Highly sensitive site-specific SUMOylation proteomics in Arabidopsis.
Journal
Nature plants
ISSN: 2055-0278
Titre abrégé: Nat Plants
Pays: England
ID NLM: 101651677
Informations de publication
Date de publication:
09 2024
09 2024
Historique:
received:
02
04
2024
accepted:
01
08
2024
medline:
19
9
2024
pubmed:
19
9
2024
entrez:
18
9
2024
Statut:
ppublish
Résumé
SUMOylation-the attachment of a small ubiquitin-like modifier (SUMO) to target proteins-plays roles in controlling plant growth, nutrient signalling and stress responses. SUMOylation studies in plants are scarce because identifying SUMOylated proteins and their sites is challenging. To date, only around 80 SUMOylation sites have been identified. Here we introduce lysine-null SUMO1 into the Arabidopsis sumo1 sumo2 mutant and establish a two-step lysine-null SUMO enrichment method. We identified a site-specific SUMOylome comprising over 2,200 SUMOylation sites from 1,300 putative acceptors that function in numerous nuclear processes. SUMOylation marks occur on several motifs, differing from the canonical ψKxE motif in distant eukaryotes. Quantitative comparisons demonstrate that SUMOylation predominantly enhances the stability of SUMO1 acceptors. Our study delivers a highly sensitive and efficient method for site-specific SUMOylome studies and provides a comprehensive catalogue of Arabidopsis SUMOylation, serving as a valuable resource with which to further explore how SUMOylation regulates protein function.
Identifiants
pubmed: 39294263
doi: 10.1038/s41477-024-01783-z
pii: 10.1038/s41477-024-01783-z
doi:
Substances chimiques
Arabidopsis Proteins
0
Small Ubiquitin-Related Modifier Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1330-1342Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Vertegaal, A. C. Uncovering ubiquitin and ubiquitin-like signaling networks. Chem. Rev. 111, 7923–7940 (2011).
pubmed: 22004258
pmcid: 3238414
doi: 10.1021/cr200187e
Augustine, R. C. & Vierstra, R. D. SUMOylation: re-wiring the plant nucleus during stress and development. Curr. Opin. Plant Biol. 45, 143–154 (2018).
pubmed: 30014889
doi: 10.1016/j.pbi.2018.06.006
Ghimire, S. et al. SUMO and SUMOylation in plant abiotic stress. Plant Growth Regul. 91, 317–325 (2020).
doi: 10.1007/s10725-020-00624-1
Pichler, A., Fatouros, C., Lee, H. & Eisenhardt, N. SUMO conjugation—a mechanistic view. Biomol. Concepts 8, 13–36 (2017).
pubmed: 28284030
doi: 10.1515/bmc-2016-0030
Saracco, S. A., Miller, M. J., Kurepa, J. & Vierstra, R. D. Genetic analysis of SUMOylation in Arabidopsis: conjugation of SUMO1 and SUMO2 to nuclear proteins is essential. Plant Physiol. 145, 119–134 (2007).
pubmed: 17644626
pmcid: 1976578
doi: 10.1104/pp.107.102285
Van den Burg, H. A., Kini, R. K., Schuurink, R. C. & Takken, F. L. Arabidopsis small ubiquitin-like modifier paralogs have distinct functions in development and defense. Plant Cell 22, 1998–2016 (2010).
pubmed: 20525853
pmcid: 2910984
doi: 10.1105/tpc.109.070961
Kurepa, J. et al. 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 (2003).
pubmed: 12482876
doi: 10.1074/jbc.M209694200
Colby, T., Matthai, A., Boeckelmann, A. & Stuible, H. P. SUMO-conjugating and SUMO-deconjugating enzymes from Arabidopsis. Plant Physiol. 142, 318–332 (2006).
pubmed: 16920872
pmcid: 1557612
doi: 10.1104/pp.106.085415
Jin, J. B. et al. 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 (2008).
