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Exploring the Protein Composition of the Plant Nuclear Envelope

  • Xiao Zhou
  • Kentaro Tamura
  • Katja Graumann
  • Iris MeierEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1411)

Abstract

Due to rather limited sequence similarity, targeted identification of plant nuclear envelope and nuclear pore complex proteins has mainly followed two routes: (1) advanced computational identification followed by experimental verification and (2) immunoaffinity purification of complexes followed by mass spectrometry. Following candidate identification, fluorescence recovery after photobleaching (FRAP) and fluorescence resonance energy transfer (FRET) provide powerful tools to verify protein–protein interactions in situ at the NE. Here, we describe these methods for the example of Arabidopsis thaliana nuclear pore and nuclear envelope protein identification.

Key words

Arabidopsis thaliana KASH protein Nuclear pore complex Bioinformatics Immunoaffinity purification Fluorescence resonance energy transfer (FRET) Fluorescence recovery after photobleaching (FRAP) 

Notes

Acknowledgments

I.M. thanks the National Science Foundation for financial support of research in this area. K.T. thanks the Grants-in-Aid for Scientific Research (nos. 15K14545 and 26711017) for supporting this work. K.G. thanks the Leverhulme Trust for an Early Career Fellowship supporting her research.

References

  1. 1.
    Zhou X, Graumann K, Meier I (2015) The plant nuclear envelope as a multifunctional platform LINCed by SUN and KASH. J Exp Bot 66:1649–1659CrossRefPubMedGoogle Scholar
  2. 2.
    Jacob Y, Mongkolsiriwatana C, Veley KM et al (2007) The nuclear pore protein AtTPR is required for RNA homeostasis, flowering time, and auxin signaling. Plant Physiol 144:1383–1390CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Xu XM, Rose A, Muthuswamy S et al (2007) NUCLEAR PORE ANCHOR, the Arabidopsis homolog of Tpr/Mlp1/Mlp2/megator, is involved in mRNA export and SUMO homeostasis and affects diverse aspects of plant development. Plant Cell 19:1537–1548CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Reeves PH, Murtas G, Dash S et al (2002) Early in short days 4, a mutation in Arabidopsis that causes early flowering and reduces the mRNA abundance of the floral repressor FLC. Development 129:5349–5361CrossRefPubMedGoogle Scholar
  5. 5.
    Murtas G, Reeves PH, Fu Y-F et al (2003) A nuclear protease required for flowering-time regulation in Arabidopsis reduces the abundance of SMALL UBIQUITIN-RELATED MODIFIER conjugates. Plant Cell 15:2308–2319CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Parry G, Ward S, Cernac A et al (2006) The Arabidopsis SUPPRESSOR OF AUXIN RESISTANCE proteins are nucleoporins with an important role in hormone signaling and development. Plant Cell 18:1590–1603CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Muthuswamy S, Meier I (2011) Genetic and environmental changes in SUMO homeostasis lead to nuclear mRNA retention in plants. Planta 233:201–208CrossRefPubMedGoogle Scholar
  8. 8.
    Zhang Y, Li X (2005) A putative nucleoporin 96 is required for both basal defense and constitutive resistance responses mediated by suppressor of npr1-1, constitutive 1. Plant Cell 17:1306–1316CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Cheng YT, Germain H, Wiermer M et al (2009) Nuclear pore complex component MOS7/Nup88 is required for innate immunity and nuclear accumulation of defense regulators in Arabidopsis. Plant Cell 21:2503–2516CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Kanamori N, Madsen LH, Radutoiu S et al (2006) A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proc Natl Acad Sci U S A 103:359–364CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Saito K, Yoshikawa M, Yano K et al (2007) NUCLEOPORIN85 is required for calcium spiking, fungal and bacterial symbioses, and seed production in Lotus japonicus. Plant Cell 19:610–624CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Tamura K, Fukao Y, Iwamoto M et al (2010) Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. Plant Cell 22:4084–4097CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Razafsky D, Hodzic D (2009) Bringing KASH under the SUN: the many faces of nucleo-cytoskeletal connections. J Cell Biol 186:461–472CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Starr DA, Fridolfsson HN (2010) Interactions between nuclei and the cytoskeleton are mediated by SUN-KASH nuclear-envelope bridges. Annu Rev Cell Dev Biol 26:421–444CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Gundersen GG, Worman HJ (2013) Nuclear positioning. Cell 152:1376–1389CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Tatout C, Evans D, Vanrobays E et al (2014) The plant LINC complex at the nuclear envelope. Chromosome Res 22:241–252CrossRefPubMedGoogle Scholar
