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Hammami NEH, Mérindol N, Plourde MB, Maisonnet T, Lebel S, Berthoux L. SUMO-3 promotes the ubiquitin-dependent turnover of TRIM55. Biochem Cell Biol 2024; 102:73-84. [PMID: 37703582 DOI: 10.1139/bcb-2023-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
Human muscle-specific RING fingers (MURFs) are members of the tripartite motif (TRIM) family of proteins characterized by their C-terminal subgroup one signature domain. MURFs play a role in sarcomere formation and microtubule dynamics. It was previously established that some TRIMs undergo post-translational modification by small ubiquitin-like modifier (SUMO). In this study, we explored the putative SUMOylation of MURF proteins as well as their interactions with SUMO. MURF proteins (TRIM54, TRIM55, and TRIM63) were not found to be SUMOylated. However, TRIM55 turnover by proteasomal and lysosomal degradation was higher upon overexpression of SUMO-3 but not of SUMO-1. Furthermore, it is predicted that TRIM55 contains two potential SUMO-interacting motifs (SIMs). We found that SIM1- and SIM2-mutated TRIM55 were more stable than the wild-type (WT) protein partly due to decreased degradation. Consistently, SIM-mutated TRIM55 was less polyubiquitinated than the WT protein, despite similar monoubiquitination levels. Using IF microscopy, we observed that SIM motifs influenced TRIM55 subcellular localization. In conclusion, our results suggest that SUMO-3 or SUMO-3-modified proteins modulate the localization, stability, and RING ubiquitin ligase activity of TRIM55.
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Affiliation(s)
- Nour-El-Houda Hammami
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Natacha Mérindol
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Mélodie B Plourde
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Tara Maisonnet
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Sophie Lebel
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Lionel Berthoux
- Department of medical biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
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Structural and Functional Insights into Human Nuclear Cyclophilins. Biomolecules 2018; 8:biom8040161. [PMID: 30518120 PMCID: PMC6315705 DOI: 10.3390/biom8040161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 02/05/2023] Open
Abstract
The peptidyl prolyl isomerases (PPI) of the cyclophilin type are distributed throughout human cells, including eight found solely in the nucleus. Nuclear cyclophilins are involved in complexes that regulate chromatin modification, transcription, and pre-mRNA splicing. This review collects what is known about the eight human nuclear cyclophilins: peptidyl prolyl isomerase H (PPIH), peptidyl prolyl isomerase E (PPIE), peptidyl prolyl isomerase-like 1 (PPIL1), peptidyl prolyl isomerase-like 2 (PPIL2), peptidyl prolyl isomerase-like 3 (PPIL3), peptidyl prolyl isomerase G (PPIG), spliceosome-associated protein CWC27 homolog (CWC27), and peptidyl prolyl isomerase domain and WD repeat-containing protein 1 (PPWD1). Each “spliceophilin” is evaluated in relation to the spliceosomal complex in which it has been studied, and current work studying the biological roles of these cyclophilins in the nucleus are discussed. The eight human splicing complexes available in the Protein Data Bank (PDB) are analyzed from the viewpoint of the human spliceophilins. Future directions in structural and cellular biology, and the importance of developing spliceophilin-specific inhibitors, are considered.
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Hendriks IA, Schimmel J, Eifler K, Olsen JV, Vertegaal ACO. Ubiquitin-specific Protease 11 (USP11) Deubiquitinates Hybrid Small Ubiquitin-like Modifier (SUMO)-Ubiquitin Chains to Counteract RING Finger Protein 4 (RNF4). J Biol Chem 2015; 290:15526-15537. [PMID: 25969536 DOI: 10.1074/jbc.m114.618132] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 11/06/2022] Open
Abstract
Ring finger protein 4 (RNF4) is a SUMO-targeted ubiquitin E3 ligase with a pivotal function in the DNA damage response (DDR). SUMO interaction motifs (SIMs) in the N-terminal part of RNF4 tightly bind to SUMO polymers, and RNF4 can ubiquitinate these polymers in vitro. Using a proteomic approach, we identified the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, as a functional interactor of RNF4. USP11 can deubiquitinate hybrid SUMO-ubiquitin chains to counteract RNF4. SUMO-enriched nuclear bodies are stabilized by USP11, which functions downstream of RNF4 as a counterbalancing factor. In response to DNA damage induced by methyl methanesulfonate, USP11 could counteract RNF4 to inhibit the dissolution of nuclear bodies. Thus, we provide novel insight into cross-talk between ubiquitin and SUMO and uncover USP11 and RNF4 as a balanced SUMO-targeted ubiquitin ligase/protease pair with a role in the DDR.
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Affiliation(s)
- Ivo A Hendriks
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Joost Schimmel
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Karolin Eifler
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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Koh MY, Nguyen V, Lemos R, Darnay BG, Kiriakova G, Abdelmelek M, Ho TH, Karam J, Monzon FA, Jonasch E, Powis G. Hypoxia-induced SUMOylation of E3 ligase HAF determines specific activation of HIF2 in clear-cell renal cell carcinoma. Cancer Res 2014; 75:316-29. [PMID: 25421578 DOI: 10.1158/0008-5472.can-13-2190] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Clear-cell renal cell cancer (CRCC) is initiated typically by loss of the tumor-suppressor VHL, driving constitutive activation of hypoxia-inducible factor-1 (HIF1) and HIF2. However, whereas HIF1 has a tumor-suppressor role, HIF2 plays a distinct role in driving CRCC. In this study, we show that the HIF1α E3 ligase hypoxia-associated factor (HAF) complexes with HIF2α at DNA to promote HIF2-dependent transcription through a mechanism relying upon HAF SUMOylation. HAF SUMOylation was induced by hypoxia, whereas HAF-mediated HIF1α degradation was SUMOylation independent. HAF overexpression in mice increased CRCC growth and metastasis. Clinically, HAF overexpression was associated with poor prognosis. Taken together, our results show that HAF is a specific mediator of HIF2 activation that is critical for CRCC development and morbidity.