pubmed: 18069938
pmcid: 2254019
doi: 10.1111/j.1365-313X.2007.03359.x
Kwak, J. S. et al. Arabidopsis HIGH PLOIDY2 sumoylates and stabilizes Flowering Locus C through its E3 ligase activity. Front. Plant Sci. 7, 530 (2016).
pubmed: 27148346
pmcid: 4837325
doi: 10.3389/fpls.2016.00530
Son, G. H., Park, B. S., Song, J. T. & Seo, H. S. FLC-mediated flowering repression is positively regulated by sumoylation. J. Exp. Bot. 65, 339–351 (2014).
pubmed: 24218331
doi: 10.1093/jxb/ert383
Conti, L. et al. Small ubiquitin-like modifier protein SUMO enables plants to control growth independently of the phytohormone gibberellin. Dev. Cell 28, 102–110 (2014).
pubmed: 24434138
doi: 10.1016/j.devcel.2013.12.004
Blanco-Tourinan, N., Serrano-Mislata, A. & Alabadi, D. Regulation of DELLA proteins by post-translational modifications. Plant Cell Physiol. 61, 1891–1901 (2020).
pubmed: 32886774
doi: 10.1093/pcp/pcaa113
Miura, K. et al. Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 negatively regulates abscisic acid signaling. Proc. Natl Acad. Sci. USA 106, 5418–5423 (2009).
pubmed: 19276109
pmcid: 2664011
doi: 10.1073/pnas.0811088106
Miura, K. et al. The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Proc. Natl Acad. Sci. USA 102, 7760–7765 (2005).
pubmed: 15894620
pmcid: 1140425
doi: 10.1073/pnas.0500778102
Park, B. S., Song, J. T. & Seo, H. S. Arabidopsis nitrate reductase activity is stimulated by the E3 SUMO ligase AtSIZ1. Nat. Commun. 2, 400 (2011).
pubmed: 21772271
doi: 10.1038/ncomms1408
Kong, X. et al. SIZ1-mediated SUMOylation of ROS1 enhances its stability and positively regulates active DNA demethylation in Arabidopsis. Mol. Plant 13, 1816–1824 (2020).
pubmed: 32927102
doi: 10.1016/j.molp.2020.09.010
Miller, M. J., Barrett-Wilt, G. A., Hua, Z. & Vierstra, R. D. 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 (2010).
pubmed: 20813957
pmcid: 2944710
doi: 10.1073/pnas.1004181107
Miller, M. J. et al. Quantitative proteomics reveals factors regulating RNA biology as dynamic targets of stress-induced SUMOylation in Arabidopsis. Mol. Cell. Proteom. 12, 449–463 (2013).
doi: 10.1074/mcp.M112.025056
Rytz, T. C. et al. SUMOylome profiling reveals a diverse array of nuclear targets modified by the SUMO ligase SIZ1 during heat stress. Plant Cell 30, 1077–1099 (2018).
pubmed: 29588388
pmcid: 6002191
doi: 10.1105/tpc.17.00993
Ingole, K. D., Dahale, S. K. & Bhattacharjee, S. Proteomic analysis of SUMO1–SUMOylome changes during defense elicitation in Arabidopsis. J. Proteom. 232, 104054 (2021).
doi: 10.1016/j.jprot.2020.104054
Hendriks, I. A. & Vertegaal, A. C. A high-yield double-purification proteomics strategy for the identification of SUMO sites. Nat. Protoc. 11, 1630–1649 (2016).
pubmed: 27560170
doi: 10.1038/nprot.2016.082
Hendriks, I. A. et al. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nat. Struct. Mol. Biol. 24, 325–336 (2017).
pubmed: 28112733
doi: 10.1038/nsmb.3366
Hendriks, I. A. et al. System-wide identification of wild-type SUMO-2 conjugation sites. Nat. Commun. 6, 7289 (2015).
pubmed: 26073453
doi: 10.1038/ncomms8289
Hendriks, I. A. et al. Site-specific characterization of endogenous SUMOylation across species and organs. Nat. Commun. 9, 2456 (2018).
