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Cates K, Hung V, Barna M. Ribosome-associated proteins: unwRAPping ribosome heterogeneity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2025; 380:20230378. [PMID: 40045784 PMCID: PMC11883435 DOI: 10.1098/rstb.2023.0378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 12/07/2024] [Accepted: 01/06/2025] [Indexed: 03/09/2025] Open
Abstract
The definition of the ribosome as the monolithic machinery in cells that synthesizes all proteins in the cell has persisted for the better part of a century. Yet, research has increasingly revealed that ribosomes are dynamic, multimodal complexes capable of fine-tuning gene expression. This translation regulation may be achieved by ribosome-associated proteins (RAPs), which play key roles as modular trans-acting factors that are dynamic across different cellular contexts and can mediate the recruitment of specific transcripts or the modification of RNA or ribosomal proteins. As a result, RAPs have the potential to rapidly regulate translation within specific subcellular regions, across different cell or tissue types, in response to signalling, or in disease states. In this article, we probe the definition of the eukaryotic ribosome and review the major layers of additional proteins that expand the definition of ribosomes in the twenty-first century. We pose RAPs as key modulators that impart ribosome function in cellular processes, development and disease.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.
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Affiliation(s)
- Kitra Cates
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305, USA
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305, USA
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2
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Gutierrez-Morton E, Wang Y. The role of SUMOylation in biomolecular condensate dynamics and protein localization. CELL INSIGHT 2024; 3:100199. [PMID: 39399482 PMCID: PMC11467568 DOI: 10.1016/j.cellin.2024.100199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/23/2024] [Accepted: 08/24/2024] [Indexed: 10/15/2024]
Abstract
As a type of protein post-translational modification, SUMOylation is the process that attaches a small ubiquitin-like modifier (SUMO) to lysine residues of protein substrates. Not only do SUMO and ubiquitin exhibit structure similarity, but the enzymatic cascades for SUMOylation and ubiquitination are also similar. It is well established that protein ubiquitination triggers proteasomal degradation, but the function of SUMOylation remains poorly understood compared to ubiquitination. Recent studies reveal the role of SUMOylation in regulating protein localization, stability, and interaction networks. SUMO can be covalently attached to substrates either as an individual monomer (monoSUMOylation) or as a polymeric SUMO chain (polySUMOylation). Strikingly, mono- and polySUMOylation likely play distinct roles in protein subcellular localization and the assembly/disassembly of biomolecular condensates, which are membraneless cellular compartments with concentrated biomolecules. In this review, we summarize the recent advances in the understanding of the function and regulation of SUMOylation, which could reveal potential therapeutic targets in disease pathogenesis.
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Affiliation(s)
- Emily Gutierrez-Morton
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306-4300, USA
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Shah RB, Li Y, Yu H, Kini E, Sidi S. Stepwise phosphorylation and SUMOylation of PIDD1 drive PIDDosome assembly in response to DNA repair failure. Nat Commun 2024; 15:9195. [PMID: 39448602 PMCID: PMC11502896 DOI: 10.1038/s41467-024-53412-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 10/08/2024] [Indexed: 10/26/2024] Open
Abstract
SUMOylation regulates numerous cellular stress responses, yet targets in the apoptotic machinery remain elusive. We show that a single, DNA damage-induced monoSUMOylation event controls PIDDosome (PIDD1/RAIDD/caspase-2) formation and apoptotic death in response to unresolved DNA interstrand crosslinks (ICLs). SUMO-1 conjugation occurs on conserved K879 in the PIDD1 death domain (DD); is catalyzed by PIAS1 and countered by SENP3; and is triggered by ATR phosphorylation of neighboring T788 in the PIDD1 DD, which enables PIAS1 docking. Phospho/SUMO-PIDD1 proteins are captured by nucleolar RAIDD monomers via a SUMO-interacting motif (SIM) in the RAIDD DD, thus compartmentalizing nascent PIDDosomes for caspase-2 recruitment. Denying SUMOylation or the SUMO-SIM interaction spares the onset of PIDDosome assembly but blocks its completion, thus eliminating the apoptotic response to ICL repair failure. Conversely, removal of SENP3 forces apoptosis, even in cells with tolerable ICL levels. SUMO-mediated PIDDosome control is also seen in response to DNA breaks but not supernumerary centrosomes. These results illuminate PIDDosome formation in space and time and identify a direct role for SUMOylation in the assembly of a major pro-apoptotic device.
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Affiliation(s)
- Richa B Shah
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuanyuan Li
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Honglin Yu
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ela Kini
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel Sidi
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Cell, Developmental and Regenerative Biology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Li Y, Yang Y, Sears RC, Dai MS, Sun XX. USP36 SUMOylates Las1L and Promotes Its Function in Pre-Ribosomal RNA ITS2 Processing. CANCER RESEARCH COMMUNICATIONS 2024; 4:2835-2845. [PMID: 39356143 PMCID: PMC11523043 DOI: 10.1158/2767-9764.crc-24-0312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 08/19/2024] [Accepted: 09/30/2024] [Indexed: 10/03/2024]
Abstract
Ribosome biogenesis is a highly regulated cellular process requiring a large cohort of accessory factors to ensure the accurate production of ribosomes. Dysregulation of ribosome biogenesis is associated with the development of various human diseases, including cancer. The Las1L-Nol9 endonuclease-kinase complex is essential for the cleavage of the rRNA internal transcribed spacer 2 (ITS2), the phosphorylation of the 5'-hydroxyl end of the resulting precursor, and, thus, the maturation of the 60S ribosome. However, how the Las1L-Nol9 complex is regulated in cells is unclear. In this study, we report that the nucleolar ubiquitin-specific protease USP36 is a novel regulator of the Las1L-Nol9 complex. USP36 interacts with both Las1L and Nol9 and regulates their stability via deubiquitination. Intriguingly, USP36 also mediates the SUMOylation of Las1L, mainly at lysine (K) 565. Mutating K565 to arginine (R) does not affect the levels of Las1L and the formation of the Las1L-Nol9 complex, but abolishes its function in ITS2 processing, as unlike wild-type Las1L, the K565R mutant failed to rescue the defects in the ITS2 processing induced by the knockdown of endogenous Las1L. These results suggest that USP36-mediated Las1L SUMOylation is critical for ITS2 processing and that USP36 plays a critical role in ribosome biogenesis by regulating the Las1L-Nol9 complex. SIGNIFICANCE This study identifies USP36 as a deubiquitinating and small ubiquitin-like modifier ligase dual-function enzyme to mediate Las1L deubiquitination and SUMOylation. Las1L SUMOylation at K565 plays a critical role in pre-rRNA ITS2 processing. Thus, our study reveals a novel downstream pathway for USP36-regulated ribosome biogenesis.
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Affiliation(s)
- Yanping Li
- Department of Molecular and Medical Genetics, School of Medicine, and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Yunhan Yang
- Department of Molecular and Medical Genetics, School of Medicine, and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Rosalie C. Sears
- Department of Molecular and Medical Genetics, School of Medicine, and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Mu-Shui Dai
- Department of Molecular and Medical Genetics, School of Medicine, and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Xiao-Xin Sun
- Department of Molecular and Medical Genetics, School of Medicine, and the OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
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Yang Y, Li Y, Sears RC, Sun XX, Dai MS. SUMOylation regulation of ribosome biogenesis: Emerging roles for USP36. FRONTIERS IN RNA RESEARCH 2024; 2:1389104. [PMID: 38764604 PMCID: PMC11101209 DOI: 10.3389/frnar.2024.1389104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Ribosome biogenesis is essential for cell growth, proliferation, and animal development. Its deregulation leads to various human disorders such as ribosomopathies and cancer. Thus, tight regulation of ribosome biogenesis is crucial for normal cell homeostasis. Emerging evidence suggests that posttranslational modifications such as ubiquitination and SUMOylation play a crucial role in regulating ribosome biogenesis. Our recent studies reveal that USP36, a nucleolar deubiquitinating enzyme (DUB), acts also as a SUMO ligase to regulate nucleolar protein group SUMOylation, thereby being essential for ribosome biogenesis. Here, we provide an overview of the current understanding of the SUMOylation regulation of ribosome biogenesis and discuss the role of USP36 in nucleolar SUMOylation.
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Affiliation(s)
- Yunhan Yang
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Yanping Li
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Rosalie C. Sears
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Xiao-Xin Sun
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
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Youssef A, Mohammed BK, Prasad A, del Aguila A, Bassi G, Yang W, Ulloa L. Splenic SUMO1 controls systemic inflammation in experimental sepsis. Front Immunol 2023; 14:1200939. [PMID: 37520526 PMCID: PMC10374847 DOI: 10.3389/fimmu.2023.1200939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The recent discovery of TAK981(Subasumstat), the first-in-class selective inhibitor of SUMOylation, enables new immune treatments. TAK981 is already in clinical trials to potentiate immunotherapy in metastatic tumors and hematologic malignancies. Cancer patients have more than ten times higher risk of infections, but the effects of TAK981 in sepsis are unknown and previous studies on SUMO in infections are conflicting. Methods We used TAK981 in two sepsis models; polymicrobial peritonitis (CLP) and LPS endotoxemia. Splenectomy was done in both models to study the role of spleen. Western blotting of SUMO-conjugated proteins in spleen lysates was done. Global SUMO1 and SUMO3 knockout mice were used to study the specific SUMO regulation of inflammation in LPS endotoxemia. Splenocytes adoptive transfer was done from SUMO knockouts to wild type mice to study the role of spleen SUMOylation in experimental sepsis. Results and discussion Here, we report that inhibition of SUMOylation with TAK981 improved survival in mild polymicrobial peritonitis by enhancing innate immune responses and peritoneal bacterial clearance. Thus, we focused on the effects of TAK981 on the immune responses to bacterial endotoxin, showing that TAK981 enhanced early TNFα production but did not affect the resolution of inflammation. Splenectomy decreased serum TNFα levels by nearly 60% and TAK981-induced TNFα responses. In the spleen, endotoxemia induced a distinct temporal and substrate specificity for SUMO1 and SUMO2/3, and both were inhibited by TAK981. Global genetic depletion of SUMO1, but not SUMO3, enhanced TNFα production and metabolic acidosis. The transfer of SUMO1-null, but not wild-type, splenocytes into splenectomized wild-type mice exacerbated TNFα production and metabolic acidosis in endotoxemia. Conclusion These results suggest that specific regulation of splenic SUMO1 can modulate immune and metabolic responses to bacterial infection.
