1,10-phenanthroline inhibits sumoylation and reveals that yeast SUMO modifications are highly transient.
1,10-Phenanthroline
Desumoylation
SUMO
Sumoylation
Ulp1
Journal
EMBO reports
ISSN: 1469-3178
Titre abrégé: EMBO Rep
Pays: England
ID NLM: 100963049
Informations de publication
Date de publication:
05 Jan 2024
05 Jan 2024
Historique:
received:
14
02
2023
accepted:
13
11
2023
revised:
31
10
2023
medline:
6
1
2024
pubmed:
6
1
2024
entrez:
5
1
2024
Statut:
aheadofprint
Résumé
The steady-state levels of protein sumoylation depend on relative rates of conjugation and desumoylation. Whether SUMO modifications are generally long-lasting or short-lived is unknown. Here we show that treating budding yeast cultures with 1,10-phenanthroline abolishes most SUMO conjugations within one minute, without impacting ubiquitination, an analogous post-translational modification. 1,10-phenanthroline inhibits the formation of the E1~SUMO thioester intermediate, demonstrating that it targets the first step in the sumoylation pathway. SUMO conjugations are retained after treatment with 1,10-phenanthroline in yeast that express a defective form of the desumoylase Ulp1, indicating that Ulp1 is responsible for eliminating existing SUMO modifications almost instantly when de novo sumoylation is inhibited. This reveals that SUMO modifications are normally extremely transient because of continuous desumoylation by Ulp1. Supporting our findings, we demonstrate that sumoylation of two specific targets, Sko1 and Tfg1, virtually disappears within one minute of impairing de novo sumoylation. Altogether, we have identified an extremely rapid and potent inhibitor of sumoylation, and our work reveals that SUMO modifications are remarkably short-lived.
Identifiants
pubmed: 38182817
doi: 10.1038/s44319-023-00010-8
pii: 10.1038/s44319-023-00010-8
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Canadian Institutes of Health Research (CIHR)
ID : PJT-178112
Organisme : Canadian Institutes of Health Research (CIHR)
ID : MOP-142282
Organisme : Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)
ID : RGPIN-04208-2014
Informations de copyright
© 2024. The Author(s).
Références
Albuquerque CP, Yeung E, Ma S, Fu T, Corbett KD, Zhou H (2015) A chemical and enzymatic approach to study site-specific sumoylation. PLoS ONE 10:e0143810
pubmed: 26633173
pmcid: 4669148
doi: 10.1371/journal.pone.0143810
Andreou AM, Tavernarakis N (2009) SUMOylation and cell signalling. Biotechnol J 4:1740–1752
pubmed: 19946876
doi: 10.1002/biot.200900219
Baig MS, Dou Y, Bergey BG, Bahar R, Burgener JM, Moallem M, McNeil JB, Akhter A, Burke GL, Sri Theivakadadcham VS et al (2021) Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II. PLoS Genet 17:e1009828
pubmed: 34587155
pmcid: 8505008
doi: 10.1371/journal.pgen.1009828
Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G (2021) SUMO and transcriptional regulation: the lessons of large-scale proteomic, modifomic and genomic studies. Molecules 26:828
pubmed: 33562565
pmcid: 7915335
doi: 10.3390/molecules26040828
Bowman EA, Kelly WG (2014) RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: a tail of two kinases. Nucleus 5:224–36
pubmed: 24879308
pmcid: 4133218
doi: 10.4161/nucl.29347
Chen Y (2023) A new immuno-oncology target—SUMOylation. Trends Cancer 9:606–608
pubmed: 37179168
doi: 10.1016/j.trecan.2023.04.010
Chymkowitch P, Nguéa PA, Enserink JM (2015) SUMO-regulated transcription: challenging the dogma. BioEssays 37:1095–1105
pubmed: 26354225
doi: 10.1002/bies.201500065
Eshleman N, Luo X, Capaldi A, Buchan JR (2020) Alterations of signaling pathways in response to chemical perturbations used to measure mRNA decay rates in yeast. RNA 26:10–18
pubmed: 31601735
pmcid: 6913126
doi: 10.1261/rna.072892.119
Esteras M, Liu I-C, Snijders AP, Jarmuz A, Aragon L (2017) Identification of SUMO conjugation sites in the budding yeast proteome. Microb Cell 4:331–341
pubmed: 29082231
pmcid: 5657824
doi: 10.15698/mic2017.10.593