pubmed: 29942033
pmcid: 6018634
doi: 10.1038/s41467-018-04957-4
Rytz, T. C., Feng, J., Barros, J. A. S. & Vierstra, R. D. Arabidopsis-expressing lysine-null SUMO1 reveals a non-essential role for secondary SUMO modifications in plants. Plant Direct 7, e506 (2023).
pubmed: 37465357
pmcid: 10350450
doi: 10.1002/pld3.506
Verma, V. et al. SUMO enables substrate selectivity by mitogen-activated protein kinases to regulate immunity in plants. Proc. Natl Acad. Sci. USA 118, e2021351118 (2021).
pubmed: 33649235
pmcid: 7958252
doi: 10.1073/pnas.2021351118
Niu, D. et al. SIZ1-mediated SUMOylation of TPR1 suppresses plant immunity in Arabidopsis. Mol. Plant 12, 215–228 (2019).
pubmed: 30543996
doi: 10.1016/j.molp.2018.12.002
Zhang, X. et al. SIZ1-mediated SUMO modification of SEUSS regulates photomorphogenesis in Arabidopsis. Plant Commun. 1, 100080 (2020).
pubmed: 33367258
pmcid: 7748021
doi: 10.1016/j.xplc.2020.100080
Liu, J. et al. A plant RNA virus inhibits NPR1 sumoylation and subverts NPR1-mediated plant immunity. Nat. Commun. 14, 2580 (2023).
Kim, J. Y. et al. Nitrate reductases are relocalized to the nucleus by AtSIZ1 and their levels are negatively regulated by COP1 and ammonium. Int. J. Mol. Sci. 19, 1202 (2018).
pubmed: 29662028
pmcid: 5979280
doi: 10.3390/ijms19041202
Zhang, T. et al. Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin. Nat. Commun. 13, 5133 (2022).
pubmed: 36050397
pmcid: 9436968
doi: 10.1038/s41467-022-32920-x
Mollapour, M. et al. Asymmetric Hsp90 N domain SUMOylation recruits Aha1 and ATP-competitive inhibitors. Mol. Cell 53, 317–329 (2014).
pubmed: 24462205
pmcid: 3964875
doi: 10.1016/j.molcel.2013.12.007
Qu, G. P. et al. Reversible SUMOylation of FHY1 regulates phytochrome A signaling in Arabidopsis. Mol. Plant 13, 879–893 (2020).
pubmed: 32298785
doi: 10.1016/j.molp.2020.04.002
Xu, X., Vatsyayan, J., Gao, C., Bakkenist, C. J. & Hu, J. Sumoylation of eIF4E activates mRNA translation. EMBO Rep. 11, 299–304 (2010).
pubmed: 20224576
pmcid: 2854592
doi: 10.1038/embor.2010.18
Liu, Y. et al. The Arabidopsis SUMO E3 ligase AtMMS21 dissociates the E2Fa/DPa complex in cell cycle regulation. Plant Cell 13, 879–893 (2016).
Kim, D. Y. et al. Arabidopsis CMT3 activity is positively regulated by AtSIZ1-mediated sumoylation. Plant Sci. 239, 209–215 (2015).
pubmed: 26398805
doi: 10.1016/j.plantsci.2015.08.003
Yang, F. et al. BubR1 is modified by sumoylation during mitotic progression. J. Biol. Chem. 287, 4875–4882 (2012).
pubmed: 22167194
doi: 10.1074/jbc.M111.318261
Zhang, J. et al. A SUMO ligase AtMMS21 regulates the stability of the chromatin remodeler BRAHMA in root development. Plant Physiol. 173, 1574–1582 (2017).
pubmed: 28115583
pmcid: 5338659
doi: 10.1104/pp.17.00014
Yu, M. et al. A SUMO ligase AtMMS21 regulates activity of the 26S proteasome in root development. Plant Sci. 280, 314–320 (2019).
