• 1
    Altmeyer M, Messner S, Hassa PO, Fey M & Hottiger MO (2009) Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites. Nucleic Acids Res 37, 37233738.
  • 2
    Corda D & Di Girolamo M (2003) Functional aspects of protein mono-ADPribosylation. EMBO J 22, 19531958.
  • 3
    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, 45654575.
  • 4
    Schreiber V, Dantzer F, Amé J-C & de Murcia G (2006) Poly(ADP-ribose): novel functions for an old molecule. Nat Rev Mol Cell Biol 7, 517528.
  • 5
    Amé J-C, Spenlehauer C & de Murcia G (2004) The PARP superfamily. Bioessays 26, 882893.
  • 6
    Otto H, Reche PA, Bazan F, Dittmar K, Haag F & Koch-Nolte F (2005) In silico characterization of the family of PARP-like poly(ADP-ribosyl)transferases (pARTs). BMC Genomics 6, 139161.
  • 7
    Kleine H, Poreba E, Lesniewicz K, Hassa PO, Hottiger MO, Litchfield DW, Shilton BH & Lüscher B (2008) Substrate-assisted catalysis by PARP10 limits its activity to mono-ADP-ribosylation. Mol Cell 32, 5769.
  • 8
    Hottiger MO, Hassa PO, Lüscher B, Schüler H & Koch-Nolte F (2010) Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem Sci 35, 208219.
  • 9
    Boehler C, Gauthier LR, Mortusewicz O, Biard DS, Saliou J-M, Bresson A, Sanglier-Cianferani S, Smith S, Schreiber V, Boussin F et al. (2011) Poly(ADP-ribose) polymerase 3 (PARP3), a newcomer in cellular response to DNA damage and mitotic progression. Proc Natl Acad Sci USA 108, 27832788.
  • 10
    Rulten SL, Fisher AE, Robert I, Zuma MC, Rouleau M, Ju L, Poirier G, Reina-San-Martin B & Caldecott KW (2011) PARP-3 and APLF function together to accelerate nonhomologous end-joining. Mol Cell 41, 3345.
  • 11
    Dantzer F, de La Rubia G, Ménissier-De Murcia J, Hostomsky Z, de Murcia G & Schreiber V (2000) Base excision repair is impaired in mammalian cells lacking Poly(ADP-ribose) polymerase-1. Biochemistry 39, 75597569.
  • 12
    Schreiber V, Amé JC, Dollé P, Schultz I, Rinaldi B, Fraulob V, Ménissier-de Murcia J & de Murcia G (2002) Poly(ADP-ribose) polymerase-2 (PARP-2) is required for efficient base excision DNA repair in association with PARP-1 and XRCC1. J Biol Chem 277, 2302823036.
  • 13
    Kickhoefer VA, Silva AC, Kedersha NL, Inman EM, Ruland C, Streuli M & Rome LH (1999) The 193-kD vault protein, VPARP, is a novel poly(ADP-ribose) polymerase. J Cell Biol 146, 917928.
  • 14
    Aravind L (2001) The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation. Trends Biochem Sci 26, 273275.
  • 15
    Yélamos J, Schreiber V & Dantzer F (2008) Toward specific functions of poly(ADP-ribose) polymerase-2. Trends Mol Med 14, 169178.
  • 16
    Isabelle M, Moreel X, Gagné J-P, Rouleau M, Ethier C, Gagné P, Hendzel MJ & Poirier GG (2010) Investigation of PARP-1, PARP-2 and PARG interactomes by affinity-purification mass spectrometry. Proteome Sci 8, 22.
  • 17
    Dantzer F, Mark M, Quenet D, Scerthan H, Huber A, Liebe B, Monaco L, Chiche Portiche A, Sassone-Corsi P, de Murcia G et al. (2006) Poly(ADP-ribose) polymerase-2 contributes to the fidelity of male meiosis I and spermiogenesis. Proc Natl Acad Sci USA 103, 1485414859.
  • 18
    Bai P, Houten SM, Huber A, Schreiber V, Watanabe M, Kiss B, de Murcia G, Auwerx J & Ménissier-de Murcia J (2007) Peroxisome proliferator-activated receptor (PPAR)-2 controls adipocyte differentiation and adipose tissue function through the regulation of the activity of the Retinoid X Receptor/PPARγ heterodimer. J Biol Chem 282, 3773837746.