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Cao Y, Huang C, Zhao X, Yu J. Regulation of SUMOylation on RNA metabolism in cancers. Front Mol Biosci 2023; 10:1137215. [PMID: 36911524 PMCID: PMC9998694 DOI: 10.3389/fmolb.2023.1137215] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Post-translational modifications of proteins play very important roles in regulating RNA metabolism and affect many biological pathways. Here we mainly summarize the crucial functions of small ubiquitin-like modifier (SUMO) modification in RNA metabolism including transcription, splicing, tailing, stability and modification, as well as its impact on the biogenesis and function of microRNA (miRNA) in particular. This review also highlights the current knowledge about SUMOylation regulation in RNA metabolism involved in many cellular processes such as cell proliferation and apoptosis, which is closely related to tumorigenesis and cancer progression.
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Affiliation(s)
- Yingting Cao
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Caihu Huang
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology and Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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Martínez-Férriz A, Ferrando A, Fathinajafabadi A, Farràs R. Ubiquitin-mediated mechanisms of translational control. Semin Cell Dev Biol 2022; 132:146-154. [PMID: 34952788 DOI: 10.1016/j.semcdb.2021.12.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/15/2022]
Abstract
mRNAs translation to proteins constitutes an important step of cellular gene expression that is highly regulated in response to different extracellular stimuli and stress situations. The fine control of protein synthesis is carried out both qualitatively and quantitatively, depending on the cellular demand at each moment. Post-translational modifications, in turn regulated by intracellular signaling pathways, play a key role in translation regulation. Among them, ubiquitination, whose role is becoming increasingly important in the control of translation, determines a correct balance between protein synthesis and degradation. In this review we focus on the role of ubiquitination (both degradative K48-linkage type and non-degradative K63-linkage type and monoubiquitination) in eukaryotic translation, both at the pre-translational level during the biogenesis/degradation of the components of translational machinery as well as at the co-translational level under stressful conditions. We also discuss other ubiquitin-dependent regulatory mechanisms of mRNA protection and resumption of translation after stress removal, where the ubiquitination of ribosomal proteins and associated regulatory proteins play an important role in the global rhythm of translation.
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Affiliation(s)
- Arantxa Martínez-Férriz
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas CSIC-Universidad Politécnica de Valencia, Valencia, Spain
| | - Alihamze Fathinajafabadi
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
| | - Rosa Farràs
- Oncogenic Signalling Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
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9
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Sheban D, Shani T, Maor R, Aguilera-Castrejon A, Mor N, Oldak B, Shmueli MD, Eisenberg-Lerner A, Bayerl J, Hebert J, Viukov S, Chen G, Kacen A, Krupalnik V, Chugaeva V, Tarazi S, Rodríguez-delaRosa A, Zerbib M, Ulman A, Masarwi S, Kupervaser M, Levin Y, Shema E, David Y, Novershtern N, Hanna JH, Merbl Y. SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity. Mol Cell 2021; 82:106-122.e9. [PMID: 34875212 DOI: 10.1016/j.molcel.2021.11.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, how the chromatin is organized to prohibit the reversal of the developmental program remains unclear. Specifically, the totipotency-to-pluripotency transition marks one of the most dramatic events to the chromatin, and yet, the nature of histone alterations underlying this process is incompletely characterized. Here, we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Furthermore, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress the totipotency program in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in facilitating chromatin repression and desolation of the totipotent identity.
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Affiliation(s)
- Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roey Maor
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bernardo Oldak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jakob Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Guoyun Chen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Valeriya Chugaeva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tarazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Ulman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Solaiman Masarwi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Meital Kupervaser
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Linking nuclear matrix-localized PIAS1 to chromatin SUMOylation via direct binding of histones H3 and H2A.Z. J Biol Chem 2021; 297:101200. [PMID: 34537242 PMCID: PMC8496182 DOI: 10.1016/j.jbc.2021.101200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/02/2022] Open
Abstract
As a conserved posttranslational modification, SUMOylation has been shown to play important roles in chromatin-related biological processes including transcription. However, how the SUMOylation machinery associates with chromatin is not clear. Here, we present evidence that multiple SUMOylation machinery components, including SUMO E1 proteins SAE1 and SAE2 and the PIAS (protein inhibitor of activated STAT) family SUMO E3 ligases, are primarily associated with the nuclear matrix rather than with chromatin. We show using nuclease digestion that all PIAS family proteins maintain nuclear matrix association in the absence of chromatin. Of importance, we identify multiple histones including H3 and H2A.Z as directly interacting with PIAS1 and demonstrate that this interaction requires the PIAS1 SAP (SAF-A/B, Acinus, and PIAS) domain. We demonstrate that PIAS1 promotes SUMOylation of histones H3 and H2B in both a SAP domain– and an E3 ligase activity–dependent manner. Furthermore, we show that PIAS1 binds to heat shock–induced genes and represses their expression and that this function also requires the SAP domain. Altogether, our study reveals for the first time the nuclear matrix as the compartment most enriched in SUMO E1 and PIAS family E3 ligases. Our finding that PIAS1 interacts directly with histone proteins also suggests a molecular mechanism as to how nuclear matrix–associated PIAS1 is able to regulate transcription and other chromatin-related processes.
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11
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Ryu HY, Hochstrasser M. Histone sumoylation and chromatin dynamics. Nucleic Acids Res 2021; 49:6043-6052. [PMID: 33885816 PMCID: PMC8216275 DOI: 10.1093/nar/gkab280] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/28/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin structure and gene expression are dynamically controlled by post-translational modifications (PTMs) on histone proteins, including ubiquitylation, methylation, acetylation and small ubiquitin-like modifier (SUMO) conjugation. It was initially thought that histone sumoylation exclusively suppressed gene transcription, but recent advances in proteomics and genomics have uncovered its diverse functions in cotranscriptional processes, including chromatin remodeling, transcript elongation, and blocking cryptic initiation. Histone sumoylation is integral to complex signaling codes that prime additional histone PTMs as well as modifications of the RNA polymerase II carboxy-terminal domain (RNAPII-CTD) during transcription. In addition, sumoylation of histone variants is critical for the DNA double-strand break (DSB) response and for chromosome segregation during mitosis. This review describes recent findings on histone sumoylation and its coordination with other histone and RNAPII-CTD modifications in the regulation of chromatin dynamics.
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Affiliation(s)
- Hong-Yeoul Ryu
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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12
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Ryu H, Sun XX, Chen Y, Li Y, Wang X, Dai RS, Zhu HM, Klimek J, David L, Fedorov LM, Azuma Y, Sears RC, Dai MS. The deubiquitinase USP36 promotes snoRNP group SUMOylation and is essential for ribosome biogenesis. EMBO Rep 2021; 22:e50684. [PMID: 33852194 DOI: 10.15252/embr.202050684] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
SUMOylation plays a crucial role in regulating diverse cellular processes including ribosome biogenesis. Proteomic analyses and experimental evidence showed that a number of nucleolar proteins involved in ribosome biogenesis are modified by SUMO. However, how these proteins are SUMOylated in cells is less understood. Here, we report that USP36, a nucleolar deubiquitinating enzyme (DUB), promotes nucleolar SUMOylation. Overexpression of USP36 enhances nucleolar SUMOylation, whereas its knockdown or genetic deletion reduces the levels of SUMOylation. USP36 interacts with SUMO2 and Ubc9 and directly mediates SUMOylation in cells and in vitro. We show that USP36 promotes the SUMOylation of the small nucleolar ribonucleoprotein (snoRNP) components Nop58 and Nhp2 in cells and in vitro and their binding to snoRNAs. It also promotes the SUMOylation of snoRNP components Nop56 and DKC1. Functionally, we show that knockdown of USP36 markedly impairs rRNA processing and translation. Thus, USP36 promotes snoRNP group SUMOylation and is critical for ribosome biogenesis and protein translation.
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Affiliation(s)
- Hyunju Ryu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiao-Xin Sun
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yingxiao Chen
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yanping Li
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiaoyan Wang
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Roselyn S Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Hong-Ming Zhu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - John Klimek
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Larry David
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Lev M Fedorov
- OHSU Transgenic Mouse Models Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Rosalie C Sears
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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13
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SUMOylation- and GAR1-Dependent Regulation of Dyskerin Nuclear and Subnuclear Localization. Mol Cell Biol 2021; 41:MCB.00464-20. [PMID: 33526451 DOI: 10.1128/mcb.00464-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
The nuclear and subnuclear compartmentalization of the telomerase-associated protein and H/ACA ribonucleoprotein component dyskerin is an important although incompletely understood aspect of H/ACA ribonucleoprotein function. Four SUMOylation sites were previously identified in the C-terminal nuclear/nucleolar localization signal (N/NoLS) of dyskerin. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS represents an under-SUMOylated variant of dyskerin compared to wild-type dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3 fusion construct can drive nuclear accumulation of this variant and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein.
