Abstract
Reversible conjugation of the small ubiquitin modifier (SUMO) peptide to proteins (SUMOylation) plays important roles in cellular processes in animals and yeasts. However, little is known about plant SUMO targets. To identify SUMO substrates in Arabidopsis and to probe for biological functions of SUMO proteins, we constructed 6xHis-3xFLAG fused AtSUMO1 (HFAtSUMO1) controlled by the CaMV35S promoter for transformation into Arabidopsis Col-0. After heat treatment, an increased sumoylation pattern was detected in the transgenic plants. SUMO1-modified proteins were selected after two-dimensional gel electrophoresis (2-DE) image analysis and identified using matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). We identified 27 proteins involved in a variety of processes such as nucleic acid metabolism, signaling, metabolism, and including proteins of unknown functions. Binding and sumoylation patterns were confirmed independently. Surprisingly, MCM3 (At5G46280), a DNA replication licensing factor, only interacted with and became sumoylated by AtSUMO1, but not by SUMO1ΔGG or AtSUMO3. The results suggest specific interactions between sumoylation targets and particular sumoylation enzymes.
Similar content being viewed by others
References
Blum, H., Beier, H., and Gross, H.J. (1987). Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 8, 93–99.
Budhiraja, R., Hermkes, R., Müller, S., Schmidt, J., Colby, T., Panigrahi, K., Coupland, G., and Bachmair, A. (2009). Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Plant Physiol. 149, 1529–1540.
Catala, R., Ouyang, J., Abreu, I.A., Hu, Y., Seo, H., Zhang, X., and Chua, N.H. (2007). The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell 19, 2952–2966.
Chen, H., Zou, Y., Shang, Y., Lin, H., Wang, Y., Cai, R., Tang, X., and Zhou, J.-M. (2008). Firefly luciferase complementation imaging assay for protein-protein interactions in plants. Plant Physiol. 146, 368–376.
Clough, S.J., and Bent, A.F. (1998). Floral dip: a simplified method for agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743.
Colby, T., Matthai, A., Boeckelmann, A., and Stuible, H.P. (2006). SUMO-conjugating and SUMO-deconjugating enzymes from Arabidopsis. Plant Physiol. 142, 318–332.
Denison, C., Rudner, A.D., Gerber, S.A., Bakalarski, C.E., Moazed, D., and Gygi, S.P. (2005). A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol. Cell. Proteomics 4, 246–254.
Elrouby, N., and Coupland, G. (2010). Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes. Proc. Natl. Acad. Sci. USA 107, 17415–17420.
Garcia-Dominguez, M., March-Diaz, R., and Reyes, J.C. (2008). The PHD domain of plant PIAS proteins mediates sumoylation of bromodomain GTE proteins. J. Biol. Chem. 283, 21469–21477.
Gill, G. (2005). Something about SUMO inhibits transcription. Curr. Opin. Genet. Dev. 15, 536–541.
Goodson, M.L., Hong, Y., Rogers, R., Matunis, M.J., Park-Sarge, O.-K., and Sarge, K.D. (2001). SUMO-1 modification regulates the DNA binding activity of heat shock transcription factor 2, a promyelocytic leukemia nuclear body associated transcription factor. J. Biol. Chem. 276, 18513–18518.
Hannich, J.T., Lewis, A., Kroetz, M.B., Li, S.-J., Heide, H., Emili, A., and Hochstrasser, M. (2005). Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem. 280, 18513–18518.
Hay, R.T. (2005). Sumo: a history of modification. Mol. Cell 18, 1–12.
Hecker, C.-M., Rabiller, M., Haglund, K., Bayer, P., and Dikic, I. (2006). Specification of SUMO1- and SUMO2-interacting motifs. J. Biol. Chem. 281, 16117–16127.
Hochstrasser, M. (2009). Origin and function of ubiquitin-like proteins. Nature 458, 422–429.
Hong, Y., Rogers, R., Matunis, M.J., Mayhew, C.N., Goodson, M., Park-Sarge, O.-K., and Sarge, K.D. (2001). Regulation of heat shock transcription factor 1 by stress-induced SUMO-1 modification. J. Biol. Chem. 276, 40263–40267.