Flotho A, Melchior F (2013) Sumoylation: a regulatory protein modification in health and disease. Annu Rev Biochem 82:357–385
pubmed: 23746258
doi: 10.1146/annurev-biochem-061909-093311
Gabellier L, De Toledo M, Chakraborty M, Akl D, Hallal R, Aqrouq M, Buonocore G, Recasens-Zorzo C, Cartron G, Delort A et al (2023) SUMOylation inhibitor TAK-981 (subasumstat) synergizes with 5-azacitidine in preclinical models of acute myeloid leukemia. Haematologica https://doi.org/10.3324/haematol.2023.282704
Goldstein AL, Pan X, McCusker JH (1999) Heterologous URA3MX cassettes for gene replacement in Saccharomyces cerevisiae. Yeast 15:507–11
pubmed: 10234788
doi: 10.1002/(SICI)1097-0061(199904)15:6<507::AID-YEA369>3.0.CO;2-P
Grigull J, Mnaimneh S, Pootoolal J, Robinson MD, Hughes TR (2004) Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol Cell Biol 24:5534–5547
pubmed: 15169913
pmcid: 419893
doi: 10.1128/MCB.24.12.5534-5547.2004
Hamza A, Tammpere E, Kofoed M, Keong C, Chiang J, Giaever G, Nislow C, Hieter P (2015) Complementation of yeast genes with human genes as an experimental platform for functional testing of human genetic variants. Genetics 201:1263–1274
pubmed: 26354769
pmcid: 4649650
doi: 10.1534/genetics.115.181099
Haruki H, Nishikawa J, Laemmli UK (2008) The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Mol Cell 31:925–932
pubmed: 18922474
doi: 10.1016/j.molcel.2008.07.020
Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal ACO, Nielsen ML (2017) Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nat Struct Mol Biol 24:325–336
pubmed: 28112733
doi: 10.1038/nsmb.3366
Hickey CM, Wilson NR, Hochstrasser M (2012) Function and regulation of SUMO proteases. Nat Rev Mol Cell Biol 13:755–766
pubmed: 23175280
pmcid: 3668692
doi: 10.1038/nrm3478
Kawamata T, Horie T, Matsunami M, Sasaki M, Ohsumi Y (2017) Zinc starvation induces autophagy in yeast. J Biol Chem 292:8520
pubmed: 28264932
pmcid: 5437255
doi: 10.1074/jbc.M116.762948
Kiss Z (1994) The zinc chelator 1,10-phenanthroline enhances the stimulatory effects of protein kinase C activators and staurosporine, but not sphingosine and H2O2, on phospholipase D activity in NIH 3T3 fibroblasts. Biochem J 298:93–98
pubmed: 8129736
pmcid: 1137987
doi: 10.1042/bj2980093
Knipscheer P, Flotho A, Klug H, Olsen JV, van Dijk WJ, Fish A, Johnson ES, Mann M, Sixma TK, Pichler A (2008) Ubc9 sumoylation regulates SUMO target discrimination. Mol Cell 31:371–382
pubmed: 18691969
doi: 10.1016/j.molcel.2008.05.022
Knop M, Siegers K, Pereira G, Zachariae W, Winsor B, Nasmyth K, Schiebel E (1999) Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines. Yeast 15:963–972
pubmed: 10407276
doi: 10.1002/(SICI)1097-0061(199907)15:10B<963::AID-YEA399>3.0.CO;2-W
Lewicki MC, Srikumar T, Johnson E, Raught B (2015) The S. cerevisiae SUMO stress response is a conjugation-deconjugation cycle that targets the transcription machinery. J Proteomics 118:39–48
pubmed: 25434491
doi: 10.1016/j.jprot.2014.11.012
Li SJ, Hochstrasser M (1999) A new protease required for cell-cycle progression in yeast. Nature 398:246–251
pubmed: 10094048
doi: 10.1038/18457
Li SJ, Hochstrasser M (2000) The yeast ULP2 (SMT4) gene encodes a novel protease specific for the ubiquitin-like Smt3 protein. Mol Cell Biol 20:2367–2377
pubmed: 10713161
pmcid: 85410
doi: 10.1128/MCB.20.7.2367-2377.2000
Liu C, Apodaca J, Davis LE, Rao H (2007) Proteasome inhibition in wild-type yeast Saccharomyces cerevisiae cells. Biotechniques 42:158,160,162
pubmed: 17373478
doi: 10.2144/000112389
Makhnevych T, Sydorskyy Y, Xin X, Srikumar T, Vizeacoumar FJ, Jeram SM, Li Z, Bahr S, Andrews BJ, Boone C et al (2009) Global map of SUMO function revealed by protein-protein interaction and genetic networks. Mol Cell 33:124–135
pubmed: 19150434
doi: 10.1016/j.molcel.2008.12.025
Martin BJE, Brind’Amour J, Kuzmin A, Jensen KN, Liu ZC, Lorincz M, Howe LJ (2021) Transcription shapes genome-wide histone acetylation patterns. Nat Commun 12:210
pubmed: 33431884
pmcid: 7801501
doi: 10.1038/s41467-020-20543-z
