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Research Paper

The nuclear envelope proteome differs notably between tissues

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Pages 552-564 | Published online: 18 Sep 2012

References

  • Dauer WT, Worman HJ. The nuclear envelope as a signaling node in development and disease. Dev Cell 2009; 17:626 - 38; http://dx.doi.org/10.1016/j.devcel.2009.10.016; PMID: 19922868
  • Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev 2009; 23:912 - 27; http://dx.doi.org/10.1101/gad.1782209; PMID: 19390086
  • Korfali N, Srsen V, Waterfall M, Batrakou DG, Pekovic V, Hutchison CJ, et al. A flow cytometry-based screen of nuclear envelope transmembrane proteins identifies NET4/Tmem53 as involved in stress-dependent cell cycle withdrawal. PLoS One 2011; 6:e18762; http://dx.doi.org/10.1371/journal.pone.0018762; PMID: 21533191
  • Lee JS, Hale CM, Panorchan P, Khatau SB, George JP, Tseng Y, et al. Nuclear lamin A/C deficiency induces defects in cell mechanics, polarization andmigration. Biophys J 2007; 93:2542 - 52; http://dx.doi.org/10.1529/biophysj.106.102426; PMID: 17631533
  • Foisner R, Aebi U, Bonne G, Gruenbaum Y, Novelli G. 141st ENMC International Workshop inaugural meeting of the EURO-Laminopathies project “Nuclear Envelope-linked Rare Human Diseases: From Molecular Pathophysiology towards Clinical Applications”, 10-12 March 2006, Naarden, The Netherlands. Neuromuscul Disord 2007; 17:655 - 60; http://dx.doi.org/10.1016/j.nmd.2007.04.003; PMID: 17587579
  • Schirmer EC, Gerace L. The nuclear membrane proteome: extending the envelope. Trends Biochem Sci 2005; 30:551 - 8; http://dx.doi.org/10.1016/j.tibs.2005.08.003; PMID: 16125387
  • Wilkie GS, Schirmer EC. Guilt by association: the nuclear envelope proteome and disease. Mol Cell Proteomics 2006; 5:1865 - 75; http://dx.doi.org/10.1074/mcp.R600003-MCP200; PMID: 16790741
  • Mootha VK, Bunkenborg J, Olsen JV, Hjerrild M, Wisniewski JR, Stahl E, et al. Integrated analysis of protein composition, tissue diversity andgene regulation in mouse mitochondria. Cell 2003; 115:629 - 40; http://dx.doi.org/10.1016/S0092-8674(03)00926-7; PMID: 14651853
  • Korfali N, Wilkie GS, Swanson SK, Srsen V, Batrakou DG, Fairley EA, et al. The leukocyte nuclear envelope proteome varies with cell activation and contains novel transmembrane proteins that affect genome architecture. Mol Cell Proteomics 2010; 9:2571 - 85; http://dx.doi.org/10.1074/mcp.M110.002915; PMID: 20693407
  • Wilkie GS, Korfali N, Swanson SK, Malik P, Srsen V, Batrakou DG, et al. Several novel nuclear envelope transmembrane proteins identified in skeletal muscle have cytoskeletal associations. Mol Cell Proteomics 2011; 10:M110 - , 003129; http://dx.doi.org/10.1074/mcp.M110.003129; PMID: 20876400
  • Schirmer EC, Florens L, Guan T, Yates JR 3rd, Gerace L. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science 2003; 301:1380 - 2; http://dx.doi.org/10.1126/science.1088176; PMID: 12958361
  • Dreger M, Bengtsson L, Schöneberg T, Otto H, Hucho F. Nuclear envelope proteomics: novel integral membrane proteins of the inner nuclear membrane. Proc Natl Acad Sci U S A 2001; 98:11943 - 8; http://dx.doi.org/10.1073/pnas.211201898; PMID: 11593002
  • Callan HG, Tomlin SG. Experimental studies on amphibian oocyte nuclei. I. Investigation of the structure of the nuclear membrane by means of the electron microscope. Proc R Soc Lond B Biol Sci 1950; 137:367 - 78; http://dx.doi.org/10.1098/rspb.1950.0047; PMID: 14786306
  • Salpingidou G, Smertenko A, Hausmanowa-Petrucewicz I, Hussey PJ, Hutchison CJ. A novel role for the nuclear membrane protein emerin in association of the centrosome to the outer nuclear membrane. J Cell Biol 2007; 178:897 - 904; http://dx.doi.org/10.1083/jcb.200702026; PMID: 17785515