  17. 17.
    Kim DI, Birendra KC, Roux KJ (2015) Making the LINC: SUN and KASH protein interactions. Biol Chem 396:295–310CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Zhou X, Graumann K, Wirthmueller L et al (2014) Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants. J Cell Biol 205:677–692CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Braun P, Aubourg S, Van Leene J et al (2013) Plant protein interactomes. Annu Rev Plant Biol 64:161–187CrossRefPubMedGoogle Scholar
  20. 20.
    Jones AM, Xuan Y, Xu M et al (2014) Border control—a membrane-linked interactome of Arabidopsis. Science 344:711–716CrossRefPubMedGoogle Scholar
  21. 21.
    Sprague BL, McNally JG (2005) FRAP analysis of binding: proper and fitting. Trends Cell Biol 15:84–91CrossRefPubMedGoogle Scholar
  22. 22.
    Martinière A, Runions J (2013) Protein diffusion in plant cell plasma membranes: the cell-wall corral. Front Plant Sci 4:515PubMedPubMedCentralGoogle Scholar
  23. 23.
    Ellenberg J, Siggia ED, Moreira JE et al (1997) Nuclear membrane dynamics and reassembly in living cells: targeting of an inner nuclear membrane protein in interphase and mitosis. J Cell Biol 138:1193–1206CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Östlund C, Sullivan T, Stewart CL et al (2006) Dependence of diffusional mobility of integral inner nuclear membrane proteins on A-type lamins. Biochemistry (Mosc) 45:1374–1382CrossRefGoogle Scholar
  25. 25.
    Graumann K, Runions J, Evans DE (2010) Characterization of SUN-domain proteins at the higher plant nuclear envelope. Plant J 61:134–144CrossRefPubMedGoogle Scholar
  26. 26.
    Graumann K (2014) Evidence for LINC1-SUN associations at the plant nuclear periphery. PLoS One 9, e93406CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Graumann K, Irons SL, Runions J et al (2007) Retention and mobility of the mammalian lamin B receptor in the plant nuclear envelope. Biol Cell 99:553–562CrossRefPubMedGoogle Scholar
  28. 28.
    Zuleger N, Kelly DA, Richardson AC et al (2011) System analysis shows distinct mechanisms and common principles of nuclear envelope protein dynamics. J Cell Biol 193:109–123CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Karpova T, Baumann C, He L et al (2003) Fluorescence resonance energy transfer from cyan to yellow fluorescent protein detected by acceptor photobleaching using confocal microscopy and a single laser. J Microsc 209:56–70CrossRefPubMedGoogle Scholar
  30. 30.
    Chen Y, Mauldin JP, Day RN et al (2007) Characterization of spectral FRET imaging microscopy for monitoring nuclear protein interactions. J Microsc 228:139–152CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Sparkes IA, Graumann K, Martinière A et al (2011) Bleach it, switch it, bounce it, pull it: using lasers to reveal plant cell dynamics. J Exp Bot 62:1–7CrossRefPubMedGoogle Scholar
  32. 32.
    Graumann K, Vanrobays E, Tutois S et al (2014) Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK. J Exp Bot 65:6499–6512CrossRefPubMedGoogle Scholar
  33. 33.
    Kall L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server. Nucleic Acids Res 35:W429–W432CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Axelrod D, Koppel D, Schlessinger J et al (1976) Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys J 16:1055CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Wilhelmsen K, Ketema M, Truong H et al (2006) KASH-domain proteins in nuclear migration, anchorage and other processes. J Cell Sci 119:5021–5029CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Xiao Zhou
    • 1
  • Kentaro Tamura
    • 2
  • Katja Graumann
    • 3
  • Iris Meier
    • 1
    Email author
  1. 1.Department of Molecular GeneticsThe Ohio State UniversityColumbusUSA
  2. 2.Department of BotanyKyoto UniversityKyotoJapan
  3. 3.Department of Biological and Medical SciencesOxford Brookes UniversityOxfordUK

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