#!/usr/bin/perl use strict; use warnings; use PDF::OCR2; $PDF::OCR2::CHECK_PDF = 1; my $pdf = PDF::OCR2->new('/home/marto/02_ProProInt2nd_Tab01.pdf'); print $pdf->text; #### TABLE 1. Examples of p53-interacting Proteins p53 domain involved in Selected p53-interacting protein Method interaction references A ctivating Tr anscription F actor 3 (ATF3) GST pull-down,co-IP FL 1 A taxia- T elangiectasia- M utated (ATM) GST pull-down FL 2 Bcl-XL co-IP,GST pull-down DNA-binding domain 3 Collaborator of ARF (CARF) co-IP FL 4 Ch eckpoint k inase 2 (Chk2) GST pull-down,co-IP amino terminal 5,6 Co nstitutively P hoto-morphogenic 1 (COP1) IP-tagged protein,silver staining 7 + mass spectrometry G lycogen S ynthase K inase-3  (GSK3  ), IP carboxyl terminal 8 H erpesvirus- A ssociated U biquitin- S pecific mass spectrometry of affinity- P rotease (HAUSP) purified p53-associated factors FL 9 H uman ortholog, S ilent i nformation r egulator (hSir2) co-IP,IF carboxyl terminal and central 10 c- J un- N -terminal k inase (JNK) co-IP amino terminal 11 M uscle S egment homeodomain family,vertebrate co-IP FL 12 homolog 1 (Msx1) N ADPH: q uinone o xidoreductase 1 (NQO1) gel filtration,co-IP FL 13,14 P oly( A DP- R ibose) P olymerase-1 (PARP-1) IP central and carboxy-terminal 15 fragments P rotein I nhibitor of A ctivated S TAT (PIAS) Y2H,co-IP FL 16,17 p 53- i nduced protein with a R ING H2 domain (Pirh2) co-IP DNA-binding domain 18 P ro m yelocytic l eukemia protein (PML) GST pull-down and IVT DNA-binding domain 19 P300/CBP co-IP,ChIP amino terminal 20 P olo- l ike k inase 1 (Plk1) co-IP DNA-binding domain 21 Re dox f actor 1/ AP - E ndonuclease 1 (Ref-1/APE1) far-western and IP-western FL 22 assays in vitro S caffold/ M atrix A ttachment R egion binding co-IP FL 23 protein-1 (SMAR1) S100B co-IP FL 24 T BP- A ssociated F actor 1 (TAF1) co-IP carboxyl terminal 25 Tr ansformation/t r anscription domain a ssociated co-IP,GST pull-down carbooxyl terminal 26 p rotein (TRRAP),hGcn5,TAF II 30 W e rn ers�syndrome protein (WRN) co-IP FL 27 14-3-3 co-IP,GST pull-down carboxyl terminal 28 The proteins listed in this table represent some (not all) of the factors identified as p53 interactors since 1998. The significa nt majority of these inter- actions were identified and characterized by targeted co-IP or by other biochemical means; in contrast, two-hybrid and other gene tic approaches have been less useful for identification of p53 interactors.IP,immunopr ecipitation;Y2H,yeast two-hybrid; IVT,in vitro translation; ChIP ,chromatin IP; FL, full length;IF,immunofluorescence. R EFERENCES (1) Yan C,Lu D,Hai T,and Boyd DD.2005.Activating transcription factor 3,a stress sensor,activates p53 by blocking its ubiquitination. EMBO J. 24: 2425�2435. (2) Khanna K.K., Keating K.E., Kozlov S., Scott S., Gatei M., Hobson K., Taya Y., Gabrielli B., Chan D., Lees-Miller S.P., and Lavin M.F. 1998. ATM associates with and phosphorylates p53: Mapping the region of interaction. Nat.Genet. 20: 398�400. (3) Mihara M.,Erster S.,Zaika A.,Petrenko O.,Chittenden T.,Pancoska P., and Moll U.M. 2003. p53 has a direct apoptogenic role at the mito- chondria. Mol.Cell 11: 577�590. (4) Hasan M.K.,Yaguchi T.,Minoda Y.,Hirano T.,Taira K.,Wadhwa R.,and Kaul S.C . 