  • 19
    Yélamos J, Monreal Y, Saenz L, Aguado E, Schreiber V, Mota R, Fuente R, Minguela A, Parrilla P, de Murcia J et al. (2006) PARP-2 deficiency affects the survival of CDC4+CD8+ double- positive thymocytes. EMBO J 25, 43504360.
  • 20
    Kun E, Kirsten E, Mendeleyev J & Ordahl CP (2004) Regulation of the enzymatic catalysis of poly(ADP-ribose) polymerase by dsDNA, polyamines, Mg2+, Ca2+, histones H1 and H3, and ATP. Biochemistry 43, 210216.
  • 21
    Kalousek F, Darigo MD & Rosenberg LE (1980) Isolation and characterization of propionyl-CoA carboxylase from normal human liver. Evidence for a protomeric tetramer of non identical subunits. J Biol Chem 255, 6065.
  • 22
    Gravel RA, Lam KF, Mahuran D & Kronis A (1980) Purification of human liver propionyl-CoA carboxylase by carbon tetrachloride extraction and monomeric avidin affinity chromatography. Arch Biochem Biophys 201, 669673.
  • 23
    Aguiar RCT, Takeyama K, He C, Kreinbrink K & Shipp MA (2005) B-aggressive lymphoma family proteins have unique domains that modulate transcription and exhibit poly(ADP-ribose) polymerase activity. J Biol Chem 280, 3375633765.
  • 24
    Kraus WL (2009) New functions for an ancient domain. Nat Struct Mol Biol 16, 904907.
  • 25
    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, 8185.
  • 26
    Gagné J-P, Isabelle M, Sin Lo K, Bourassa S, Hendzel MJ, Dawson VL, Dawson TM & Poirier GG (2008) Proteome-wide identification of poly(ADP-ribose) binding proteins and poy(ADP-ribose)-associated protein complexes. Nucleic Acids Res 36, 69596976.
  • 27
    Krishnakumar R & Kraus WL (2010) The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Mol Cell 39, 824.
  • 28
    Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211D215.
  • 29
    Rulten SL, Cortes-Ledesma F, Guo L, Iles NJ & Caldecott KW (2008) APLF (C2orf13) is a novel component of poly(ADP-ribose) signaling in mammalian cells. Mol Cell Biol 28, 46204628.
  • 30
    Kanno S, Kuzuoka H, Sasao S, Hong Z, Lan L, Nakajima S & Yasui A (2007) A novel human AP endonuclease with conserved zinc-finger-like motifs involved in DNA strand break responses. EMBO J 26, 20942103.
  • 31
    Meder VS, Boeglin M, de Murcia G & Schreiber V (2005) PARP-1 and PARP-2 interact with nucleophosmin/B23 and accumulate in transcriptionally active nucleoli. J Cell Sci 118, 211222.
  • 32
    Saxena A, Wong LH, Kalitsis P, Earle E, Shaffer LG & Choo KH (2002) Poly(ADP-ribose) polymerase 2 localizes to mammalian active centromeres and interacts with PARP-1, Cenpa, Cenpb and Bub3, but not Cenpc. Hum Mol Genet 11, 23192329.
  • 33
    Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A & Narechania A (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13, 21292141.
  • 34
    Anderson NL & Anderson NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1, 845867.
  • 35
    Tao Z, Gao P & Liu H-w (2009) Studies of expression of human poly(ADP-ribose) polymerase-1 in Saccharomyces cerevisiae and identification of PARP-1 substrates by yeast proteome microarray screening. Biochemistry 48, 1174511754.
  • 36
    Hanus J, Kalinowska-Herok M & Widlak P (2008) The major apoptotic endonuclease DFF40/CAD is a deoxyribose-specific and double-strand-specific enzyme. Apoptosis 13, 377382.
  • 37
    Höck J, Weinmann L, Ender C, Rüdel S, Kremmer E, Raabe M, Urlaub H & Meister G (2007) Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells. EMBO Rep 8, 10521060.
  • 38
    Galat A, Lane WS, Standaert RF & Schreiber SL (1992) A rapamycin-selective 25-kDa immunophilin. Biochemistry 31, 24272434.
  • 39
    Yang WM, Yao YL & Seto E (2001) The FK506-binding protein 25 functionally associates with histone deacetylases and with transcription factor YY1. EMBO J 20, 48144825.
  • 40
    Ahn J, Murphy M, Kratowicz S, Wang A, Levine AJ & George DL (1999) Down-regulation of the stathmin/Op18 and FKBP25 genes following p53 induction. Oncogene 18, 59545958.
