Abstract
The organization of the nuclear periphery is crucial for many nuclear functions. Nuclear lamins form dense network at the nuclear periphery and play a substantial role in chromatin organization, transcription regulation and in organization of nuclear pore complexes (NPCs). Here, we show that TPR, the protein located preferentially within the nuclear baskets of NPCs, associates with lamin B1. The depletion of TPR affects the organization of lamin B1 but not lamin A/C within the nuclear lamina as shown by stimulated emission depletion microscopy. Finally, reduction of TPR affects the distribution of NPCs within the nuclear envelope and the effect can be reversed by simultaneous knock-down of lamin A/C or the overexpression of lamin B1. Our work suggests a novel role for the TPR at the nuclear periphery: the TPR contributes to the organization of the nuclear lamina and in cooperation with lamins guards the interphase assembly of nuclear pore complexes.
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Gruenbaum Y, Foisner R (2015) Lamins: nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu Rev Biochem 84:131–164. https://doi.org/10.1146/annurev-biochem-060614-034115
Naetar N, Ferraioli S, Foisner R (2017) Lamins in the nuclear interior—life outside the lamina. J Cell Sci 130(13):2087–2096. https://doi.org/10.1242/jcs.203430
de Leeuw R, Gruenbaum Y, Medalia O (2017) Nuclear lamins: thin filaments with major functions. Trends Cell Biol. https://doi.org/10.1016/j.tcb.2017.08.004
Schermelleh L, Carlton PM, Haase S, Shao L, Winoto L, Kner P, Burke B, Cardoso MC, Agard DA, Gustafsson MG, Leonhardt H, Sedat JW (2008) Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320(5881):1332–1336. https://doi.org/10.1126/science.1156947
Shimi T, Kittisopikul M, Tran J, Goldman AE, Adam SA, Zheng Y, Jaqaman K, Goldman RD (2015) Structural organization of nuclear lamins A, C, B1, and B2 revealed by superresolution microscopy. Mol Biol Cell 26(22):4075–4086. https://doi.org/10.1091/mbc.E15-07-0461
Xie W, Chojnowski A, Boudier T, Lim JS, Ahmed S, Ser Z, Stewart C, Burke B (2016) A-type lamins form distinct filamentous networks with differential nuclear pore complex associations. Curr Biol 26(19):2651–2658. https://doi.org/10.1016/j.cub.2016.07.049
Cho S, Irianto J, Discher DE (2017) Mechanosensing by the nucleus: from pathways to scaling relationships. J Cell Biol 216(2):305–315. https://doi.org/10.1083/jcb.201610042
Lammerding J, Fong LG, Ji JY, Reue K, Stewart CL, Young SG, Lee RT (2006) Lamins A and C but not lamin B1 regulate nuclear mechanics. J Biol Chem 281(35):25768–25780. https://doi.org/10.1074/jbc.M513511200
Swift J, Ivanovska IL, Buxboim A, Harada T, Dingal PC, Pinter J, Pajerowski JD, Spinler KR, Shin JW, Tewari M, Rehfeldt F, Speicher DW, Discher DE (2013) Nuclear lamin-A scales with tissue stiffness and enhances matrix-directed differentiation. Science 341(6149):1240104. https://doi.org/10.1126/science.1240104
Daigle N, Beaudouin J, Hartnell L, Imreh G, Hallberg E, Lippincott-Schwartz J, Ellenberg J (2001) Nuclear pore complexes form immobile networks and have a very low turnover in live mammalian cells. J Cell Biol 154(1):71–84
Lenz-Bohme B, Wismar J, Fuchs S, Reifegerste R, Buchner E, Betz H, Schmitt B (1997) Insertional mutation of the Drosophila nuclear lamin Dm0 gene results in defective nuclear envelopes, clustering of nuclear pore complexes, and accumulation of annulate lamellae. J Cell Biol 137(5):1001–1016