  • Walter P, Blobel G. Preparation of microsomal membranes for cotranslational protein translocation. Methods Enzymol 1983; 96:84 - 93; http://dx.doi.org/10.1016/S0076-6879(83)96010-X; PMID: 6656655
  • Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, et al. A mammalian organelle map by protein correlation profiling. Cell 2006; 125:187 - 99; http://dx.doi.org/10.1016/j.cell.2006.03.022; PMID: 16615899
  • Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, et al. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A 2006; 103:18928 - 33; http://dx.doi.org/10.1073/pnas.0606379103; PMID: 17138671
  • Zhang Y, Wen Z, Washburn MP, Florens L. Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins. Anal Chem 2010; 82:2272 - 81; http://dx.doi.org/10.1021/ac9023999; PMID: 20166708
  • Washburn MP, Wolters D, Yates JR 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001; 19:242 - 7; http://dx.doi.org/10.1038/85686; PMID: 11231557
  • Wolters DA, Washburn MP, Yates JR 3rd. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001; 73:5683 - 90; http://dx.doi.org/10.1021/ac010617e; PMID: 11774908
  • Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002; 99:4465 - 70; http://dx.doi.org/10.1073/pnas.012025199; PMID: 11904358
  • Wu C,, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, et al. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 2009; 10:R130; http://dx.doi.org/10.1186/gb-2009-10-11-r130; PMID: 19919682
  • Lui PP, Chan FL, Suen YK, Kwok TT, Kong SK. The nucleus of HeLa cells contains tubular structures for Ca2+ signaling with the involvement of mitochondria. Biochem Biophys Res Commun 2003; 308:826 - 33; http://dx.doi.org/10.1016/S0006-291X(03)01469-4; PMID: 12927793
  • Malik P, Korfali N, Srsen V, Lazou V, Batrakou DG, Zuleger N, et al. Cell-specific and lamin-dependent targeting of novel transmembrane proteins in the nuclear envelope. Cell Mol Life Sci 2010; 67:1353 - 69; http://dx.doi.org/10.1007/s00018-010-0257-2; PMID: 20091084
  • Ulbert S, Platani M, Boue S, Mattaj IW. Direct membrane protein-DNA interactions required early in nuclear envelope assembly. J Cell Biol 2006; 173:469 - 76; http://dx.doi.org/10.1083/jcb.200512078; PMID: 16717124
  • Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group. AmiGO: online access to ontology and annotation data. Bioinformatics 2009; 25:288 - 9; http://dx.doi.org/10.1093/bioinformatics/btn615; PMID: 19033274
  • Helbig AO, Heck AJ, Slijper M. Exploring the membrane proteome--challenges and analytical strategies. J Proteomics 2010; 73:868 - 78; http://dx.doi.org/10.1016/j.jprot.2010.01.005; PMID: 20096812
  • Savas JN, Stein BD, Wu CC, Yates JR 3rd. Mass spectrometry accelerates membrane protein analysis. Trends Biochem Sci 2011; 36:388 - 96; PMID: 21616670
  • Cízková A, Stránecký V, Mayr JA, Tesarová M, Havlícková V, Paul J, et al. TMEM70 mutations cause isolated ATP synthase deficiency and neonatal mitochondrial encephalocardiomyopathy. Nat Genet 2008; 40:1288 - 90; http://dx.doi.org/10.1038/ng.246; PMID: 18953340
  • Karbowski M, Neutzner A, Youle RJ. The mitochondrial E3 ubiquitin ligase MARCH5 is required for Drp1 dependent mitochondrial division. J Cell Biol 2007; 178:71 - 84; http://dx.doi.org/10.1083/jcb.200611064; PMID: 17606867
  • Yazawa M, Ferrante C, Feng J, Mio K, Ogura T, Zhang M, et al. TRIC channels are essential for Ca2+ handling in intracellular stores. Nature 2007; 448:78 - 82; http://dx.doi.org/10.1038/nature05928; PMID: 17611541
  • Lattanzi G, Ognibene A, Sabatelli P, Capanni C, Toniolo D, Columbaro M, et al. Emerin expression at the early stages of myogenic differentiation. Differentiation 2000; 66:208 - 17; http://dx.doi.org/10.1111/j.1432-0436.2000.660407.x; PMID: 11269947