2004.Alternative reading frame protein (ARF)-independent function of CARF (collaborator of ARF) involves its interactions with p53:Evidence for a novel p53-activation pathway and its negative feed- back control. Biochem.J. 380: 605�610. (5) Shieh S.Y., Ahn J., Tamai K., Taya Y., and Proves C. 2000. The human homologs ofcheckpoint kinases C hk1 and Cds1 (Chk2) phosphorylate p53 at multiple DNA damage-inducible sites. Genes Dev . 14: 289�300. (6) Berger M.,Stahl N.,Del Sal G.,and Haupt Y.2005.Mutations in proline 82 of p53 impair its activation by Pin1 and Chk2 in response to DNA damage. Mol.Cell.Biol. 25: 5380�5388. (7) Dornan D., Wertz I., Shimizu H., Arnott D., Frantz G.D., Dowd P., O�Rourke K., Koeppen H., and Dixit V.M. 2004 . The ubiquitin ligase COP1 is a critical negative regulator of p53. Nature 429: 86�92. (8) Watcharasit P.,Bijur G.N.,Song L.,Zhu J.,Chen X.,and Jope R.S.2003. Glycogen synthase kinase-3beta (GSK3beta) binds to and promotes the actions of p53. J.Biol.Chem. 278: 48872�48879. (9) Li M.,Chen D.,Shiloh A.,Luo J.,Nikolaev A.Y.,Qin J.,and Gu W.2002. Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416: 648-653. ( 10) Vaziri H.,Dessain S.K.,Ng Eaton E.,Imai S.I.,Frye R.A.,Pandita T.K., Guarente L., and Weinberg R.A. 2001. hSir2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell 107: 149�159. (11) Fuchs S.Y.,Adler V.,Buschmann T.,Yin Z.,Wu X.,Jones S.N.,and Ronai Z.1998.JNK targets p53 ubiquitination and degradation in nonstressed cells. Genes Dev. 12: 2658�2663. (12) Park K.,Kim K.,Rho S.B.,Choi K.,Kim D.,Oh S.H.,Park J.,Lee S.H., and Lee J.H.2005.Homeobox Msx1 interacts with p53 tumor suppres- sor and inhibits tumor growth by inducing apoptosis. Cancer Res. 65: 749�757. 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NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA oligomers. J. Biol.Chem. 279: 31455�31461. (18) Leng R.P., Lin Y., Ma W., Wu H., Lemmers B., Chung S., Parant J.M., Lozano G., Hakem R., and Benchimol S. 2003. Pirh2, a p53-induced ubiquitin-protein ligase,promotes p53 degradation. Cell 112: 779�791. (19) Zhong S.,Salomoni P.,and Pandolfi P.P.2000.The transcriptional role of PML and the nuclear body. Nature Cell Biol. 2: E85�E90. (20) Ito A.,Lai C.H.,Zhao X.,Saito S.,Hamilton M.H.,Appella E.,and Yao T.P.2001.p300/CBP-mediated p53 acetylation is commonly induced by p53-activating agents and inhibited by MDM2. EMBO J. 20: 1331�1340. (21) Ando K., Ozaki T.,Yamamoto H., Furuya K., Hosoda M., Hayashi S., Fukuzawa M., and Nakagawara A. 2004. Polo-like kinase 1 (Plk1) inhibits p53 function by physical interaction and phosphorylation. J. Biol.Chem . 279: 25549�25561. (22) Hanson S., Kim E., and Deppert W. 2005. 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Acetylation of p53 activates transcription through recruitment of coactivators/histone acetyltrans- ferases. Mol.Cell 8: 1243�1254. (27) Sommers J.A.,Sharma S.,Doherty K.M.,Karmakar P.,Yang Q.,Kenny M.K., Harris C.C., and Brosh R.M., Jr. 2005. p53 modulates RPA- dependent and RPA-independent WRN helicase activity. Cancer Res. 65: 1223�1233. (28) Waterman M.J., Stavridi E.S., Waterman J.L., and Halazonetis T.D. 1998. ATM-dependent activation of p53 involves dephosphorylation and association with 14-3-3 proteins. Nat.Genet. 19: 175�178. �2005 by Cold Spring Harbor Laboratory Press.All rights reserved. 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