Comprehensive Nuclear Proteome of Arabidopsis Obtained by Sequential Extraction

Overview

Journal Nucleus

Date 2019 Apr 10

PMID 30961429

Citations 13

Authors

Chieko Goto

Shoko Hashizume

Yoichiro Fukao

Ikuko Hara-Nishimura

Kentaro Tamura

Affiliations

Soon will be listed here.

Abstract

In eukaryotes, the nucleus plays key roles in fundamental cellular processes, including DNA replication, chromatin maintenance, transcription, and translation. To better understand the functional diversity of nuclei, we developed a method for the comprehensive extraction of the nuclear proteome from Arabidopsis. We used a buffer with a high sucrose concentration to purify nuclei and then conducted solubility-based fractionation to increase proteome coverage. We identified 1539 proteins and two novel nuclear envelope (NE) proteins in the nuclear fraction of Arabidopsis cultured cells. The localization of 25 proteins was determined by GFP fusion analyses; 23 of these proteins were localized either in the nucleus or the NE-associated endoplasmic reticulum. This result was indicative of the high quality of the proteome. These findings will be useful for clarifying novel nuclear functions in plants.

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References

Saitoh N, Spahr C, Patterson S, Bubulya P, Neuwald A, Spector D . Proteomic analysis of interchromatin granule clusters. Mol Biol Cell. 2004; 15(8):3876-90. PMC: 491843. DOI: 10.1091/mbc.e04-03-0253. View

Nasrabadi D, Rezaei Larijani M, Fathi A, Gourabi H, Dizaj A, Baharvand H . Nuclear proteome analysis of monkey embryonic stem cells during differentiation. Stem Cell Rev Rep. 2010; 6(1):50-61. DOI: 10.1007/s12015-009-9109-6. View

Zhao Q, Brkljacic J, Meier I . Two distinct interacting classes of nuclear envelope-associated coiled-coil proteins are required for the tissue-specific nuclear envelope targeting of Arabidopsis RanGAP. Plant Cell. 2008; 20(6):1639-51. PMC: 2483365. DOI: 10.1105/tpc.108.059220. View

Tamura K, Hara-Nishimura I . Involvement of the nuclear pore complex in morphology of the plant nucleus. Nucleus. 2011; 2(3):168-72. PMC: 3149876. DOI: 10.4161/nucl.2.3.16175. View

Fakih Z, Bulbul Ahmed M, Letanneur C, Germain H . An unbiased nuclear proteomics approach reveals novel nuclear protein components that participates in MAMP-triggered immunity. Plant Signal Behav. 2016; 11(6):e1183087. PMC: 4977454. DOI: 10.1080/15592324.2016.1183087. View

Starr D, Fischer J . KASH 'n Karry: the KASH domain family of cargo-specific cytoskeletal adaptor proteins. Bioessays. 2005; 27(11):1136-46. DOI: 10.1002/bies.20312. View

Fernandez-Irigoyen J, Zelaya M, Tunon T, Santamaria E . Anatomo-proteomic characterization of human basal ganglia: focus on striatum and globus pallidus. Mol Brain. 2014; 7:83. PMC: 4236423. DOI: 10.1186/s13041-014-0083-9. View

Aki T, Yanagisawa S . Application of rice nuclear proteome analysis to the identification of evolutionarily conserved and glucose-responsive nuclear proteins. J Proteome Res. 2009; 8(8):3912-24. DOI: 10.1021/pr900187e. View

Zhou X, Graumann K, Evans D, Meier I . Novel plant SUN-KASH bridges are involved in RanGAP anchoring and nuclear shape determination. J Cell Biol. 2012; 196(2):203-11. PMC: 3265956. DOI: 10.1083/jcb.201108098. View

10.

Engelke R, Riede J, Hegermann J, Wuerch A, Eimer S, Dengjel J . The quantitative nuclear matrix proteome as a biochemical snapshot of nuclear organization. J Proteome Res. 2014; 13(9):3940-56. DOI: 10.1021/pr500218f. View

11.

Wu X, Xiong E, An S, Gong F, Wang W . Sequential extraction results in improved proteome profiling of medicinal plant Pinellia ternata tubers, which contain large amounts of high-abundance proteins. PLoS One. 2012; 7(11):e50497. PMC: 3502364. DOI: 10.1371/journal.pone.0050497. View

12.

Turck N, Richert S, Gendry P, Stutzmann J, Kedinger M, Leize E . Proteomic analysis of nuclear proteins from proliferative and differentiated human colonic intestinal epithelial cells. Proteomics. 2004; 4(1):93-105. DOI: 10.1002/pmic.200300480. View

13.

Gottschalk A, Neubauer G, Banroques J, Mann M, Luhrmann R, Fabrizio P . Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP. EMBO J. 1999; 18(16):4535-48. PMC: 1171528. DOI: 10.1093/emboj/18.16.4535. View

14.

Yin X, Komatsu S . Nuclear Proteomics Reveals the Role of Protein Synthesis and Chromatin Structure in Root Tip of Soybean during the Initial Stage of Flooding Stress. J Proteome Res. 2016; 15(7):2283-98. DOI: 10.1021/acs.jproteome.6b00330. View

15.

Lam Y, Evans V, Heesom K, Lamond A, Matthews D . Proteomics analysis of the nucleolus in adenovirus-infected cells. Mol Cell Proteomics. 2009; 9(1):117-30. PMC: 2808258. DOI: 10.1074/mcp.M900338-MCP200. View

16.

Andersen J, Lyon C, Fox A, Leung A, Lam Y, Steen H . Directed proteomic analysis of the human nucleolus. Curr Biol. 2002; 12(1):1-11. DOI: 10.1016/s0960-9822(01)00650-9. View

17.

Rose A, Schraegle S, Stahlberg E, Meier I . Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control. BMC Evol Biol. 2005; 5:66. PMC: 1322226. DOI: 10.1186/1471-2148-5-66. View

18.

Wang X, Xie B, Zhu M, Zhang Z, Hong Z . Nucleostemin-like 1 is required for embryogenesis and leaf development in Arabidopsis. Plant Mol Biol. 2011; 78(1-2):31-44. DOI: 10.1007/s11103-011-9840-7. View

19.

Zhang Y, Fang C, Bao H, Fan H, Shen H, Yang P . Nuclear proteome profile of C57BL/6J mouse liver. Sci China Life Sci. 2013; 56(6):513-23. DOI: 10.1007/s11427-013-4488-y. View

20.

Hill T, Broadhvest J, Kuzoff R, Gasser C . Arabidopsis SHORT INTEGUMENTS 2 is a mitochondrial DAR GTPase. Genetics. 2006; 174(2):707-18. PMC: 1602101. DOI: 10.1534/genetics.106.060657. View