talk in cell death: parthanatos. Ann NY Acad Sci 1147:233–241
21. de Murcia G, Huletsky A, Lamarre D, Gaudreau A, Pouyet J, Daune M, Poirier GG (1986) Modulation of chromatin superstructure induced by poly(ADP-ribose) synthesis and degradation. J Biol Chem 261:7011–7017
22. de Murcia G, Huletsky A, Poirier GG (1988) Modulation of chromatin structure by poly(ADP-ribosyl)ation. Biochem Cell Biol 66:626–635
23. Egloff MP, Malet H, Putics A, Heinonen M, Dutartre H, Frangeul A, Gruez A, Campanacci V, Cambillau C, Ziebuhr J, Ahola T, Canard B (2006) Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains. J Virol 80:8493–8502
24. Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG (2005) The macro domain is an ADP-ribose binding module. EMBO J 24:1911–1920
25. Till S, Ladurner AG (2009) Sensing NAD metabolites through macro domains. Front Biosci 14:3246–3258
26. Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC (2008) Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/ checkpoint proteins. Nature 451:81–85
27. Li GY, McCulloch RD, Fenton AL, Cheung M, Meng L, Ikura M, Koch CA (2010) Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response. Proc Natl Acad Sci USA 107(20):9129–9134
28. Timinszky G, Till S, Hassa PO, Hothorn M, Kustatscher G, Nijmeijer B, Colombelli J, Altmeyer M, Stelzer EH, Scheffzek K, Hottiger MO, Ladurner AG (2009) A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat Struct Mol Biol 16:923–929
29. Pleschke JM, Kleczkowska HE, Strohm M, Althaus FR (2000) Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins. J Biol Chem 275:40974–40980
30. Gagné JP, Isabelle M, Lo KS, Bourassa S, Hendzel MJ, Dawson VL, Dawson TM, Poirier GG (2008) Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes. Nucleic Acids Res 36:6959–6976
31. Malanga M, Pleschke JM, Kleczkowska HE, Althaus FR (1998) Poly(ADP-ribose) binds to specific domains of p53 and alters its DNA binding functions. J Biol Chem 273:11839–11843
32. Dani N, Stilla A, Marchegiani A, Tamburro A, Till S, Ladurner AG, Corda D, Di Girolamo M (2009) Combining affinity purification by ADP-ribose-binding macro domains with mass spectrometry to define the mammalian ADP-ribosyl proteome. Proc Natl Acad Sci USA 106:4243–4248
33. Riggs AD, Bourgeois S, Newby RF, Cohn M (1968) DNA binding of the lac repressor. J Mol Biol 34:365–368
34. Fahrer J, Kranaster R, Altmeyer M, Marx A, Burkle A (2007) Quantitative analysis of the binding affinity of poly(ADP-ribose) to specific binding proteins as a function of chain length. Nucleic Acids Res 35:e143
35. Slama JT, Aboul-Ela N, Goli DM, Cheesman BV, Simmons AM, Jacobson MK (1995) Specific inhibition of poly(ADP-ribose) glycohydrolase by adenosine diphosphate (hydroxymethyl)pyr-rolidinediol. J Med Chem 38:389–393
36. Slama JT, Aboul-Ela N, Jacobson MK (1995) Mechanism of inhibition of poly(ADP-ribose) glycohydrolase by adenosine diphosphate (hydroxymethyl)pyrrolidinediol. J Med Chem 38:4332–4336
37. Kawamitsu H, Hoshino H, Okada H, Miwa M, Momoi H, Sugimura T (1984) Monoclonal antibodies to poly(adenosine diphosphate ribose) recognize different structures. Biochemistry 23:3771–3777
38. Kawamitsu H, Hoshino H, Miwa M, Sugimura T (1983) Monoclonal antibodies against poly(ADP-ribose) recognize different structures of poly(ADP-ribose). Princess Takamatsu Symp 13:41–47
39. Affar EB, Duriez PJ, Shah RG, Winstall E, Germain M, Boucher C, Bourassa S, Kirkland JB, Poirier GG (1999) Immunological determination and size characterization of poly(ADP-ribose) synthesized in vitro and in vivo. Biochim Biophys Acta 1428:137–146