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14
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An interaction between PRRT2 and Na +/K + ATPase contributes to the control of neuronal excitability. Cell Death Dis 2021; 12:292. [PMID: 33731672 PMCID: PMC7969623 DOI: 10.1038/s41419-021-03569-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/18/2021] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Mutations in PRoline Rich Transmembrane protein 2 (PRRT2) cause pleiotropic syndromes including benign infantile epilepsy, paroxysmal kinesigenic dyskinesia, episodic ataxia, that share the paroxysmal character of the clinical manifestations. PRRT2 is a neuronal protein that plays multiple roles in the regulation of neuronal development, excitability, and neurotransmitter release. To better understand the physiopathology of these clinical phenotypes, we investigated PRRT2 interactome in mouse brain by a pulldown-based proteomic approach and identified α1 and α3 Na+/K+ ATPase (NKA) pumps as major PRRT2-binding proteins. We confirmed PRRT2 and NKA interaction by biochemical approaches and showed their colocalization at neuronal plasma membrane. The acute or constitutive inactivation of PRRT2 had a functional impact on NKA. While PRRT2-deficiency did not modify NKA expression and surface exposure, it caused an increased clustering of α3-NKA on the plasma membrane. Electrophysiological recordings showed that PRRT2-deficiency in primary neurons impaired NKA function during neuronal stimulation without affecting pump activity under resting conditions. Both phenotypes were fully normalized by re-expression of PRRT2 in PRRT2-deficient neurons. In addition, the NKA-dependent afterhyperpolarization that follows high-frequency firing was also reduced in PRRT2-silenced neurons. Taken together, these results demonstrate that PRRT2 is a physiological modulator of NKA function and suggest that an impaired NKA activity contributes to the hyperexcitability phenotype caused by PRRT2 deficiency.
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15
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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16
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Urinary proteomics reveals key markers of salt sensitivity in hypertensive patients during saline infusion. J Nephrol 2021; 34:739-751. [PMID: 33398797 DOI: 10.1007/s40620-020-00877-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hypertension is a complex disease and is the major cause of cardiovascular complications. In the vast majority of individuals, the aetiology of elevated blood pressure (BP) cannot be determined, thus impairing optimized therapies and prognosis for individual patients. A more precise understanding of the molecular pathogenesis of hypertension remains a pressing priority for both basic and translational research. Here we investigated the effect of salt on naive hypertensive patients in order to better understand the salt intake-blood pressure relationship. METHODS Patients underwent an acute saline infusion and were defined as salt-sensitive or salt-resistant according to mean blood pressure changes. Urinary proteome changes during the salt load test were analysed by a label-free quantitative proteomics approach. RESULTS Our data show that salt-sensitive patients display equal sodium reabsorption as salt-resistant patients, as major sodium transporters show the same behaviour during the salt load. However, salt-sensitive patients regulate the renin angiotensin system (RAS) differently from salt-resistant patients, and upregulate proteins, as epidermal growth factor (EGF) and plasminogen activator, urokinase (PLAU), involved in the regulation of epithelial sodium channel ENaC activity. CONCLUSIONS Salt-sensitive and salt-resistant subjects have similar response to a saline/volume infusion as detected by urinary proteome. However, we identified glutamyl aminopeptidase (ENPEP), PLAU, EGF and Xaa-Pro aminopeptidase 2 precursor XPNPEP2 as key molecules of salt-sensitivity, through modulation of ENaC-dependent sodium reabsorption along the distal tubule.
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17
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Ryu HY, Zhao D, Li J, Su D, Hochstrasser M. Histone sumoylation promotes Set3 histone-deacetylase complex-mediated transcriptional regulation. Nucleic Acids Res 2020; 48:12151-12168. [PMID: 33231641 PMCID: PMC7708062 DOI: 10.1093/nar/gkaa1093] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/12/2020] [Accepted: 10/27/2020] [Indexed: 12/02/2022] Open
Abstract
Histones are substrates of the SUMO (small ubiquitin-like modifier) conjugation pathway. Several reports suggest histone sumoylation affects transcription negatively, but paradoxically, our genome-wide analysis shows the modification concentrated at many active genes. We find that trans-tail regulation of histone-H2B ubiquitylation and H3K4 di-methylation potentiates subsequent histone sumoylation. Consistent with the known control of the Set3 histone deacetylase complex (HDAC) by H3K4 di-methylation, histone sumoylation directly recruits the Set3 complex to both protein-coding and noncoding RNA (ncRNA) genes via a SUMO-interacting motif in the HDAC Cpr1 subunit. The altered gene expression profile caused by reducing histone sumoylation matches well to the profile in cells lacking Set3. Histone H2B sumoylation and the Set3 HDAC coordinately suppress cryptic ncRNA transcription initiation internal to mRNA genes. Our results reveal an elaborate co-transcriptional histone crosstalk pathway involving the consecutive ubiquitylation, methylation, sumoylation and deacetylation of histones, which maintains transcriptional fidelity by suppressing spurious transcription.
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Affiliation(s)
- Hong-Yeoul Ryu
- Correspondence may also be addressed to Hong-Yeoul Ryu. Tel: +82 53 950 6352;
| | - Dejian Zhao
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06520, USA
| | - Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dan Su
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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18
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Matafora V, Farris F, Restuccia U, Tamburri S, Martano G, Bernardelli C, Sofia A, Pisati F, Casagrande F, Lazzari L, Marsoni S, Bonoldi E, Bachi A. Amyloid aggregates accumulate in melanoma metastasis modulating YAP activity. EMBO Rep 2020; 21:e50446. [PMID: 32749065 PMCID: PMC7507035 DOI: 10.15252/embr.202050446] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/27/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022] Open
Abstract
Melanoma progression is generally associated with increased transcriptional activity mediated by the Yes-associated protein (YAP). Mechanical signals from the extracellular matrix are sensed by YAP, which then activates the expression of proliferative genes, promoting melanoma progression and drug resistance. Which extracellular signals induce mechanotransduction, and how this is mediated, is not completely understood. Here, using secretome analyses, we reveal the extracellular accumulation of amyloidogenic proteins, i.e. premelanosome protein (PMEL), in metastatic melanoma, together with proteins that assist amyloid maturation into fibrils. We also confirm the accumulation of amyloid-like aggregates, similar to those detected in Alzheimer disease, in metastatic cell lines, as well as in human melanoma biopsies. Mechanistically, beta-secretase 2 (BACE2) regulates the maturation of these aggregates, which in turn induce YAP activity. We also demonstrate that recombinant PMEL fibrils are sufficient to induce mechanotransduction, triggering YAP signaling. Finally, we demonstrate that BACE inhibition affects cell proliferation and increases drug sensitivity, highlighting the importance of amyloids for melanoma survival, and the use of beta-secretase inhibitors as potential therapeutic approach for metastatic melanoma.
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Affiliation(s)
| | | | - Umberto Restuccia
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
- Present address:
ADIENNE Pharma & BiotechCaponagoItaly
| | - Simone Tamburri
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
- Present address:
Department of Experimental OncologyIEO‐European Institute of Oncology IRCCSMilanItaly
| | | | - Clara Bernardelli
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
- Present address:
Fondazione Politecnico di MilanoMilanItaly
| | - Andrea Sofia
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
- University of InsubriaVareseItaly
| | - Federica Pisati
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
- Cogentech SRL Benefit CorporationMilanItaly
| | | | - Luca Lazzari
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
| | | | - Emanuela Bonoldi
- Department of Laboratory MedicineDivision of PathologyGrande Ospedale Metropolitano NiguardaMilanItaly
| | - Angela Bachi
- IFOM‐ FIRC Institute of Molecular OncologyMilanItaly
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19
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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20
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Zhao X. SUMO-Mediated Regulation of Nuclear Functions and Signaling Processes. Mol Cell 2019; 71:409-418. [PMID: 30075142 DOI: 10.1016/j.molcel.2018.07.027] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022]
Abstract
Since the discovery of SUMO twenty years ago, SUMO conjugation has become a widely recognized post-translational modification that targets a myriad of proteins in many processes. Great progress has been made in understanding the SUMO pathway enzymes, substrate sumoylation, and the interplay between sumoylation and other regulatory mechanisms in a variety of contexts. As these research directions continue to generate insights into SUMO-based regulation, several mechanisms by which sumoylation and desumoylation can orchestrate large biological effects are emerging. These include the ability to target multiple proteins within the same cellular structure or process, respond dynamically to external and internal stimuli, and modulate signaling pathways involving other post-translational modifications. Focusing on nuclear function and intracellular signaling, this review highlights a broad spectrum of historical data and recent advances with the aim of providing an overview of mechanisms underlying SUMO-mediated global effects to stimulate further inquiry into intriguing roles of SUMO.