Liu J, Rolef Ben-Shahar T, Riemer D, Treinin M, Spann P, Weber K, Fire A, Gruenbaum Y (2000) Essential roles for Caenorhabditis elegans lamin gene in nuclear organization, cell cycle progression, and spatial organization of nuclear pore complexes. Mol Biol Cell 11(11):3937–3947
Guo Y, Kim Y, Shimi T, Goldman RD, Zheng Y (2014) Concentration-dependent lamin assembly and its roles in the localization of other nuclear proteins. Mol Biol Cell 25(8):1287–1297. https://doi.org/10.1091/mbc.E13-11-0644
Sullivan T, Escalante-Alcalde D, Bhatt H, Anver M, Bhat N, Nagashima K, Stewart CL, Burke B (1999) Loss of A-type lamin expression compromises nuclear envelope integrity leading to muscular dystrophy. J Cell Biol 147(5):913–920
Maeshima K, Iino H, Hihara S, Funakoshi T, Watanabe A, Nishimura M, Nakatomi R, Yahata K, Imamoto F, Hashikawa T, Yokota H, Imamoto N (2010) Nuclear pore formation but not nuclear growth is governed by cyclin-dependent kinases (Cdks) during interphase. Nat Struct Mol Biol 17(9):1065–1071. https://doi.org/10.1038/nsmb.1878
Vietri M, Schink KO, Campsteijn C, Wegner CS, Schultz SW, Christ L, Thoresen SB, Brech A, Raiborg C, Stenmark H (2015) Spastin and ESCRT-III coordinate mitotic spindle disassembly and nuclear envelope sealing. Nature 522(7555):231–235. https://doi.org/10.1038/nature14408
Maeshima K, Yahata K, Sasaki Y, Nakatomi R, Tachibana T, Hashikawa T, Imamoto F, Imamoto N (2006) Cell-cycle-dependent dynamics of nuclear pores: pore-free islands and lamins. J Cell Sci 119(Pt 21):4442–4451. https://doi.org/10.1242/jcs.03207
Hurt E, Beck M (2015) Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis. Curr Opin Cell Biol 34:31–38. https://doi.org/10.1016/j.ceb.2015.04.009
Walther TC, Fornerod M, Pickersgill H, Goldberg M, Allen TD, Mattaj IW (2001) The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins. EMBO J 20(20):5703–5714. https://doi.org/10.1093/emboj/20.20.5703
Smythe C, Jenkins HE, Hutchison CJ (2000) Incorporation of the nuclear pore basket protein nup153 into nuclear pore structures is dependent upon lamina assembly: evidence from cell-free extracts of Xenopus eggs. EMBO J 19(15):3918–3931. https://doi.org/10.1093/emboj/19.15.3918
Al-Haboubi T, Shumaker DK, Koser J, Wehnert M, Fahrenkrog B (2011) Distinct association of the nuclear pore protein Nup153 with A- and B-type lamins. Nucleus 2(5):500–509. https://doi.org/10.4161/nucl.2.5.17913
Pal K, Bandyopadhyay A, Zhou XE, Xu Q, Marciano DP, Brunzelle JS, Yerrum S, Griffin PR, Vande Woude G, Melcher K, Xu HE (2017) Structural basis of TPR-mediated oligomerization and activation of oncogenic fusion kinases. Structure 25(6):867–877 e863. https://doi.org/10.1016/j.str.2017.04.015
Coyle JH, Bor YC, Rekosh D, Hammarskjold ML (2011) The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway. RNA 17(7):1344–1356. https://doi.org/10.1261/rna.2616111
Fontoura BM, Dales S, Blobel G, Zhong H (2001) The nucleoporin Nup98 associates with the intranuclear filamentous protein network of TPR. Proc Natl Acad Sci USA 98(6):3208–3213. https://doi.org/10.1073/pnas.061014698
Rajanala K, Sarkar A, Jhingan GD, Priyadarshini R, Jalan M, Sengupta S, Nandicoori VK (2014) Phosphorylation of nucleoporin Tpr governs its differential localization and is required for its mitotic function. J Cell Sci 127(Pt 16):3505–3520. https://doi.org/10.1242/jcs.149112
Vomastek T, Iwanicki MP, Burack WR, Tiwari D, Kumar D, Parsons JT, Weber MJ, Nandicoori VK (2008) Extracellular signal-regulated kinase 2 (ERK2) phosphorylation sites and docking domain on the nuclear pore complex protein Tpr cooperatively regulate ERK2–Tpr interaction. Mol Cell Biol 28(22):6954–6966. https://doi.org/10.1128/MCB.00925-08