Jin, J.B., Jin, Y.H., Lee, J., Miura, K., Yoo, C.Y., Kim, W.-Y., Van Oosten, M., Hyun, Y., Somers, D.E., Lee, I., et al. (2008). The SUMO E3 ligase, AtSIZ1, regulates flowering by controlling a salicylic acid-mediated floral promotion pathway and through affects on FLC chromatin structure. Plant J. 53, 530–540.
Johnson, E.S. (2004). Protein modification by SUMO. Annu. Rev. Biochem. 73, 355–382.
Kim, S.T., Kim, S.G., Hwang, D.H., Kang, S.Y., Kim, H.J., Lee, B.H., Lee, J.J., and Kang, K.Y. (2004). Proteomic analysis of pathogen-responsive proteins from rice leaves induced by rice blast fungus, Magnaporthe grisea. Proteomics 4, 3569–3578.
Kurepa, J., Walker, J.M., Smalle, J., Gosink, M.M., Davis, S.J., Durham, T.L., Sung, D.-Y., and Vierstra, R.D. (2003). The small ubiquitin-like modifier (SUMO) protein modification system in Arabidopsis: Accumulation of SUMO1 and -2 conjugates is increased by stress. J. Biol. Chem. 278, 6862–6872.
Lakatos, L., Szittya, G., Silhavy, D., and Burgyan, J. (2004). Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses. EMBO 23, 876–884.
Laser, H., Bongards, C., Schuller, J., Heck, S., Johnsson, N., and Lehming, N. (2000). A new screen for protein interactions reveals that the Saccharomyces cerevisiae high mobility group proteins Nhp6A/B are involved in the regulation of the GAL1 promoter. Proc. Natl. Acad. Sci. USA 97, 13732–13737.
Lee, J., Nam, J., Park, H.C., Na, G., Miura, K., Jin, J.B., Yoo, C.Y., Baek, D., Kim, D.H., Jeong, J.C., et al. (2007). Salicylic acidmediated innate immunity in Arabidopsis is regulated by SIZ SUMO E3 ligase. Plant J. 49, 79–90.
Lois, L.M., Lima, C.D., and Chua, N.H. (2003). Small ubiquitin-like modifier modulates abscisic acid signaling in Arabidopsis. Plant Cell 15, 1347–1359.
Mao, Y., Desai, S.D., and Liu, L.F. (2000). SUMO-1 conjugation to human DNA topoisomerase II isozymes. J. Biol. Chem. 275, 26066–26073.
Matunis, M.J., Coutavas, E., and Blobel, G. (1996). A novel ubiquitin-like modification modulates the partitioning of the Ran-GAPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex. J. Cell Biol. 135, 1457–1470.
Melchior, F. (2000). SUMO-nonclassical ubiquitin. Annu. Rev. Cell Dev. Biol. 16, 591–626.
Meulmeester, E., and Melchior, F. (2008). Cell biology: SUMO. Nature 452, 709–711.
Miller, M.J., Barrett-Wilt, G.A., Hua, Z., and Vierstra, R.D. (2010). Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc. Natl. Acad. Sci. USA 107, 16512–16517.
Minty, A., Dumont, X., Kaghad, M., and Caput, D. (2000). Covalent modification of p73α by SUMO-1. J. Biol. Chem. 275, 36316–36323.
Miura, K., and Hasegawa, P.M. (2010). Sumoylation and other ubiquitin-like post-translational modifications in plants. Trend Cell Biol. 20, 223–232.
Miura, K., Rus, A., Sharkhuu, A., Yokoi, S., Karthikeyan, A.S., Raghothama, K.G., Baek, D., Koo, Y.D., Jin, J.B., Bressan, R.A., et al. (2005). The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Proc. Natl. Acad. Sci. USA 102, 7760–7765.
Miura, K., Jin, J.B., Lee, J., Yoo, C.Y., Stirm, V., Miura, T., Ashworth, E.N., Bressan, R.A., Yun, D.-J., and Hasegawa, P.M. (2007). SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell 19, 1403–1414.
Miura, K., Lee, J., Jin, J.B., Yoo, C.Y., Miura, T., and Hasegawa, P.M. (2009). Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling. Proc. Natl. Acad. Sci. USA 106, 5418–5423.
Novatchkova, M., Budhiraja, R., Coupland, G., Eisenhaber, F., and Bachmair, A. (2004). SUMO conjugation in plants. Planta 220, 1–8.
O’Farrell, P.H. (1975). High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250, 4007–4021.