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Affiliation(s)
- Xiaolan Zhao
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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21
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Umbaugh CS, Figueiredo ML. Lysines residing in putative Small Ubiquitin-like MOdifier (SUMO) motifs regulate fate and function of 37 KDa laminin receptor. Biochimie 2019; 156:92-99. [DOI: 10.1016/j.biochi.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/06/2018] [Indexed: 01/17/2023]
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22
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Jeong J, Jin S, Choi H, Kwon JT, Kim J, Kim J, Park ZY, Cho C. Characterization of MAGEG2 with testis-specific expression in mice. Asian J Androl 2018; 19:659-665. [PMID: 27852984 PMCID: PMC5676425 DOI: 10.4103/1008-682x.192033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Male germ cell development is a well-defined process occurring in numerous seminiferous tubules of the testis. Uncovering testicular novel genes related to intrinsic regulation of spermatogenesis is essential for the understanding of spermatogenesis. In the present study, we investigated mouse Mageg2, which belongs to a group of melanoma-associated antigens (MAGEs). Mageg2 is transcribed in the testis specifically, and its expression level is increased at the pachytene spermatocyte stage, indicating that Mageg2 is expressed predominantly in germ cells. We generated an antibody against mouse MAGEG2 for further characterization at the protein level. Immunoblot analysis suggested that MAGEG2 has specific testicular expression and the expression primarily occurred in pachytene spermatocytes. Proteomic analyses demonstrated that mouse MAGEG2 binded to testicular germ cell-specific serine/threonine-protein kinase 31 (STK31) and heat shock protein 9 (HSPA9). Direct binding with both interaction partners was confirmed by co-immunoprecipitation. We found that STK31 and HSPA9 bind MAGEG2 directly but not with each other. Interestingly, MAGEG2 reduced the kinase activity of STK31. Our study suggests that mouse MAGEG2 has at least two functions, including chaperone activity related to HSPA9 and regulation of pachytene spermatocyte-specific kinase, STK31. Altogether, our results provide the first information about MAGEG2 at the transcript and protein levels and suggest its potential molecular functions.
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Affiliation(s)
- Juri Jeong
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Sora Jin
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Heejin Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Jun Tae Kwon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Jihye Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Jaehwan Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Zee Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
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23
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Morozov VM, Giovinazzi S, Ishov AM. CENP-B protects centromere chromatin integrity by facilitating histone deposition via the H3.3-specific chaperone Daxx. Epigenetics Chromatin 2017; 10:63. [PMID: 29273057 PMCID: PMC5741900 DOI: 10.1186/s13072-017-0164-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/24/2017] [Indexed: 12/27/2022] Open
Abstract
Background The main chromatin unit, the nucleosome, can be modulated by the incorporation of histone variants that, in combination with posttranslational histones modifications, determine epigenetics properties of chromatin. Understanding the mechanism that creates a histone variants landscape at different genomic elements is expected to elevate our comprehension of chromatin assembly and function. The Daxx chaperone deposits transcription-associated histone H3.3 at centromeres, but mechanism of centromere-specific Daxx targeting remains unclear. Results In this study, we identified an unexpected function of the constitutive centromeric protein CENP-B that serves as a “beacon” for H3.3 incorporation. CENP-B depletion reduces Daxx association and H3.3 incorporation at centromeres. Daxx/CENP-B interaction and Daxx centromeric association are SUMO dependent and requires SIMs of Daxx. Depletion of SUMO-2, but not SUMO-1, decreases Daxx/CENP-B interaction and reduces centromeric accumulation of Daxx and H3.3, demonstrating distinct functions of SUMO paralogs in H3.3 chaperoning. Finally, disruption of CENP-B/Daxx-dependent H3.3 pathway deregulates heterochromatin marks H3K9me3, ATRX and HP1α at centromeres and elevates chromosome instability. Conclusion The demonstrated roles of CENP-B and SUMO-2 in H3.3 loading reveal a novel mechanism controlling chromatin maintenance and genome stability. Given that CENP-B is the only centromere protein that binds centromere-specific DNA elements, our study provides a new link between centromere DNA and unique epigenetic landscape of centromere chromatin. Electronic supplementary material The online version of this article (10.1186/s13072-017-0164-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viacheslav M Morozov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA
| | - Serena Giovinazzi
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA.,Division of Food Safety, Florida Department of Agriculture and Consumer Services, Tallahassee, FL, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA.
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24
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Jung Y, Kim HD, Yang HW, Kim HJ, Jang CY, Kim J. Modulating cellular balance of Rps3 mono-ubiquitination by both Hel2 E3 ligase and Ubp3 deubiquitinase regulates protein quality control. Exp Mol Med 2017; 49:e390. [PMID: 29147007 PMCID: PMC5704183 DOI: 10.1038/emm.2017.128] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/25/2017] [Accepted: 03/27/2017] [Indexed: 12/14/2022] Open
Abstract
When a ribosome complex is stalled during the translation elongation process in eukaryotes, the mono-ubiquitination of Rps3 has recently been shown to be critical to ribosome quality control. We have discovered that the regulatory role of Rps3 mono-ubiquitination is controlled by a deubiquitinase. We also showed that an autophagic signal appears to be coupled to the mono-ubiquitination of Rps3p through the entrance of Ubp3p into the autophagosome in yeasts. The mono-ubiquitination of the Rps3 protein is tightly modulated by reciprocal action between the Hel2p E3 ligase and the Ubp3p deubiquitinase in yeasts and the reciprocal action between the RNF123 E3 ligase and the USP10 deubiquitinase in mammalian cells. We also found that the Ubp3p/USP10 deubiquitinases critically modulate Hel2p/RNF123-mediated Rps3p mono-ubiquitination. In addition, we found that Hel2p/RNF123 and Ubp3p/USP10 appeared to be differently localized in the ribosome complex after ultraviolet irradiation. Together, our results support a model in which coordinated ubiquitination and deubiquitination activities can finely balance the level of regulatory Rps3p mono-ubiquitination in ribosome-associated quality control and autophagy processes.
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Affiliation(s)
- Youjin Jung
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building 603-3, Korea University, Seoul, Republic of Korea
| | - Hee Woong Yang
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hye Jin Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Chang-Young Jang
- Laboratory of Cell Biology, Research Center for Cell Fate Control, College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, TechnoComplex Building 603-3, Korea University, Seoul, Republic of Korea
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25
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Hughes DJ, Tiede C, Penswick N, Tang AAS, Trinh CH, Mandal U, Zajac KZ, Gaule T, Howell G, Edwards TA, Duan J, Feyfant E, McPherson MJ, Tomlinson DC, Whitehouse A. Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Sci Signal 2017; 10:10/505/eaaj2005. [PMID: 29138295 DOI: 10.1126/scisignal.aaj2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells. Crucially, these synthetic proteins did not prevent SUMO conjugation either in vitro or in cell-based systems, enabling the specific analysis of SUMO-mediated protein-protein interactions. Furthermore, through structural analysis and molecular modeling, we explored the molecular mechanisms that may underlie their specificity in interfering with either SUMO-1-mediated interactions or interactions mediated by either SUMO-2 or SUMO-3. Not only will these reagents enable investigation of the biological roles of SUMOylation, but the Affimer technology used to generate these synthetic binding proteins could also be exploited to design or validate reagents or therapeutics that target other protein-protein interactions.
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Affiliation(s)
- David J Hughes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalie Penswick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anna Ah-San Tang
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Upasana Mandal
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katarzyna Z Zajac
- BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thembaninskosi Gaule
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth Howell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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26
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Liang Z, Yang Y, He Y, Yang P, Wang X, He G, Zhang P, Zhu H, Xu N, Zhao X, Liang S. SUMOylation of IQGAP1 promotes the development of colorectal cancer. Cancer Lett 2017; 411:90-99. [PMID: 28987385 DOI: 10.1016/j.canlet.2017.09.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 02/05/2023]
Abstract
IQGAP1 is a conserved multifunctional protein implicated in tumorigenesis. An aberrant expression of IQGAP1 widely exists in many cancers, but the SUMOylation modification of IQGAP1 in carcinogenesis is unknown by now. Here we first time explore biological functions of IQGAP1 SUMOylation in promoting colorectal cancer progression in vitro and in vivo. The expression of IQGAP1 and its SUMOylation level are both increased in human colorectal carcinoma (CRC) cells and tissues. IQGAP1 is mainly SUMOylated by SUMO1 at the K1445 residue, which could stabilize IQGAP1 by reducing protein ubiquitination. IQGAP1 SUMOylation improves CRC cell growth, cell migration and tumorigenesis in vivo through activating the phosphorylation of ERK, MEK and AKT. While the SUMOylation site mutation at K1445 of IQGAP1 greatly reduces CRC cell proliferation, migration ability and tumor growth of CRC-xenograft mice by suppressing phosphorylation of ERK, MEK and AKT. Our findings discover the IQGAP1 SUMOylation is a novel regulatory mechanism to enhance tumorigenesis and development of CRC in vitro and in vivo.
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Affiliation(s)
- Ziwei Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China
| | - Yanfang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China
| | - Yu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China
| | - Pengbo Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China
| | - Xixi Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, 100034, PR China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China; Laboratory of Cell and Molecular Biology & State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, 100034, PR China
| | - Xia Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China; Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, 610041, PR China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, No.17, 3rd Section of People's South Road, Chengdu, 610041, PR China.
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27
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Regulation of Cellular Processes by SUMO: Understudied Topics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:89-97. [PMID: 28197907 DOI: 10.1007/978-3-319-50044-7_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SUMO plays a multiple role in maintenance of cellular homeostasis, both under normal conditions and under cell stress . Considerable effort has been devoted to unraveling the functions of SUMO in regulation of transcription and preservation of genome stability. However, it is clear from high-throughput SUMO proteome studies that SUMO likely regulates many more cellular processes. The function of SUMO in these processes has hardly been explored. This review will focus on the emerging function of SUMO in regulation of several of these processes.