Nakano H, Funasaka T, Hashizume C, Wong RW (2010) Nucleoporin translocated promoter region (Tpr) associates with dynein complex, preventing chromosome lagging formation during mitosis. J Biol Chem 285(14):10841–10849. https://doi.org/10.1074/jbc.M110.105890
Lee SH, Sterling H, Burlingame A, McCormick F (2008) Tpr directly binds to Mad1 and Mad2 and is important for the Mad1–Mad2-mediated mitotic spindle checkpoint. Genes Dev 22(21):2926–2931. https://doi.org/10.1101/gad.1677208
Schweizer N, Ferras C, Kern DM, Logarinho E, Cheeseman IM, Maiato H (2013) Spindle assembly checkpoint robustness requires Tpr-mediated regulation of Mad1/Mad2 proteostasis. J Cell Biol 203(6):883–893. https://doi.org/10.1083/jcb.201309076
David-Watine B (2011) Silencing nuclear pore protein Tpr elicits a senescent-like phenotype in cancer cells. PLoS One 6(7):e22423. https://doi.org/10.1371/journal.pone.0022423
Snow CJ, Paschal BM (2014) Roles of the nucleoporin Tpr in cancer and aging. Adv Exp Med Biol 773:309–322. https://doi.org/10.1007/978-1-4899-8032-8_14
Krull S, Dorries J, Boysen B, Reidenbach S, Magnius L, Norder H, Thyberg J, Cordes VC (2010) Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion. EMBO J 29(10):1659–1673. https://doi.org/10.1038/emboj.2010.54
Vaquerizas JM, Suyama R, Kind J, Miura K, Luscombe NM, Akhtar A (2010) Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS Genet 6(2):e1000846. https://doi.org/10.1371/journal.pgen.1000846
Funasaka T, Tsuka E, Wong RW (2012) Regulation of autophagy by nucleoporin Tpr. Sci Rep 2:878. https://doi.org/10.1038/srep00878
McCloskey A, Ibarra A, Hetzer MW (2018) Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes Dev 32(19–20):1321–1331. https://doi.org/10.1101/gad.315523.118
Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T, Goldman RD (2008) The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev 22(24):3409–3421. https://doi.org/10.1101/gad.1735208
Wu R, Terry AV, Singh PB, Gilbert DM (2005) Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol Biol Cell 16(6):2872–2881. https://doi.org/10.1091/mbc.E04-11-0997
Vollmer B, Lorenz M, Moreno-Andres D, Bodenhofer M, De Magistris P, Astrinidis SA, Schooley A, Flotenmeyer M, Leptihn S, Antonin W (2015) Nup153 recruits the Nup107–160 complex to the inner nuclear membrane for interphasic nuclear pore complex assembly. Dev Cell 33(6):717–728. https://doi.org/10.1016/j.devcel.2015.04.027
Hase ME, Cordes VC (2003) Direct interaction with nup153 mediates binding of Tpr to the periphery of the nuclear pore complex. Mol Biol Cell 14(5):1923–1940. https://doi.org/10.1091/mbc.E02-09-0620
Belgareh N, Rabut G, Bai SW, van Overbeek M, Beaudouin J, Daigle N, Zatsepina OV, Pasteau F, Labas V, Fromont-Racine M, Ellenberg J, Doye V (2001) An evolutionarily conserved NPC subcomplex, which redistributes in part to kinetochores in mammalian cells. J Cell Biol 154(6):1147–1160. https://doi.org/10.1083/jcb.200101081
Fiserova J, Efenberkova M, Sieger T, Maninova M, Uhlirova J, Hozak P (2017) Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data. J Cell Sci 130(12):2066–2077. https://doi.org/10.1242/jcs.198424
Ball G, Demmerle J, Kaufmann R, Davis I, Dobbie IM, Schermelleh L (2015) SIMcheck: a toolbox for successful super-resolution structured illumination microscopy. Sci Rep 5:15915. https://doi.org/10.1038/srep15915
Tsai W (1985) Moment-preserving tresholding: a new approach. Comput Vis Graph Image Process 29:377–393
Arganda-Carreras I, Fernandez-Gonzalez R, Munoz-Barrutia A, Ortiz-De-Solorzano C (2010) 3D reconstruction of histological sections: application to mammary gland tissue. Microsc Res Tech 73(11):1019–1029. https://doi.org/10.1002/jemt.20829