Okada, S., Nagabuchi, M., Takamura, Y., Nakagawa, T., Shinmyozu, K., Nakayama, J.-I., and Tanaka, K. (2009). Reconstitution of Arabidopsis thaliana SUMO pathway in E. coli: functional evaluation of SUMO machinery proteins and mapping of sumoylation sites by mass spectrometry. Plant Cell Physiol. 50, 1049–1061.
Panse, V.G., Hardeland, U., Werner, T., Kuster, B., and Hurt, E. (2004). A proteome-wide approach identifies sumoylated substrate proteins in yeast. J. Biol. Chem. 279, 41346–41351.
Park, H.C., Kim, M.L., Kang, Y.H., Jeong, J.C., Cheong, M.S., Choi, W., Lee, S.Y., Cho, M.J., Kim, M.C., Chung, W.S., et al. (2009). Functional analysis of the stress-inducible soybean calmodulin isoform-4 (GmCaM-4) promoter in transgenic tobacco plants. Mol. Cells 27, 475–480.
Saitoh, H., and Hinchey, J. (2000). Functional heterogeneity of small ubiquitin-related protein modifiers SUMO-1 versus SUMO-2/3. J. Biol. Chem. 275, 6252–6258.
Saracco, S.A., Miller, M.J., Kurepa, J., and Vierstra, R.D. (2007). Genetic analysis of SUMOylation in Arabidopsis: conjugation of SUMO1 and SUMO2 to nuclear proteins is essential. Plant Physiol. 145, 119–134.
Schmidt, D., and Müller, S. (2003). PIAS/SUMO: new partners in transcriptional regulation. Cell. Mol. Life Sci. 60, 2561–2574.
Seeler, J.S., and Dejean, A. (2003). Nuclear and unclear functions of SUMO. Nat. Rev. Mol. Cell Biol. 4, 690–699.
Stagljar, I., Korostensky, C., Johnsson, N., and te Heesen, S. (1998). A new genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl. Acad. Sci. USA 95, 5187–5192.
Stevens, R., Mariconti, L., Rossignol, P., Perennes, C., Cella, R., and Bergounioux, C. (2002). Two E2F sites in the Arabidopsis MCM3 promoter have different roles in cell cycle activation and meristematic expression. J. Biol. Chem. 277, 32978–32984.
van den Burg, H.A., Kini, R.K., Schuurink, R.C., and Takken, F.L.W. (2010). Arabidopsis small ubiquitin-like modifier paralogs have distinct functions in development and defense. Plant Cell 22, 1998–2016.
Varshavsky, A. (1996). The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93, 12142–12149.
Wykoff, D.D., and O’shea, E.K. (2005). Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome. Mol. Cell. Proteomics 4, 73–83.
Yoo, J.H., Park, C.Y., Kim, J.C., Heo, W.D., Cheong, M.S., Park, H.C., Kim, M.C., Moon, B.C., Choi, M.S., Kang, Y.H., et al. (2005). Direct interaction of a divergent CaM isoform and the transcription factor, MYB2, enhances salt tolerance in Arabidopsis. J. Biol. Chem. 280, 3697–3706.
Yoo, C.Y., Miura, K., Jin, J.B., Lee, J., Park, H.C., Salt, D.E., Yun, D.-J., Bressan, R.A., and Hasegawa, P.M. (2006) SIZ1 small ubiquitin-like modifier E3 ligase facilitates basal thermotolerance in Arabidopsis independent of salicylic acid. Plant Physiol. 142, 1548–1558.
Zhao, Y., Kwon, S.W., Anselmo, A., Kaur, K., and White, M.A. (2004). Broad spectrum identification of cellular small ubiquitinrelated modifier (SUMO) substrate proteins. J. Biol. Chem. 279, 20999–21002.
Zhou, W., Ryan, J.J., and Zhou, H. (2004). Global analyses of sumoylated proteins in Saccharomyces cerevisiae: induction of protein sumoylation by cellular stresses. J. Biol. Chem. 279, 32262–32268.
Author information
Authors and Affiliations
Corresponding authors
Additional information
These authors contributed equally to this work.
About this article
Cite this article
Park, H.C., Choi, W., Park, H.J. et al. Identification and molecular properties of SUMO-binding proteins in Arabidopsis . Mol Cells 32, 143–151 (2011). https://doi.org/10.1007/s10059-011-2297-3
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10059-011-2297-3