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Abstract
Many of the known SUMO substrates are nuclear proteins, which regulate gene expression and chromatin dynamics. Sumoylation, in general, appears to correlate with decreased transcriptional activity, and in many cases modulation of the chromatin template is implicated. Sumoylation of the core histones is associated with transcriptional silencing, and transcription factor sumoylation can decrease gene expression by promoting recruitment of chromatin modifying enzymes. Additionally, sumoylation of transcriptional corepressors and chromatin remodeling enzymes can influence interactions with other transcriptional regulators, and alter their enzymatic activity. In some cases, proteins that are components of transcriptional corepressor complexes have been shown to be SUMO E3 ligases, further emphasizing the integration of sumoylation with the regulation of chromatin remodeling. Despite the evidence suggesting that sumoylation is primarily repressive for access to chromatin, recent analyses suggest that protein sumoylation on the chromatin template may play important roles at highly expressed genes. Elucidating the dynamic interplay of sumoylation with other post-translational modifications of histones and chromatin associated proteins will be key to fully understanding the regulation of access to the chromatin template.
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Pérez-Garrastachu M, Arluzea J, Andrade R, Díez-Torre A, Urtizberea M, Silió M, Aréchaga J. Nucleoporins redistribute inside the nucleus after cell cycle arrest induced by histone deacetylases inhibition. Nucleus 2017; 8:515-533. [PMID: 28696859 DOI: 10.1080/19491034.2017.1320001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nucleoporins are the main components of the nuclear-pore complex (NPC) and were initially considered as mere structural elements embedded in the nuclear envelope, being responsible for nucleocytoplasmic transport. Nevertheless, several recent scientific reports have revealed that some nucleoporins participate in nuclear processes such as transcription, replication, DNA repair and chromosome segregation. Thus, the interaction of NPCs with chromatin could modulate the distribution of chromosome territories relying on the epigenetic state of DNA. In particular, the nuclear basket proteins Tpr and Nup153, and the FG-nucleoporin Nup98 seem to play key roles in all these novel functions. In this work, histone deacetylase inhibitors (HDACi) were used to induce a hyperacetylated state of chromatin and the behavior of the mentioned nucleoporins was studied. Our results show that, after HDACi treatment, Tpr, Nup153 and Nup98 are translocated from the nuclear pore toward the interior of the cell nucleus, accumulating as intranuclear nucleoporin clusters. These transitory structures are highly dynamic, and are mainly present in the population of cells arrested at the G0/G1 phase of the cell cycle. Our results indicate that the redistribution of these nucleoporins from the nuclear envelope to the nuclear interior may be implicated in the early events of cell cycle initialization, particularly during the G1 phase transition.
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Affiliation(s)
- Miguel Pérez-Garrastachu
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Jon Arluzea
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain.,b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Ricardo Andrade
- b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Alejandro Díez-Torre
- b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Marta Urtizberea
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Margarita Silió
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
| | - Juan Aréchaga
- a Laboratory of Stem Cells, Development & Cancer, Department of Cell Biology and Histology, Faculty of Medicine and Nursing , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain.,b High Resolution and Analytical Biomedical Microscopy Core Facility, SGIKer , University of the Basque Country (UPV/EHU) , Leioa , Biscay , Spain
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30
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Cai L, Tu J, Song L, Gao Z, Li K, Wang Y, Liu Y, Zhong F, Ge R, Qin J, Ding C, He F. Proteome-wide Mapping of Endogenous SUMOylation Sites in Mouse Testis. Mol Cell Proteomics 2017; 16:717-727. [PMID: 28289178 PMCID: PMC5417816 DOI: 10.1074/mcp.m116.062125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 02/27/2017] [Indexed: 01/12/2023] Open
Abstract
SUMOylation is a reversible post-translational modification involved in various critical biological processes. To date, there is limited approach for endogenous wild-type SUMO-modified peptides enrichment and SUMOylation sites identification. In this study, we generated a high-affinity SUMO1 antibody to facilitate the enrichment of endogenous SUMO1-modified peptides from Trypsin/Lys-C protease digestion. Following secondary Glu-C protease digestion, we identified 53 high-confidence SUMO1-modified sites from mouse testis by using high-resolution mass spectrometry. Bioinformatics analyses showed that SUMO1-modified proteins were enriched in transcription regulation and DNA repair. Nab1 was validated to be an authentic SUMOylated protein and Lys479 was identified to be the major SUMOylation site. The SUMOylation of Nab1 enhanced its interaction with HDAC2 and maintained its inhibitory effect on EGR1 transcriptional activity. Therefore, we provided a novel approach to investigating endogenous SUMOylation sites in tissue samples.
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Affiliation(s)
- Lili Cai
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Jun Tu
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China.,¶Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Song
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Zhihua Gao
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Kai Li
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Yunzhi Wang
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yang Liu
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Fan Zhong
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Rui Ge
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Jun Qin
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Chen Ding
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China; .,§State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
| | - Fuchu He
- From the ‡State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institutes of Biomedical Sciences, School of Life Sciences, Fudan University, Shanghai 200032, China; .,§State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX center, Beijing), Beijing 102206, China
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31
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Xiao Y, Pollack D, Andrusier M, Levy A, Callaway M, Nieves E, Reddi P, Vigodner M. Identification of cell-specific targets of sumoylation during mouse spermatogenesis. Reproduction 2016; 151:149-66. [PMID: 26701181 DOI: 10.1530/rep-15-0239] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent findings suggest diverse and potentially multiple roles of small ubiquitin-like modifier (SUMO) in testicular function and spermatogenesis. However, SUMO targets remain uncharacterized in the testis due to the complex multicellular nature of testicular tissue, the inability to maintain and manipulate spermatogenesis in vitro, and the technical challenges involved in identifying low-abundance endogenous SUMO targets. In this study, we performed cell-specific identification of sumoylated proteins using concentrated cell lysates prepared with de-sumoylation inhibitors from freshly purified spermatocytes and spermatids. One-hundred and twenty proteins were uniquely identified in the spermatocyte and/or spermatid fractions. The identified proteins are involved in the regulation of transcription, stress response, microRNA biogenesis, regulation of major enzymatic pathways, nuclear-cytoplasmic transport, cell-cycle control, acrosome biogenesis, and other processes. Several proteins with important roles during spermatogenesis were chosen for further characterization by co-immunoprecipitation, co-localization, and in vitro sumoylation studies. GPS-SUMO Software was used to identify consensus and non-consensus sumoylation sites within the amino acid sequences of the proteins. The analyses confirmed the cell-specific sumoylation and/or SUMO interaction of several novel, previously uncharacterized SUMO targets such as CDK1, RNAP II, CDC5, MILI, DDX4, TDP-43, and STK31. Furthermore, several proteins that were previously identified as SUMO targets in somatic cells (KAP1 and MDC1) were identified as SUMO targets in germ cells. Many of these proteins have a unique role in spermatogenesis and during meiotic progression. This research opens a novel avenue for further studies of SUMO at the level of individual targets.
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Affiliation(s)
| | | | | | | | - Myrasol Callaway
- Department of BiologyStern College, Yeshiva University, New York, New York, USALaboratory for Macromolecular Analysis and ProteomicsAlbert Einstein College of Medicine, Bronx, New York, USADepartment of BiologyStern College, Yeshiva University, 245 Lexington Avenue, New York, New York 10016, USADepartment of Developmental and Molecular BiologyAlbert Einstein College of Medicine, Bronx, New York, USADepartment of PathologyUniversity of Virginia, Charlottesville, Virginia, USA
| | - Edward Nieves
- Department of BiologyStern College, Yeshiva University, New York, New York, USALaboratory for Macromolecular Analysis and ProteomicsAlbert Einstein College of Medicine, Bronx, New York, USADepartment of BiologyStern College, Yeshiva University, 245 Lexington Avenue, New York, New York 10016, USADepartment of Developmental and Molecular BiologyAlbert Einstein College of Medicine, Bronx, New York, USADepartment of PathologyUniversity of Virginia, Charlottesville, Virginia, USA
| | - Prabhakara Reddi
- Department of BiologyStern College, Yeshiva University, New York, New York, USALaboratory for Macromolecular Analysis and ProteomicsAlbert Einstein College of Medicine, Bronx, New York, USADepartment of BiologyStern College, Yeshiva University, 245 Lexington Avenue, New York, New York 10016, USADepartment of Developmental and Molecular BiologyAlbert Einstein College of Medicine, Bronx, New York, USADepartment of PathologyUniversity of Virginia, Charlottesville, Virginia, USA
| | - Margarita Vigodner
- Department of BiologyStern College, Yeshiva University, New York, New York, USALaboratory for Macromolecular Analysis and ProteomicsAlbert Einstein College of Medicine, Bronx, New York, USADepartment of BiologyStern College, Yeshiva University, 245 Lexington Avenue, New York, New York 10016, USADepartment of Developmental and Molecular BiologyAlbert Einstein College of Medicine, Bronx, New York, USADepartment of PathologyUniversity of Virginia, Charlottesville, Virginia, USA Department of BiologyStern College, Yeshiva University, New York, New York, USALaboratory for Macromolecular Analysis and ProteomicsAlbert Einstein College of Medicine, Bronx, New York, USADepartment of BiologyStern College, Yeshiva University, 245 Lexington Avenue, New York, New York 10016, USADepartment of Developmental and Molecular BiologyAlbert Einstein College of Medicine, Bronx, New York, USADepartment of PathologyUniversity of Virginia, Charlottesville, Virginia, USA
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32
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Abstract
Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication and the DNA-damage response.