pubmed: 30824010
doi: 10.1016/j.plantsci.2018.12.014
Elrouby, N. & Coupland, G. 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 (2010).
pubmed: 20855607
pmcid: 2951436
doi: 10.1073/pnas.1005452107
Park, H. C. et al. Identification and molecular properties of SUMO-binding proteins in Arabidopsis. Mol. Cells 32, 143–151 (2011).
pubmed: 21607647
pmcid: 3887670
doi: 10.1007/s10059-011-2297-3
Lopez-Torrejon, G. et al. Identification of SUMO targets by a novel proteomic approach in plants. J. Integr. Plant Biol. 55, 96–107 (2013).
pubmed: 23164430
doi: 10.1111/jipb.12012
Budhiraja, R. et al. 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 (2009).
pubmed: 19151129
pmcid: 2649401
doi: 10.1104/pp.108.135053
Huang, J. W. et al. An effective in vitro SUMOylation detection system for plant proteins. Chin. Bull. Bot. 57, 490–499 (2022).
Okada, S. et al. Reconstitution of Arabidopsis thaliana SUMO pathways in E. coli: functional evaluation of SUMO machinery proteins and mapping of SUMOylation sites by mass spectrometry. Plant Cell Physiol. 50, 1049–1061 (2009).
pubmed: 19376783
doi: 10.1093/pcp/pcp056
Kwak, J. S., Song, J. T. & Seo, H. S. E3 SUMO ligase SIZ1 splicing variants localize and function according to external conditions. Plant Physiol. 195, 1601–1623 (2024).
pubmed: 38497423
pmcid: 11142376
doi: 10.1093/plphys/kiae108
Kim, J. Y., Song, J. T. & Seo, H. S. Post-translational modifications of Arabidopsis E3 SUMO ligase AtSIZ1 are controlled by environmental conditions. FEBS Open. Bio. 7, 1622–1634 (2017).
pubmed: 28979848
pmcid: 5623694
doi: 10.1002/2211-5463.12309
Skilton, A. et al. SUMO chain formation is required for response to replication arrest in S. pombe. PLoS ONE 4, e6750 (2009).
pubmed: 19707600
pmcid: 2727700
doi: 10.1371/journal.pone.0006750
Guerra, D. et al. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms. Front. Plant Sci. 6, 57 (2015).
pubmed: 25717333
pmcid: 4324062
doi: 10.3389/fpls.2015.00057
Lubkowska, A., Pluta, W., Strońska, A. & Lalko, A. Role of heat shock proteins (HSP70 and HSP90) in viral infection. Int. J. Mol. Sci. 22, 9366 (2021).
pubmed: 34502274
pmcid: 8430838
doi: 10.3390/ijms22179366
Schramm, F. et al. A cascade of transcription factor DREB2A and heat stress transcription factor HsfA3 regulates the heat stress response of Arabidopsis. Plant J. 53, 264–274 (2008).
pubmed: 17999647
doi: 10.1111/j.1365-313X.2007.03334.x
Song, C. et al. VOZ1, a transcriptional repressor of DREB2C, mediates heat stress responses in Arabidopsis. Planta 247, 1439–1448 (2018).
pubmed: 29536220
doi: 10.1007/s00425-018-2879-9
Wang, H. et al. Thermosensitive SUMOylation of TaHsfA1 defines a dynamic ON/OFF molecular switch for the heat stress response in wheat. Plant Cell 35, 3889–3910 (2023).
pubmed: 37399070
pmcid: 10533334
doi: 10.1093/plcell/koad192
Hammoudi, V. et al. The protein modifier SUMO is critical for integrity of the Arabidopsis shoot apex at warm ambient temperatures. J. Exp. Bot. 9, erab262 (2021).
doi: 10.1093/jxb/erab262
Zhang, S. et al. SUMO E3 ligase SlSIZ1 facilitates heat tolerance in tomato. Plant Cell Physiol. 59, 58–71 (2018).