  • 41
    Ochocka AM, Kampanis P, Nicol S, Allende-Vega N, Cox M, Marcar L, Milne D, Fuller-Pace F & Meek D (2009) FKBP25, a novel regulator of the p53 pathway, induces the degradation of MDM2 and activation of p53. FEBS Lett 583, 621626.
  • 42
    Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ & Gygi SP (2008) A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci USA 105, 1076210767.
  • 43
    Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther T, Olsen JV & Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834840.
  • 44
    Jiang H, Kim JH, Frizzell KM, Kraus WL & Lin H (2010) Clickable NAD analogues for labelling substrate proteins of poly(ADP-ribose) polymerases. J Am Chem Soc 132, 93639372.
  • 45
    Suzuki H, Kawai J, Taga C, Yaoi T, Hara A, Hirose K, Hayashizaki Y & Watanabe S (1996) Stac, a novel neuron-specific protein with cysteine-rich and SH3 domains. Biochem Biophys Res Commun 229, 902909.
  • 46
    Satoh J, Nanri Y & Yamamura T (2006) Rapid identification of 14-3-3-binding proteins by protein microarray analysis. J Neurosci Methods 152, 278288.
  • 47
    Mitra S, Mazumder Indra D, Bhattacharya N, Singh RK, Basu PS, Mondal RK, Roy A, Zabarovsky ER, Roychoudhury S & Panda CK (2010) RBSP3 is frequently altered in premalignant cervical lesions: clinical and prognostic significance. Genes Chromosom Cancer 49, 155170.
  • 48
    Kofler J, Otsuka T, Zhang Z, Nopppens R, Grafe MR, Koh DW, Dawson VL, Ménissiewr de Murcia J, Hurn PD & Traystman RJ (2006) Differential effect of PARP-2 deletion on brain injury after focal and global cerebral ischemia. J Cereb Blood Flow Metab 26, 135141.
  • 49
    Moroni F, Formentini L, Gerace E, Camaioni E, Pellegrini-Giampietro DE, Chiarugi A & Pellicciari R (2009) Selective PARP-2 inhibitors increase apoptosis in hippocampal slices but protect cortical cells in models of post-ischaemic brain damage. Br J Pharmacol 157, 854862.
  • 50
    Schnack C, Hengerer B & Gillardon F (2008) Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high-density protein microarrays. Proteomics 8, 19801986.
  • 51
    Zhu J, Liao G, Shan L, Zhang J, Chen M-R, Hayward GS, Hayward SD, Desai P & Zhu H (2009) Protein array identification of substrates of the Epstein-Barr virus protein kinase BGLF4. J Virol 83, 52195231.
  • 52
    Foster MW, Forrester MT & Stamler JS (2009) A protein microarray-based analysis of S-nitrosylation. Proc Natl Acad Sci USA 106, 1894818953.
  • 53
    Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J & Rotin D (2007) Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Syst Biol 3, 116.
  • 54
    Lu J-y, Lin Y-y, Qian J, Tao S-c, Zhu J, Pickart C & Zhu H (2008) Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics 7, 3545.
  • 55
    Persaud A, Alberts P, Amsen EM, Xiong X, Wasmuth J, Saadon Z, Fladd C, Parkinson J & Rotin D (2009) Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrrays. Mol Syst Biol 5, 333.
  • 56
    Fenner BJ, Scannell M & Prehn JHM (2010) Expanding the substantial interactome of NEMO using protein microarrays. PLoS ONE 5, e8799.
  • 57
    del Rincón SV, Rogers J, Widschwendter M, Sun D, Sieburg HB & Spruck C (2010) Development and validation of a method for profiling post-translational modification activities using protein microarrays. PLoS ONE 5, e11332.
  • 58
    Montagnoli A, Bosotti R, Villa F, Rialland M, Brotherton D, Mercurio C, Berthelsen J & Santocanale C (2002) Drf1, a novel regulatory subunit for human Cdc7 kinase. EMBO J 21, 31713181.
  • 59
    Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41, 207234.
  • 60
    Rosa JL, Pérez JX, Ventura F, Tauler A, Gil J, Shimoyama M, Pilkis SJ & Bartrons R (1995) Role of the N-terminal region in covalent modification of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase: comparison of phosphorylation and ADP-ribosylation. Biochem J 309, 119125.