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33
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Jongjitwimol J, Baldock RA, Morley SJ, Watts FZ. Sumoylation of eIF4A2 affects stress granule formation. J Cell Sci 2016; 129:2407-15. [PMID: 27160682 PMCID: PMC4920252 DOI: 10.1242/jcs.184614] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/29/2016] [Indexed: 01/27/2023] Open
Abstract
Regulation of protein synthesis is crucial for cells to maintain viability and to prevent unscheduled proliferation that could lead to tumorigenesis. Exposure to stress results in stalling of translation, with many translation initiation factors, ribosomal subunits and mRNAs being sequestered into stress granules or P bodies. This allows the re-programming of the translation machinery. Many aspects of translation are regulated by post-translational modification. Several proteomic screens have identified translation initiation factors as targets for sumoylation, although in many cases the role of this modification has not been determined. We show here that eIF4A2 is modified by SUMO, with sumoylation occurring on a single residue (K226). We demonstrate that sumoylation of eIF4A2 is modestly increased in response to arsenite and ionising radiation, but decreases in response to heat shock or hippuristanol. In arsenite-treated cells, but not in hippuristanol-treated cells, eIF4A2 is recruited to stress granules, suggesting sumoylation of eIF4A2 correlates with its recruitment to stress granules. Furthermore, we demonstrate that the inability to sumoylate eIF4A2 results in impaired stress granule formation, indicating a new role for sumoylation in the stress response. Summary: In response to stress, proteins required to initiate protein synthesis are modified; we demonstrate that sumoylation of eIF4A2 correlates with its recruitment to stress granules.
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Affiliation(s)
- Jirapas Jongjitwimol
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Robert A Baldock
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Simon J Morley
- Department of Biochemistry and Biomedical Science, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Felicity Z Watts
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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34
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Intense Resistance Exercise Promotes the Acute and Transient Nuclear Translocation of Small Ubiquitin-Related Modifier (SUMO)-1 in Human Myofibres. Int J Mol Sci 2016; 17:ijms17050646. [PMID: 27136539 PMCID: PMC4881472 DOI: 10.3390/ijms17050646] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 01/14/2023] Open
Abstract
Protein sumoylation is a posttranslational modification triggered by cellular stress. Because general information concerning the role of small ubiquitin-related modifier (SUMO) proteins in adult skeletal muscle is sparse, we investigated whether SUMO-1 proteins will be subjected to time-dependent changes in their subcellular localization in sarcoplasmic and nuclear compartments of human type I and II skeletal muscle fibers in response to acute stimulation by resistance exercise (RE). Skeletal muscle biopsies were taken at baseline (PRE), 15, 30, 60, 240 min and 24 h post RE from 6 male subjects subjected to a single bout of one-legged knee extensions. SUMO-1 localization was determined via immunohistochemistry and confocal laser microscopy. At baseline SUMO-1 was localized in perinuclear regions of myonuclei. Within 15 and up to 60 min post exercise, nuclear SUMO-1 localization was significantly increased (p < 0.01), declining towards baseline levels within 240 min post exercise. Sarcoplasmic SUMO-1 localization was increased at 15 min post exercise in type I and up to 30 min post RE in type II myofibres. The changing localization of SUMO-1 proteins acutely after intense muscle contractions points to a role for SUMO proteins in the acute regulation of the skeletal muscle proteome after exercise.
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35
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Matafora V, Cuccurullo M, Beneduci A, Petrazzuolo O, Simeone A, Anastasio P, Mignani R, Feriozzi S, Pisani A, Comotti C, Bachi A, Capasso G. Early markers of Fabry disease revealed by proteomics. MOLECULAR BIOSYSTEMS 2016; 11:1543-51. [PMID: 25666440 DOI: 10.1039/c4mb00707g] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Fabry disease (FD) is an X-linked lysosomal storage disorder caused by a deficiency of the lysosomal hydrolase α-galactosidase A (α-GalA) that leads to the intra-lysosomal accumulation of globotriaosylceramide (Gb3) in various organ systems. As a consequence, a multisystems disorder develops, culminating in stroke, progressive renal and cardiac dysfunction. Enzyme replacement therapy (ERT) offers a specific treatment for patients affected by FD, though the monitoring of treatment is hindered by a lack of surrogate markers of response. Remarkably, due to the high heterogeneity of the Fabry phenotype, both diagnostic testing and treatment decisions are more challenging in females than in males; thus, reliable biomarkers for Fabry disease are needed, particularly for female patients. Here, we use a proteomic approach for the identification of disease-associated markers that can be used for the early diagnosis of FD as well as for monitoring the effectiveness of ERT. Our data show that the urinary proteome of Fabry naïve patients is different from that of normal subjects. In addition, biological pathways mainly affected by FD are related to immune response, inflammation, and energetic metabolism. In particular, the up-regulation of uromodulin, prostaglandin H2 d-isomerase and prosaposin in the urine of FD patients was demonstrated; these proteins might be involved in kidney damage at the tubular level, inflammation and immune response. Furthermore, comparing the expression of these proteins in Fabry patients before and after ERT treatment, a decrease of their concentration was observed, thus demonstrating the correlation between the identified markers and the effectiveness of the pharmacological treatment.
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Affiliation(s)
- V Matafora
- Department of Cardiovascular Medicine, Second University of Naples, Naples, Italy
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36
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Tu J, Chen Y, Cai L, Xu C, Zhang Y, Chen Y, Zhang C, Zhao J, Cheng J, Xie H, Zhong F, He F. Functional Proteomics Study Reveals SUMOylation of TFII-I is Involved in Liver Cancer Cell Proliferation. J Proteome Res 2015; 14:2385-97. [PMID: 25869096 DOI: 10.1021/acs.jproteome.5b00062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SUMOylation has emerged as a new regulatory mechanism for proteins involved in multiple physiological and pathological processes. However, the detailed function of SUMOylation in liver cancer is still elusive. This study reveals that the SUMOylation-activating enzyme UBA2 is highly expressed in liver cancer cells and clinical samples. Silencing of UBA2 expression could to some extent suppress cell proliferation. To elucidate the function of UBA2, we used a large scale proteomics strategy to identify SUMOylation targets in HepG2 cells. We characterized 827 potential SUMO1-modified proteins that were not present in the control samples. These proteins were enriched in gene expression processes. Twelve candidates were validated as SUMO1-modified proteins by immunoprecipitation-Western blotting. We further characterized SUMOylated protein TFII-I that was identified in this study and determined that TFII-I was modified by SUMO1 at K221 and K240. PIAS4 was an E3 ligase for TFII-I SUMOylation, and SENP2 was responsible for deSUMOylating TFII-I in HepG2 cells. SUMOylation reduced TFII-I binding to its repressor HDAC3 and thus promoted its transcriptional activity. We further show that SUMOylation is critical for TFII-I to promote cell proliferation and colony formation. Our findings contribute to understanding the role of SUMOylation in liver cancer development.
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Affiliation(s)
- Jun Tu
- †Department of Chemistry, Fudan University, Shanghai 200433, China.,‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yalan Chen
- ∥Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lili Cai
- ‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Changming Xu
- #College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China
| | - Yang Zhang
- ‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,§Department of Systems Biology for Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yanmei Chen
- ‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chen Zhang
- ‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jian Zhao
- ‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jinke Cheng
- ∥Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongwei Xie
- #College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China
| | - Fan Zhong
- ‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,§Department of Systems Biology for Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fuchu He
- †Department of Chemistry, Fudan University, Shanghai 200433, China.,‡Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,⊥State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
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Pentecost M, Vashisht AA, Lester T, Voros T, Beaty SM, Park A, Wang YE, Yun TE, Freiberg AN, Wohlschlegel JA, Lee B. Evidence for ubiquitin-regulated nuclear and subnuclear trafficking among Paramyxovirinae matrix proteins. PLoS Pathog 2015; 11:e1004739. [PMID: 25782006 PMCID: PMC4363627 DOI: 10.1371/journal.ppat.1004739] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 02/10/2015] [Indexed: 11/24/2022] Open
Abstract
The paramyxovirus matrix (M) protein is a molecular scaffold required for viral morphogenesis and budding at the plasma membrane. Transient nuclear residence of some M proteins hints at non-structural roles. However, little is known regarding the mechanisms that regulate the nuclear sojourn. Previously, we found that the nuclear-cytoplasmic trafficking of Nipah virus M (NiV-M) is a prerequisite for budding, and is regulated by a bipartite nuclear localization signal (NLSbp), a leucine-rich nuclear export signal (NES), and monoubiquitination of the K258 residue within the NLSbp itself (NLSbp-lysine). To define whether the sequence determinants of nuclear trafficking identified in NiV-M are common among other Paramyxovirinae M proteins, we generated the homologous NES and NLSbp-lysine mutations in M proteins from the five major Paramyxovirinae genera. Using quantitative 3D confocal microscopy, we determined that the NES and NLSbp-lysine are required for the efficient nuclear export of the M proteins of Nipah virus, Hendra virus, Sendai virus, and Mumps virus. Pharmacological depletion of free ubiquitin or mutation of the conserved NLSbp-lysine to an arginine, which inhibits M ubiquitination, also results in nuclear and nucleolar retention of these M proteins. Recombinant Sendai virus (rSeV-eGFP) bearing the NES or NLSbp-lysine M mutants rescued at similar efficiencies to wild type. However, foci of cells expressing the M mutants displayed marked fusogenicity in contrast to wild type, and infection did not spread. Recombinant Mumps virus (rMuV-eGFP) bearing the homologous mutations showed similar defects in viral morphogenesis. Finally, shotgun proteomics experiments indicated that the interactomes of Paramyxovirinae M proteins are significantly enriched for components of the nuclear pore complex, nuclear transport receptors, and nucleolar proteins. We then synthesize our functional and proteomics data to propose a working model for the ubiquitin-regulated nuclear-cytoplasmic trafficking of cognate paramyxovirus M proteins that show a consistent nuclear trafficking phenotype. Elucidating virus-cell interactions is fundamental to understanding viral replication and identifying targets for therapeutic control of viral infection. Paramyxoviruses include human and animal pathogens of medical and agricultural significance. Their matrix (M) structural protein organizes virion assembly at the plasma membrane and mediates viral budding. While nuclear localization of M proteins has been described for some paramyxoviruses, the underlying mechanisms of nuclear trafficking and the biological relevance of this observation have remained largely unexamined. Through comparative analyses of M proteins across five Paramyxovirinae genera, we identify M proteins from at least three genera that exhibit similar nuclear trafficking phenotypes regulated by an NLSbp as well as an NES sequence within M that may mediate the interaction of M with host nuclear transport receptors. Additionally, a conserved lysine within the NLSbp of some M proteins is required for nuclear export by regulating M ubiquitination. Sendai virus engineered to express a ubiquitination-defective M does not produce infectious virus but instead displays extensive cell-cell fusion while M is retained in the nucleolus. Thus, some Paramyxovirinae M proteins undergo regulated and active nuclear and subnuclear transport, a prerequisite for viral morphogenesis, which also suggests yet to be discovered roles for M in the nucleus.