  • Wheeler MA, Warley A, Roberts RG, Ehler E, Ellis JA. Identification of an emerin-beta-catenin complex in the heart important for intercalated disc architecture and beta-catenin localisation. Cell Mol Life Sci 2010; 67:781 - 96; http://dx.doi.org/10.1007/s00018-009-0219-8; PMID: 19997769
  • Arteaga MF, Gutiérrez R, Avila J, Mobasheri A, Díaz-Flores L, Martín-Vasallo P. Regeneration influences expression of the Na+, K+-atpase subunit isoforms in the rat peripheral nervous system. Neuroscience 2004; 129:691 - 702; http://dx.doi.org/10.1016/j.neuroscience.2004.08.041; PMID: 15541890
  • Bkaily G, Nader M, Avedanian L, Jacques D, Perrault C, Abdel-Samad D, et al. Immunofluorescence revealed the presence of NHE-1 in the nuclear membranes of rat cardiomyocytes and isolated nuclei of human, rabbit andrat aortic and liver tissues. Can J Physiol Pharmacol 2004; 82:805 - 11; http://dx.doi.org/10.1139/y04-119; PMID: 15523538
  • Cruttwell C, Bernard J, Hilly M, Nicolas V, Tunwell RE, Mauger JP. Dynamics of the inositol 1,4,5-trisphosphate receptor during polarisation of MDCK cells. Biol Cell 2005; http://dx.doi.org/10.1042/BC20040503; PMID: 15730344
  • Erickson ES, Mooren OL, Moore-Nichols D, Dunn RC. Activation of ryanodine receptors in the nuclear envelope alters the conformation of the nuclear pore complex. Biophys Chem 2004; 112:1 - 7; http://dx.doi.org/10.1016/j.bpc.2004.06.010; PMID: 15501570
  • Klein C, Gensburger C, Freyermuth S, Nair BC, Labourdette G, Malviya AN. A 120 kDa nuclear phospholipase Cgamma1 protein fragment is stimulated in vivo by EGF signal phosphorylating nuclear membrane EGFR. Biochemistry 2004; 43:15873 - 83; http://dx.doi.org/10.1021/bi048604t; PMID: 15595842
  • Paine PL, Moore LC, Horowitz SB. Nuclear envelope permeability. Nature 1975; 254:109 - 14; http://dx.doi.org/10.1038/254109a0; PMID: 1117994
  • Maissel A, Marom M, Shtutman M, Shahaf G, Livneh E. PKCeta is localized in the Golgi, ER and nuclear envelope and translocates to the nuclear envelope upon PMA activation and serum-starvation: C1b domain and the pseudosubstrate containing fragment target PKCeta to the Golgi and the nuclear envelope. Cell Signal 2006; 18:1127 - 39; http://dx.doi.org/10.1016/j.cellsig.2005.09.003; PMID: 16242915
  • Deng M, Hochstrasser M. Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase. Nature 2006; 443:827 - 31; http://dx.doi.org/10.1038/nature05170; PMID: 17051211
  • Lin F, Morrison JM, Wu W, Worman HJ. MAN1, an integral protein of the inner nuclear membrane, binds Smad2 and Smad3 and antagonizes transforming growth factor-beta signaling. Hum Mol Genet 2005; 14:437 - 45; http://dx.doi.org/10.1093/hmg/ddi040; PMID: 15601644
  • Markiewicz E, Tilgner K, Barker N, van de Wetering M, Clevers H, Dorobek M, et al. The inner nuclear membrane protein emerin regulates beta-catenin activity by restricting its accumulation in the nucleus. EMBO J 2006; 25:3275 - 85; http://dx.doi.org/10.1038/sj.emboj.7601230; PMID: 16858403
  • Furukawa K. LAP2 binding protein 1 (L2BP1/BAF) is a candidate mediator of LAP2-chromatin interaction. J Cell Sci 1999; 112:2485 - 92; PMID: 10393804
  • Somech R, Shaklai S, Geller O, Amariglio N, Simon AJ, Rechavi G, et al. The nuclear-envelope protein and transcriptional repressor LAP2beta interacts with HDAC3 at the nuclear periphery andinduces histone H4 deacetylation. J Cell Sci 2005; 118:4017 - 25; http://dx.doi.org/10.1242/jcs.02521; PMID: 16129885
  • Chi YH, Haller K, Peloponese JM Jr., Jeang KT. Histone acetyltransferase hALP and nuclear membrane protein hsSUN1 function in de-condensation of mitotic chromosomes. J Biol Chem 2007; 282:27447 - 58; http://dx.doi.org/10.1074/jbc.M703098200; PMID: 17631499
  • Holaska JM, Rais-Bahrami S, Wilson KL. Lmo7 is an emerin-binding protein that regulates the transcription of emerin and many other muscle-relevant genes. Hum Mol Genet 2006; 15:3459 - 72; http://dx.doi.org/10.1093/hmg/ddl423; PMID: 17067998