40. Panzeter PL, Realini CA, Althaus FR (1992) Noncovalent interactions of poly(adenosine diphosphate ribose) with histones. Biochemistry 31:1379–1385
41. Gagné JP, Hunter JM, Labrecque B, Chabot B, Poirier GG (2003) A proteomic approach to the identification of heterogeneous nuclear ribonucleoproteins as a new family of poly (ADP-ribose)-binding proteins. Biochem J 371:331–340
42. Shah GM, Poirier D, Duchaine C, Brochu G, Desnoyers S, Lagueux J, Verreault A, Hoflack JC, Kirkland JB, Poirier GG (1995) Methods for biochemical study of poly(ADP-ribose) metabolism in vitro and in vivo. Anal Biochem 227:1–13
43. Fried MG (1989) Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10:366–376
44. Willander M, Al-Hilli S (2009) Analysis of biomolecules using surface plasmons. Methods Mol Biol 544:201–229
45. Panzeter PL, Zweifel B, Althaus FR (1992) Synthesis of poly(ADP-ribose)-agarose beads: an affinity resin for studying (ADP-ribose)n-protein interactions. Anal Biochem 207:157–162
46. Combet C, Blanchet C, Geourjon C, Deleage G (2000) NPS@: network protein sequence analysis. Trends Biochem Sci 25:147–150
47. Ménard L, Poirier GG (1987) Rapid assay of poly(ADP-ribose) glycohydrolase. Biochem Cell Biol 65:668–673
48. Cardenas-Corona ME, Jacobson EL, Jacobson MK (1987) Endogenous polymers of ADP-ribose are associated with the nuclear matrix. J Biol Chem 262:14863–14866
49. Alvarez-Gonzalez R, Jacobson MK (1987) Characterization of polymers of adenosine diphosphate ribose generated in vitro and in vivo. Biochemistry 26:3218–3224
50. Wielckens K, Schmidt A, George E, Bredehorst R, Hilz H (1982) DNA fragmentation and NAD depletion. Their relation to the turnover of endogenous mono(ADP-ribosyl) and poly(ADP-ribosyl) proteins. J Biol Chem 257:12872–12877
51. Juarez-Salinas H, Sims JL, Jacobson MK (1979) Poly(ADP-ribose) levels in carcinogen-treated cells. Nature 282:740–741
52. Hall RA (2004) Studying protein-protein interactions via blot overlay or Far Western blot. Methods Mol Biol 261:167–174
53. Kiehlbauch CC, Aboul-Ela N, Jacobson EL, Ringer DP, Jacobson MK (1993) High resolution fractionation and characterization of ADP-ribose polymers. Anal Biochem 208:26–34
54. Isogai S, Kanno S, Ariyoshi M, Tochio H, Ito Y, Yasui A, Shirakawa M (2010) Solution structure of a zinc-finger domain that binds to poly-ADP-ribose. Genes Cells 15:101–110
55. Shuman S (2001) Analysis of topoisomerase-DNA interactions by electrophoretic mobility shift assay. Methods Mol Biol 95:65–74
56. Affar EB, Duriez PJ, Shah RG, Sallmann FR, Bourassa S, Kupper JH, Burkle A, Poirier GG (1998) Immunodot blot method for the detection of poly(ADP-ribose) synthesized in vitro and in vivo. Anal Biochem 259:280–283
57. Eustermann S, Brockmann C, Mehrotra PV, Yang JC, Loakes D, West SC, Ahel I, Neuhaus D (2010) Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Nat Struct Mol Biol 17:241–243
58. Ahel D, Horejsi Z, Wiechens N, Polo SE, Garcia-Wilson E, Ahel I, Flynn H, Skehel M, West SC, Jackson SP, Owen-Hughes T, Boulton SJ (2009) Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 325:1240–1243
59. Malanga M, Althaus FR (2005) The role of poly(ADP-ribose) in the DNA damage signaling network. Biochem Cell Biol 83:354–364
60. Althaus FR, Kleczkowska HE, Malanga M, Muntener CR, Pleschke JM, Ebner M, Auer B (1999) Poly ADP-ribosylation: a DNA break signal mechanism. Mol Cell Biochem 193:5–11