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Affiliation(s)
- Mickey Pentecost
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ajay A. Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Talia Lester
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tim Voros
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shannon M. Beaty
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Arnold Park
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Yao E. Wang
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tatyana E Yun
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - James A. Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Benhur Lee
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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38
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Camerini S, Mauri P. The role of protein and peptide separation before mass spectrometry analysis in clinical proteomics. J Chromatogr A 2014; 1381:1-12. [PMID: 25618357 DOI: 10.1016/j.chroma.2014.12.035] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 11/25/2022]
Abstract
The purpose of clinical proteomics is to characterise protein profiles of a plethora of diseases with the aim of finding specific biomarkers. These are particularly valuable for early diagnosis, and represent key molecules suitable to elucidate pathogenic mechanisms. Samples deriving from patients (i.e. blood, urine, cerebrospinal fluid, biopsies) are the sources for clinical proteomics. Due to the complexity of the extracted samples their direct analysis is unachievable. Any analytical clinical proteomics study should start with the choice of the optimal combination of strategies with respect to both sample preparations and MS approaches. Protein or peptide fractionation (off-line or on-line) is essential to reduce complexity of biological samples and to achieve the most complete and reproducible analysis. The aim of this review is to introduce the readers to a functional range of strategies to help scientists in their proteomics set up. In particular, the separation approaches of proteins or peptides (both gel-based and gel-free) are reviewed with special attention paid to their advantages and limitations, and to the different liquid chromatography techniques used to peptide fractionation after protein enzymatic digestion and before their detection. Finally, the role of mass spectrometry (MS) for protein identification and quantification is discussed including emerging MS data acquisition strategies.
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Affiliation(s)
- Serena Camerini
- Dept of Cell Biology and Neurosciences Higher Institute of Health (ISS), Rome, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies (ITB-CNR), Segrate, and Institute of Life Science - Scuola Superiore Sant'Anna, Pisa, Italy.
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39
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Lamoliatte F, Caron D, Durette C, Mahrouche L, Maroui MA, Caron-Lizotte O, Bonneil E, Chelbi-Alix MK, Thibault P. Large-scale analysis of lysine SUMOylation by SUMO remnant immunoaffinity profiling. Nat Commun 2014; 5:5409. [PMID: 25391492 DOI: 10.1038/ncomms6409] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/29/2014] [Indexed: 01/11/2023] Open
Abstract
Small ubiquitin-related modifiers (SUMO) are evolutionarily conserved ubiquitin-like proteins that regulate several cellular processes including cell cycle progression, intracellular trafficking, protein degradation and apoptosis. Despite the importance of protein SUMOylation in different biological pathways, the global identification of acceptor sites in complex cell extracts remains a challenge. Here we generate a monoclonal antibody that enriches for peptides containing SUMO remnant chains following tryptic digestion. We identify 954 SUMO3-modified lysine residues on 538 proteins and profile by quantitative proteomics the dynamic changes of protein SUMOylation following proteasome inhibition. More than 86% of these SUMOylation sites have not been reported previously, including 5 sites on the tumour suppressor parafibromin (CDC73). The modification of CDC73 at K136 affects its nuclear retention within PML nuclear bodies on proteasome inhibition. In contrast, a CDC73 K136R mutant translocates to the cytoplasm under the same conditions, further demonstrating the effectiveness of our method to characterize the dynamics of lysine SUMOylation.
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Affiliation(s)
- Frédéric Lamoliatte
- 1] Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7 [2] Department of Chemistry, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Danielle Caron
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Louiza Mahrouche
- 1] Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7 [2] Department of Biochemistry, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | | | - Olivier Caron-Lizotte
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | | | - Pierre Thibault
- 1] Institute for Research in Immunology and Cancer, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7 [2] Department of Chemistry, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7 [3] Department of Biochemistry, Université de Montréal, PO Box 6128, Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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40
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Watts FZ, Baldock R, Jongjitwimol J, Morley SJ. Weighing up the possibilities: Controlling translation by ubiquitylation and sumoylation. ACTA ACUST UNITED AC 2014; 2:e959366. [PMID: 26779408 DOI: 10.4161/2169074x.2014.959366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/01/2014] [Accepted: 05/12/2014] [Indexed: 12/15/2022]
Abstract
Regulation of protein synthesis is of fundamental importance to cells. It has a critical role in the control of gene expression, and consequently cell growth and proliferation. The importance of this control is supported by the fact that protein synthesis is frequently upregulated in tumor cells. The major point at which regulation occurs is the initiation stage. Initiation of translation involves the interaction of several proteins to form the eIF4F complex, the recognition of the mRNA by this complex, and the subsequent recruitment of the 40S ribosomal subunit to the mRNA. This results in the formation of the 48S complex that then scans the mRNA for the start codon, engages the methionyl-tRNA and eventually forms the mature 80S ribosome which is elongation-competent. Formation of the 48S complex is regulated by the availability of individual initiation factors and through specific protein-protein interactions. Both of these events can be regulated by post-translational modification by ubiquitin or Ubls (ubiquitin-like modifiers) such as SUMO or ISG15. We provide here a summary of translation initiation factors that are modified by ubiquitin or Ubls and, where they have been studied in detail, describe the role of these modifications and their effects on regulating protein synthesis.
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Affiliation(s)
- Felicity Z Watts
- Genome Damage and Stability Center; School of Life Sciences; University of Sussex ; Falmer, Brighton, UK
| | - Robert Baldock
- Genome Damage and Stability Center; School of Life Sciences; University of Sussex ; Falmer, Brighton, UK
| | - Jirapas Jongjitwimol
- Genome Damage and Stability Center; School of Life Sciences; University of Sussex ; Falmer, Brighton, UK
| | - Simon J Morley
- Department of Biochemistry and Biomedical Science; School of Life Sciences; University of Sussex ; Brighton, UK
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41
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Yang W, Paschen W. SUMO proteomics to decipher the SUMO-modified proteome regulated by various diseases. Proteomics 2014; 15:1181-91. [PMID: 25236368 DOI: 10.1002/pmic.201400298] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/18/2014] [Accepted: 09/15/2014] [Indexed: 01/14/2023]
Abstract
Small ubiquitin-like modifier (SUMO1-3) conjugation is a posttranslational protein modification whereby SUMOs are conjugated to lysine residues of target proteins. SUMO conjugation can alter the activity, stability, and function of target proteins, and thereby modulate almost all major cellular pathways. Many diseases are associated with SUMO conjugation, including heart failure, arthritis, cancer, degenerative diseases, and brain ischemia/stroke. It is, therefore, of major interest to characterize the SUMO-modified proteome regulated by these disorders. SUMO proteomics analysis is hampered by low levels of SUMOylated proteins. Several strategies have, therefore, been developed to enrich SUMOylated proteins from cell/tissue extracts. These include proteomics analysis on cells expressing epitope-tagged SUMO isoforms, use of monoclonal SUMO antibodies for immunoprecipitation and epitope-specific peptides for elution, and affinity purification with peptides containing SUMO interaction motifs to specifically enrich polySUMOylated proteins. Recently, two mouse models were generated and characterized that express tagged SUMO isoforms, and allow purification of SUMOylated proteins from complex organ extracts. Ultimately, these new analytical tools will help to decipher the SUMO-modified proteome regulated by various human diseases, and thereby, identify new targets for preventive and therapeutic purposes.
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Affiliation(s)
- Wei Yang
- Molecular Neurobiology Laboratory, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
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42
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Matafora V, Zagato L, Ferrandi M, Molinari I, Zerbini G, Casamassima N, Lanzani C, Delli Carpini S, Trepiccione F, Manunta P, Bachi A, Capasso G. Quantitative proteomics reveals novel therapeutic and diagnostic markers in hypertension. BBA CLINICAL 2014; 2:79-87. [PMID: 26672470 PMCID: PMC4633972 DOI: 10.1016/j.bbacli.2014.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 01/13/2023]
Abstract
Hypertension is a prevalent disorder in the world representing one of the major risk factors for heart attack and stroke. These risks are increased in salt sensitive individuals. Hypertension and salt sensitivity are complex phenotypes whose pathophysiology remains poorly understood and, remarkably, salt sensitivity is still laborious to diagnose. Here we present a urinary proteomic study specifically designed to identify urinary proteins relevant for the pathogenesis of hypertension and salt sensitivity. Despite previous studies that underlined the association of UMOD gene variants with hypertension, this work provides novel evidence showing different uromodulin protein level in the urine of hypertensive patients compared to healthy individuals. Notably, we also show that patients with higher level of uromodulin are homozygous for UMOD risk variant and display a decreased level of salt excretion, highlighting the essential role of UMOD in the regulation of salt reabsorption in hypertension. Additionally, we found that urinary nephrin 1, a marker of glomerular slit diaphragm, may predict a salt sensitive phenotype and positively correlate with increased albuminuria associated with this type of hypertension. We identified urinary proteins differently excreted in hypertensive patients. Nephrin 1 might predict salt sensitive phenotype and glomerular complications. Uromodulin impacts salt homeostasis in hypertension. We provide new insights into the pathogenesis of hypertension and salt sensitivity.