Wee CY, Parmesran R (2007) Measure of image sharpness using eigenvalues. Inf Sci 177(12):2533–2552
Razafsky D, Ward C, Potter C, Zhu W, Xue Y, Kefalov VJ, Fong LG, Young SG, Hodzic D (2016) Lamin B1 and lamin B2 are long-lived proteins with distinct functions in retinal development. Mol Biol Cell 27(12):1928–1937. https://doi.org/10.1091/mbc.E16-03-0143
Jacinto FV, Benner C, Hetzer MW (2015) The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes Dev 29(12):1224–1238. https://doi.org/10.1101/gad.260919.115
Nanni S, Re A, Ripoli C, Gowran A, Nigro P, D’Amario D, Amodeo A, Crea F, Grassi C, Pontecorvi A, Farsetti A, Colussi C (2016) The nuclear pore protein Nup153 associates with chromatin and regulates cardiac gene expression in dystrophic mdx hearts. Cardiovasc Res 112(2):555–567. https://doi.org/10.1093/cvr/cvw204
Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer MW, Gage FH (2017) Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell 21(5):618–634 e617. https://doi.org/10.1016/j.stem.2017.08.012
Freund A, Laberge RM, Demaria M, Campisi J (2012) Lamin B1 loss is a senescence-associated biomarker. Mol Biol Cell 23(11):2066–2075. https://doi.org/10.1091/mbc.E11-10-0884
Otsuka S, Bui KH, Schorb M, Hossain MJ, Politi AZ, Koch B, Eltsov M, Beck M, Ellenberg J (2016) Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope. Elife 5:e19071. https://doi.org/10.7554/elife.19071
Otsuka S, Steyer AM, Schorb M, Heriche JK, Hossain MJ, Sethi S, Kueblbeck M, Schwab Y, Beck M, Ellenberg J (2018) Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings. Nat Struct Mol Biol 25(1):21–28. https://doi.org/10.1038/s41594-017-0001-9
Acknowledgements
We thank to Iva Jelinkova for the help with immunofluorescence and HeLa cell culture. We thank the Microscopy Centre, Light Microscopy Core Facility, IMG ASCR, Prague, Czech Republic for the help with imaging, especially to Ivan Novotny for the help with microscope settings and acquisitions by SIM and STED.
Funding
This work was supported by the Grant Agency of the Czech Republic: [15-08835Y], [16-03346S], [16-03403S], [17-09103S], [18-19714S], by the institutional support of long-term conceptual support of development of the scientific organization (RVO: 68378050) and by the project “BIOCEV—Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University” (CZ.1.05/1.1.00/02.0109), from the European Regional Development Fund. M.M. was supported by grant of ASCR (L200521801). J.U. was supported by GAUK (930218). We acknowledge the Light and Electron Microscopy Core Facility, IMG CAS supported by the MEYS CR (LM2015062), OPPK (CZ.2.16/3.1.00/21547), NPU I (LO1419) and ERDF (Project no. CZ.02.1.01/0.0/0.0/16_013/0001775).
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JF was responsible for conception, JF and MM for design of the experiments, JF, MM, KF and PH for the biological data analysis; JF, MM, JU and LS for the experimental execution; ME for the Matlab programming, TS for statistical analysis; JF and MC for the image analysis, JF for drafting the article and JF, MM, TS, ME, MC, JU, LS, KF and PH for editing the article prior to submission.
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Fišerová, J., Maninová, M., Sieger, T. et al. Nuclear pore protein TPR associates with lamin B1 and affects nuclear lamina organization and nuclear pore distribution. Cell. Mol. Life Sci. 76, 2199–2216 (2019). https://doi.org/10.1007/s00018-019-03037-0
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DOI: https://doi.org/10.1007/s00018-019-03037-0