  • Guarda A, Bolognese F, Bonapace IM, Badaracco G. Interaction between the inner nuclear membrane lamin B receptor and the heterochromatic methyl binding protein, MeCP2. Exp Cell Res 2009; 315:1895 - 903; http://dx.doi.org/10.1016/j.yexcr.2009.01.019; PMID: 19331822
  • Ye Q, Worman HJ. Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1. J Biol Chem 1996; 271:14653 - 6; http://dx.doi.org/10.1074/jbc.271.25.14653; PMID: 8663349
  • Pegoraro G, Kubben N, Wickert U, Göhler H, Hoffmann K, Misteli T. Ageing-related chromatin defects through loss of the NURD complex. Nat Cell Biol 2009; 11:1261 - 7; http://dx.doi.org/10.1038/ncb1971; PMID: 19734887
  • Pestov NB, Korneenko TV, Zhao H, Adams G, Kostina MB, Shakhparonov MI, et al. The betam protein, a member of the X,K-ATPase beta-subunits family, is located intracellularly in pig skeletal muscle. Arch Biochem Biophys 2001; 396:80 - 8; http://dx.doi.org/10.1006/abbi.2001.2599; PMID: 11716465
  • Pestov NB, Ahmad N, Korneenko TV, Zhao H, Radkov R, Schaer D, et al. Evolution of Na,K-ATPase beta m-subunit into a coregulator of transcription in placental mammals. Proc Natl Acad Sci U S A 2007; 104:11215 - 20; http://dx.doi.org/10.1073/pnas.0704809104; PMID: 17592128
  • Stewart CL, Roux KJ, Burke B. Blurring the boundary: the nuclear envelope extends its reach. Science 2007; 318:1408 - 12; http://dx.doi.org/10.1126/science.1142034; PMID: 18048680
  • Worman HJ, Bonne G. “Laminopathies”: a wide spectrum of human diseases. Exp Cell Res 2007; 313:2121 - 33; http://dx.doi.org/10.1016/j.yexcr.2007.03.028; PMID: 17467691
  • Florens L, Korfali N, Schirmer EC. Subcellular fractionation and proteomics of nuclear envelopes. Methods Mol Biol 2008; 432:117 - 37; http://dx.doi.org/10.1007/978-1-59745-028-7_8; PMID: 18370014
  • Florens L, Washburn MP. Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol 2006; 328:159 - 75; PMID: 16785648
  • Wu CC, MacCoss MJ, Howell KE, Yates JR 3rd. A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 2003; 21:532 - 8; http://dx.doi.org/10.1038/nbt819; PMID: 12692561
  • McDonald WH, Tabb DL, Sadygov RG, MacCoss MJ, Venable J, Graumann J, et al. MS1, MS2 andSQT-three unified, compact andeasily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun Mass Spectrom 2004; 18:2162 - 8; http://dx.doi.org/10.1002/rcm.1603; PMID: 15317041
  • Venable JD, Dong MQ, Wohlschlegel J, Dillin A, Yates JR. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat Methods 2004; 1:39 - 45; http://dx.doi.org/10.1038/nmeth705; PMID: 15782151
  • Eng J, McCormack A. Yates Jr. An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database. J Am Soc Mass Spectrom 1994; 5:976 - 89; http://dx.doi.org/10.1016/1044-0305(94)80016-2
  • Tabb DL, McDonald WH, Yates JR 3rd. DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 2002; 1:21 - 6; http://dx.doi.org/10.1021/pr015504q; PMID: 12643522
  • Zybailov BL, Florens L, Washburn MP. Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol Biosyst 2007; 3:354 - 60; http://dx.doi.org/10.1039/b701483j; PMID: 17460794
  • Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, et al. Ensembl 2008. Nucleic Acids Res 2008; 36:Database issue D707 - 14; http://dx.doi.org/10.1093/nar/gkm988; PMID: 18000006
  • Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002; 12:1611 - 8; http://dx.doi.org/10.1101/gr.361602; PMID: 12368254
  • Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000; 16:276 - 7; http://dx.doi.org/10.1016/S0168-9525(00)02024-2; PMID: 10827456
  • Nakai K, Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 1999; 24:34 - 6; http://dx.doi.org/10.1016/S0968-0004(98)01336-X; PMID: 10087920
  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567 - 80; http://dx.doi.org/10.1006/jmbi.2000.4315; PMID: 11152613