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Affiliation(s)
- Mei Yee Koh
- Sanford-Burnham Medical Research Institute, La Jolla, California.
| | - Vuvi Nguyen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert Lemos
- Sanford-Burnham Medical Research Institute, La Jolla, California
| | - Bryant G Darnay
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Galina Kiriakova
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mena Abdelmelek
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Thai H Ho
- Department of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Jose Karam
- Department of GU Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Federico A Monzon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Eric Jonasch
- Department of GU Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Garth Powis
- Sanford-Burnham Medical Research Institute, La Jolla, California
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Multiple crosstalks between mRNA biogenesis and SUMO. Chromosoma 2013; 122:387-99. [PMID: 23584125 DOI: 10.1007/s00412-013-0408-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/10/2013] [Accepted: 03/13/2013] [Indexed: 12/26/2022]
Abstract
mRNA metabolism involves the orchestration of multiple nuclear events, including transcription, processing (e.g., capping, splicing, polyadenylation), and quality control. This leads to the accurate formation of messenger ribonucleoparticles (mRNPs) that are finally exported to the cytoplasm for translation. The production of defined sets of mRNAs in given environmental or physiological situations relies on multiple regulatory mechanisms that target the mRNA biogenesis machineries. Among other regulations, post-translational modification by the small ubiquitin-like modifier SUMO, whose prominence in several cellular processes has been largely demonstrated, also plays a key role in mRNA biogenesis. Analysis of the multiple available SUMO proteomes and functional validations of an increasing number of sumoylated targets have revealed the key contribution of SUMO-dependent regulation in nuclear mRNA metabolism. While sumoylation of transcriptional activators and repressors is so far best documented, SUMO contribution to other stages of mRNA biogenesis is also emerging. Modification of mRNA metabolism factors by SUMO determine their subnuclear targeting and biological activity, notably by regulating their molecular interactions with nucleic acids or protein partners. In particular, sumoylation of DNA-bound transcriptional regulators interfere with their association to target sequences or chromatin modifiers. In addition, the recent identification of enzymes of the SUMO pathway within specialized mRNA biogenesis machineries may provide a further level of regulation to their specificity. These multiple crosstalks between mRNA metabolism and SUMO appear therefore as important players in cellular regulatory networks.
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Allen WL, Stevenson L, Coyle VM, Jithesh PV, Proutski I, Carson G, Gordon MA, Lenz HJD, Van Schaeybroeck S, Longley DB, Johnston PG. A systems biology approach identifies SART1 as a novel determinant of both 5-fluorouracil and SN38 drug resistance in colorectal cancer. Mol Cancer Ther 2012; 11:119-31. [PMID: 22027693 PMCID: PMC3272421 DOI: 10.1158/1535-7163.mct-11-0510] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemotherapy response rates for advanced colorectal cancer remain disappointingly low, primarily because of drug resistance, so there is an urgent need to improve current treatment strategies. To identify novel determinants of resistance to the clinically relevant drugs 5-fluorouracil (5-FU) and SN38 (the active metabolite of irinotecan), transcriptional profiling experiments were carried out on pretreatment metastatic colorectal cancer biopsies and HCT116 parental and chemotherapy-resistant cell line models using a disease-specific DNA microarray. To enrich for potential chemoresistance-determining genes, an unsupervised bioinformatics approach was used, and 50 genes were selected and then functionally assessed using custom-designed short interfering RNA (siRNA) screens. In the primary siRNA screen, silencing of 21 genes sensitized HCT116 cells to either 5-FU or SN38 treatment. Three genes (RAPGEF2, PTRF, and SART1) were selected for further analysis in a panel of 5 colorectal cancer cell lines. Silencing SART1 sensitized all 5 cell lines to 5-FU treatment and 4/5 cell lines to SN38 treatment. However, silencing of RAPGEF2 or PTRF had no significant effect on 5-FU or SN38 sensitivity in the wider cell line panel. Further functional analysis of SART1 showed that its silencing induced apoptosis that was caspase-8 dependent. Furthermore, silencing of SART1 led to a downregulation of the caspase-8 inhibitor, c-FLIP, which we have previously shown is a key determinant of drug resistance in colorectal cancer. This study shows the power of systems biology approaches for identifying novel genes that regulate drug resistance and identifies SART1 as a previously unidentified regulator of c-FLIP and drug-induced activation of caspase-8.
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Affiliation(s)
- Wendy L. Allen
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Leanne Stevenson
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Vicky M. Coyle
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Puthen V. Jithesh
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Irina Proutski
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Gail Carson
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Michael A Gordon
- Division of Medical Oncology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, USA
| | - Heinz-Josef D Lenz
- Division of Medical Oncology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90033, USA
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Daniel B. Longley
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
| | - Patrick G. Johnston
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, Northern Ireland
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Affiliation(s)
- Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands.
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Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC. Site-Specific Identification of SUMO-2 Targets in Cells Reveals an Inverted SUMOylation Motif and a Hydrophobic Cluster SUMOylation Motif. Mol Cell 2010; 39:641-52. [DOI: 10.1016/j.molcel.2010.07.026] [Citation(s) in RCA: 203] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/22/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]
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