McNeil JB, Agah H, Bentley D (1998) Activated transcription independent of the RNA polymerase II holoenzyme in budding yeast. Genes Dev 12:2510–2521
pubmed: 9716404
pmcid: 317099
doi: 10.1101/gad.12.16.2510
Moallem M, Akhter A, Burke GL, Babu J, Bergey BG, McNeil JB, Baig MS, Rosonina E (2023) Sumoylation is largely dispensable for normal growth but facilitates heat tolerance in yeast. Mol Cell Biol 43:64–84
pubmed: 36720466
pmcid: 9936996
doi: 10.1080/10985549.2023.2166320
Morawska M, Ulrich HD (2013) An expanded tool kit for the auxin-inducible degron system in budding yeast. Yeast 30:341–351
pubmed: 23836714
doi: 10.1002/yea.2967
Nasir AM, Yang Q, Chalker DL, Forney JD (2015) SUMOylation is developmentally regulated and required for cell pairing during conjugation in Tetrahymena thermophila. Eukaryot Cell 14:170–81
pubmed: 25527524
pmcid: 4311922
doi: 10.1128/EC.00252-14
Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ (2017) A high throughput mutagenic analysis of yeast sumo structure and function. PLoS Genet 13:e1006612
pubmed: 28166236
pmcid: 5319795
doi: 10.1371/journal.pgen.1006612
Nishimura K, Kanemaki MT (2014) Rapid depletion of budding yeast proteins via the fusion of an auxin-inducible degron (AID). Current Protocols in Cell Biology 64:20
Nonet M, Scafe C, Sexton J, Young R (1987) Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol 7:1602–1611
pubmed: 3299050
pmcid: 365259
Olsen SK, Capili AD, Lu X, Tan DS, Lima CD (2010) Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature 463:906–912
pubmed: 20164921
pmcid: 2866016
doi: 10.1038/nature08765
Pinto MP, Carvalho AF, Grou CP, Rodríguez-Borges JE, Sá-Miranda C, Azevedo JE (2012) Heat shock induces a massive but differential inactivation of SUMO-specific proteases. Biochim Biophys Acta Mol Cell Res 1823:1958–1966
doi: 10.1016/j.bbamcr.2012.07.010
Qiu C, Malik I, Arora P, Laperuta AJ, Pavlovic EM, Ugochuckwu S, Naik M, Kaplan C (2021) Thiolutin is a direct inhibitor of RNA Polymerase II. Preprint at https://www.biorxiv.org/content/10.1101/2021.05.05.442806v1
Rao MS, Gupta R, Liguori MJ, Hu M, Huang X, Mantena SR, Mittelstadt SW, Blomme EAG, Van Vleet TR (2019) Novel computational approach to predict off-target interactions for small molecules. Front Big Data 2:25
pubmed: 33693348
pmcid: 7931946
doi: 10.3389/fdata.2019.00025
Rape M (2018) Ubiquitylation at the crossroads of development and disease. Nat Rev Mol Cell Biol 19:59–70
pubmed: 28928488
doi: 10.1038/nrm.2017.83
Rosonina E, Akhter A, Dou Y, Babu J, Sri Theivakadadcham VS (2017) Regulation of transcription factors by sumoylation. Transcription 8:220–231
pubmed: 28379052
pmcid: 5574528
doi: 10.1080/21541264.2017.1311829
Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27
pubmed: 2659436
pmcid: 1203683
doi: 10.1093/genetics/122.1.19
Soustelle C, Vernis L, Freon K, Reynaud-Angelin A, Chanet R, Fabre F, Heude M (2004) A new Saccharomyces cerevisiae strain with a mutant Smt3-deconjugating Ulp1 protein is affected in DNA replication and requires Srs2 and homologous recombination for its viability. Mol Cell Biol 24:5130–5143
pubmed: 15169880
pmcid: 419856
doi: 10.1128/MCB.24.12.5130-5143.2004
Sri Theivakadadcham VS, Bergey BG, Rosonina E (2019) Sumoylation of DNA-bound transcription factor Sko1 prevents its association with nontarget promoters. PLoS Genet 15:e1007991
pubmed: 30763307
pmcid: 6392331
doi: 10.1371/journal.pgen.1007991
Sydorskyy Y, Srikumar T, Jeram SM, Wheaton S, Vizeacoumar FJ, Makhnevych T, Chong YT, Gingras A-C, Raught B (2010) A novel mechanism for SUMO system control: regulated Ulp1 nucleolar sequestration. Mol Cell Biol 30:4452–4462
pubmed: 20647537
pmcid: 2937538
doi: 10.1128/MCB.00335-10
Wallace EWJ, Beggs JD (2017) Extremely fast and incredibly close: cotranscriptional splicing in budding yeast. RNA 23:601–610
pubmed: 28153948
pmcid: 5393171
doi: 10.1261/rna.060830.117
Zhao X (2018) SUMO-mediated regulation of nuclear functions and signaling processes. Mol Cell 71:409–418
pubmed: 30075142
pmcid: 6095470
doi: 10.1016/j.molcel.2018.07.027