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

• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Chapter Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Beneke S, Burkle A (2007) Poly(ADP-ribosyl)ation in mammalian ageing. Nucleic Acids Res 35:7456–7465
  Article PubMed CAS Google Scholar
• Chang P, Jacobson MK, Mitchison TJ (2004) Poly(ADP-ribose) is required for spindle assembly and structure. Nature 432:645–649
  Article PubMed CAS Google Scholar
• 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
  PubMed Google Scholar
• Kraus WL (2008) Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr Opin Cell Biol 20:294–302
  Article PubMed CAS Google Scholar
• Hassa PO (2009) The molecular “Jekyll and Hyde” duality of PARP1 in cell death and cell survival. Front Biosci 14:72–111
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed Google Scholar
• 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
  PubMed CAS Google Scholar
• Minaga T, Kun E (1983) Spectral analysis of the conformation of polyadenosine diphosphoribose. Evidence indicating secondary structure. J Biol Chem 258:725–730
  PubMed CAS Google Scholar
• 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-ribosylation. Mol Cell 32:57–69
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed Google Scholar
• Andrabi SA, Dawson TM, Dawson VL (2008) Mitochondrial and nuclear cross talk in cell death: parthanatos. Ann NY Acad Sci 1147:233–241
  Article PubMed CAS Google Scholar
• 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
  PubMed Google Scholar
• de Murcia G, Huletsky A, Poirier GG (1988) Modulation of chromatin structure by poly(ADP-ribosyl)ation. Biochem Cell Biol 66:626–635
  Article PubMed Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Till S, Ladurner AG (2009) Sensing NAD metabolites through macro domains. Front Biosci 14:3246–3258
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Riggs AD, Bourgeois S, Newby RF, Cohn M (1968) DNA binding of the lac repressor. J Mol Biol 34:365–368
  Article PubMed CAS Google Scholar
• 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
  Article PubMed Google Scholar
• 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)pyrrolidinediol. J Med Chem 38:389–393
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Panzeter PL, Realini CA, Althaus FR (1992) Noncovalent interactions of poly(adenosine diphosphate ribose) with histones. Biochemistry 31:1379–1385
  Article PubMed CAS Google Scholar
• 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
  Article PubMed Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Fried MG (1989) Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 10:366–376
  Article PubMed CAS Google Scholar
• Willander M, Al-Hilli S (2009) Analysis of biomolecules using surface plasmons. Methods Mol Biol 544:201–229
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Combet C, Blanchet C, Geourjon C, Deleage G (2000) NPS@: network protein sequence analysis. Trends Biochem Sci 25:147–150
  Article PubMed CAS Google Scholar
• Ménard L, Poirier GG (1987) Rapid assay of poly(ADP-ribose) glycohydrolase. Biochem Cell Biol 65:668–673
  Article PubMed Google Scholar
• 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
  PubMed CAS Google Scholar
• Alvarez-Gonzalez R, Jacobson MK (1987) Characterization of polymers of adenosine diphosphate ribose generated in vitro and in vivo. Biochemistry 26:3218–3224
  Article PubMed CAS Google Scholar
• 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
  PubMed CAS Google Scholar
• Juarez-Salinas H, Sims JL, Jacobson MK (1979) Poly(ADP-ribose) levels in carcinogen-treated cells. Nature 282:740–741
  Article PubMed CAS Google Scholar
• Hall RA (2004) Studying protein-protein interactions via blot overlay or Far Western blot. Methods Mol Biol 261:167–174
  PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Shuman S (2001) Analysis of topoisomerase-DNA interactions by electrophoretic mobility shift assay. Methods Mol Biol 95:65–74
  PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar
• Malanga M, Althaus FR (2005) The role of poly(ADP-ribose) in the DNA damage signaling network. Biochem Cell Biol 83:354–364
  Article PubMed CAS Google Scholar
• 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
  Article PubMed CAS Google Scholar