pubmed: 29069432
doi: 10.1093/pcp/pcx160
Zhang, H., Lang, Z. & Zhu, J.-K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 (2018).
pubmed: 29784956
doi: 10.1038/s41580-018-0016-z
Liu, J. et al. An H3K27me3 demethylase–HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis. Cell Res. 29, 379–390 (2019).
pubmed: 30778176
pmcid: 6796840
doi: 10.1038/s41422-019-0145-8
Malabarba, J., Windels, D., Xu, W. & Verdier, J. Regulation of DNA (de)methylation positively impacts seed germination during seed development under heat stress. Genes 12, 457 (2021).
pubmed: 33807066
pmcid: 8005211
doi: 10.3390/genes12030457
Lee, J. et al. Salicylic acid-mediated innate immunity in Arabidopsis is regulated by SIZ1 SUMO E3 ligase. Plant J. 49, 79–90 (2007).
pubmed: 17163880
doi: 10.1111/j.1365-313X.2006.02947.x
Saleh, A. et al. Posttranslational modifications of the master transcriptional regulator NPR1 enable dynamic but tight control of plant immune responses. Cell Host Microbe 18, 169–182 (2015).
pubmed: 26269953
pmcid: 4537515
doi: 10.1016/j.chom.2015.07.005
Yip Delormel, T. & Boudsocq, M. Properties and functions of calcium-dependent protein kinases and their relatives in Arabidopsis thaliana. New Phytol. 224, 585–604 (2019).
pubmed: 31369160
doi: 10.1111/nph.16088
Tang, R. J., Wang, C., Li, K. & Luan, S. The CBL–CIPK calcium signaling network: unified paradigm from 20 years of discoveries. Trends Plant Sci. 25, 604–617 (2020).
pubmed: 32407699
doi: 10.1016/j.tplants.2020.01.009
Dong, Q., Wallrad, L., Almutairi, B. O. & Kudla, J. Ca
pubmed: 35048537
doi: 10.1111/jipb.13228
Mori, I. C. et al. CDPKs CPK6 and CPK3 function in ABA regulation of guard cell S-type anion- and Ca
pubmed: 17032064
pmcid: 1592316
doi: 10.1371/journal.pbio.0040327
Wang, P. et al. Mapping proteome-wide targets of protein kinases in plant stress responses. Proc. Natl Acad. Sci. USA 117, 3270–3280 (2020).
pubmed: 31992638
pmcid: 7022181
doi: 10.1073/pnas.1919901117
Mertins, P. et al. Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry. Nat. Protoc. 13, 1632–1661 (2018).
pubmed: 29988108
pmcid: 6211289
doi: 10.1038/s41596-018-0006-9
Hendriks, I. A., Akimov, V., Blagoev, B. & Nielsen, M. L. MaxQuant.Live enables enhanced selectivity and identification of peptides modified by endogenous SUMO and ubiquitin. J. Proteome Res. 20, 2042–2055 (2021).
pubmed: 33539096
doi: 10.1021/acs.jproteome.0c00892
Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).
pubmed: 34557778
pmcid: 8454663
Sherman, B. T. et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 50, W216–W221 (2022).
pubmed: 35325185
pmcid: 9252805
doi: 10.1093/nar/gkac194
Crooks, G. E., Hon, G., Chandonia, J.-M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188–1190 (2004).
pubmed: 15173120
pmcid: 419797
doi: 10.1101/gr.849004
Bailey, T. L., Johnson, J., Grant, C. E. & Noble, W. S. The MEME suite. Nucleic Acids Res. 43, W39–W49 (2015).
pubmed: 25953851
pmcid: 4489269
doi: 10.1093/nar/gkv416
Sang, T. et al. DIA-based phosphoproteomics identifies early phosphorylation events in response to EGTA and mannitol in Arabidopsis. Mol. Cell. Proteom. 18, 100804 (2024).
doi: 10.1016/j.mcpro.2024.100804
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022).
pubmed: 34723319
doi: 10.1093/nar/gkab1038