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Key Words
- BMI, body mass index
- BP, blood pressure
- DBP, diastolic BP
- GO, Gene Ontology
- Glomerular injury
- LC–MS/MS, liquid chromatography coupled to tandem mass spectrometry
- MBP, mean BP.
- MQ, MaxQuant
- Nephrinuria
- Quantitative proteomics
- SBP, systolic BP
- SR, salt resistant
- SS, salt sensitive
- Salt homeostasis
- Salt sensitive hypertension
- Urinary biomarker
- Uromodulin
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Affiliation(s)
- Vittoria Matafora
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy ; Chair of Nephrology, Department of Cardio-Vascular Medicine, Second University of Naples, Naples, Italy
| | - Laura Zagato
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Mara Ferrandi
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Isabella Molinari
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Gianpaolo Zerbini
- Division of Metabolic and Cardiovascular Sciences, San Raffaele Scientific Institute, Milan, Italy
| | - Nunzia Casamassima
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Lanzani
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Simona Delli Carpini
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Trepiccione
- Chair of Nephrology, Department of Cardio-Vascular Medicine, Second University of Naples, Naples, Italy
| | - Paolo Manunta
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics & Cell Biology, San Raffaele Scientific Institute, Milan, Italy ; Chair of Nephrology, University Vita-Salute San Raffaele, Milan, Italy
| | - Angela Bachi
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Giovambattista Capasso
- Chair of Nephrology, Department of Cardio-Vascular Medicine, Second University of Naples, Naples, Italy
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Sumoylation is Required for the Cytoplasmic Accumulation of a Subset of mRNAs. Genes (Basel) 2014; 5:982-1000. [PMID: 25333844 PMCID: PMC4276922 DOI: 10.3390/genes5040982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/26/2014] [Accepted: 10/04/2014] [Indexed: 12/17/2022] Open
Abstract
In order to discover novel proteins that promote the nuclear export of newly synthesized mRNAs in mammalian cells, we carried out a limited RNAi screen for proteins required for the proper cytoplasmic distribution of a model intronless mRNA. From this screen we obtained two hits, Ubc9 (SUMO-conjugating E2 enzyme) and GANP (germinal center-associated nuclear protein). Depletion of Ubc9 inhibited the proper cytoplasmic distribution of certain overexpressed intronless mRNAs, while depletion of GANP affected all tested mRNAs. Depletion of Sae1, which is also required for sumoylation, partially inhibited the cytoplasmic distribution of our model mRNA. Interestingly, the block in cytoplasmic accumulation in Ubc9-depleted cells could be overcome if an intron was incorporated into the mRNA. Surprisingly, Ubc9-depleted cells had normal nuclear export of newly synthesized intronless mRNAs, indicating that the observed accumulation of the model mRNA in the nuclei of transfected cells was likely due to some more general perturbation. Indeed, depletion of Ubc9, coupled with the overexpression of the intronless mRNAs, caused the redistribution of the nuclear speckle protein SC35 to cytoplasmic foci. Our results suggest that sumoylation may play a role in the proper assembly of mRNPs and/or the distribution of key RNA binding proteins, and may thus contribute to general protein expression patterns.
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44
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Dhall A, Wei S, Fierz B, Woodcock CL, Lee TH, Chatterjee C. Sumoylated human histone H4 prevents chromatin compaction by inhibiting long-range internucleosomal interactions. J Biol Chem 2014; 289:33827-37. [PMID: 25294883 DOI: 10.1074/jbc.m114.591644] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of eukaryotic chromatin directly influences gene function, and is regulated by chemical modifications of the core histone proteins. Modification of the human histone H4 N-terminal tail region by the small ubiquitin-like modifier protein, SUMO-3, is associated with transcription repression. However, the direct effect of sumoylation on chromatin structure and function remains unknown. Therefore, we employed a disulfide-directed strategy to generate H4 homogenously and site-specifically sumoylated at Lys-12 (suH4ss). Chromatin compaction and oligomerization assays with nucleosomal arrays containing suH4ss established that SUMO-3 inhibits array folding and higher order oligomerization, which underlie chromatin fiber formation. Moreover, the effect of sumoylation differed from that of acetylation, and could be recapitulated with the structurally similar protein ubiquitin. Mechanistic studies at the level of single nucleosomes revealed that, unlike acetylation, the effect of SUMO-3 arises from the attenuation of long-range internucleosomal interactions more than from the destabilization of a compacted dinucleosome state. Altogether, our results present the first insight on the direct structural effects of histone H4 sumoylation and reveal a novel mechanism by which SUMO-3 inhibits chromatin compaction.
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Affiliation(s)
- Abhinav Dhall
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Sijie Wei
- the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Beat Fierz
- the Institute of Chemical Sciences and Engineering, Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and
| | | | - Tae-Hee Lee
- the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802,
| | - Champak Chatterjee
- From the Department of Chemistry, University of Washington, Seattle, Washington 98195,
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45
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Wen D, Xu Z, Xia L, Liu X, Tu Y, Lei H, Wang W, Wang T, Song L, Ma C, Xu H, Zhu W, Chen G, Wu Y. Important role of SUMOylation of Spliceosome factors in prostate cancer cells. J Proteome Res 2014; 13:3571-82. [PMID: 25027693 DOI: 10.1021/pr4012848] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sentrin/SUMO (small ubiquitin-like modifier)-specific proteases (SENPs) have been implicated in the development of prostate cancer. However, due to the low abundance of SUMO-modified proteins and high activity of SENPs, the SUMO substrates affected by SENPs in prostate cancer cells are largely unknown. Here, we identified SI2, a novel cell-permeable SENP-specific inhibitor, by high-throughput screening. Using SI2 as a way of inhibiting the activity of SENPs and the SUMO stably transfected PC3 cells as a prostate cancer model, in combination with the stable isotope labeling with amino acids (SILAC) quantitative proteomic technique, we identified more than 900 putative target proteins of SUMO, in which 231 proteins were further subjected to bioinformatic analysis. In the highly enriched spliceosome pathway, we validated that USP39, HSPA1A, and HSPA2 were novel target proteins of SUMO. Furthermore, we demonstrated that K6, K16, K29, K51, and K73 were the SUMOylation sites of USP39. Mutation of these SUMO modification sites of USP39 further promoted the proliferation-enhancing effect of USP39 on prostate cancer cells. This study provides the SUMOproteome of PC3 cells and reveals that SUMOylation of spliceosome factors may be implicated in the pathogenesis of prostate cancer. Optimization of SI2 for isotype-specific SENP inhibitors warrants further investigation.
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Affiliation(s)
- Donghua Wen
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Shanghai Jiao Tong University School of Medicine , Shanghai 200025, China
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46
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Jongjitwimol J, Feng M, Zhou L, Wilkinson O, Small L, Baldock R, Taylor DL, Smith D, Bowler LD, Morley SJ, Watts FZ. The S. pombe translation initiation factor eIF4G is Sumoylated and associates with the SUMO protease Ulp2. PLoS One 2014; 9:e94182. [PMID: 24818994 PMCID: PMC4018355 DOI: 10.1371/journal.pone.0094182] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/13/2014] [Indexed: 12/03/2022] Open
Abstract
SUMO is a small post-translational modifier, that is attached to lysine residues in target proteins. It acts by altering protein-protein interactions, protein localisation and protein activity. SUMO chains can also act as substrates for ubiquitination, resulting in proteasome-mediated degradation of the target protein. SUMO is removed from target proteins by one of a number of specific proteases. The processes of sumoylation and desumoylation have well documented roles in DNA metabolism and in the maintenance of chromatin structure. To further analyse the role of this modification, we have purified protein complexes containing the S. pombe SUMO protease, Ulp2. These complexes contain proteins required for ribosome biogenesis, RNA stability and protein synthesis. Here we have focussed on two translation initiation factors that we identified as co-purifying with Ulp2, eIF4G and eIF3h. We demonstrate that eIF4G, but not eIF3h, is sumoylated. This modification is increased under conditions that produce cytoplasmic stress granules. Consistent with this we observe partial co-localisation of eIF4G and SUMO in stressed cells. Using HeLa cells, we demonstrate that human eIF4GI is also sumoylated; in vitro studies indicate that human eIF4GI is modified on K1368 and K1588, that are located in the C-terminal eIF4A- and Mnk-binding sites respectively.
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Affiliation(s)
- Jirapas Jongjitwimol
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Min Feng
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Oliver Wilkinson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Lauren Small
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Robert Baldock
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Deborah L. Taylor
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Duncan Smith
- Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom
| | - Lucas D. Bowler
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Simon J. Morley
- Biochemistry and Biomedical Sciences, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
| | - Felicity Z. Watts
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom
- * E-mail:
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Tammsalu T, Matic I, Jaffray EG, Ibrahim AFM, Tatham MH, Hay RT. Proteome-wide identification of SUMO2 modification sites. Sci Signal 2014; 7:rs2. [PMID: 24782567 PMCID: PMC4051997 DOI: 10.1126/scisignal.2005146] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Posttranslational modification with small ubiquitin-like modifiers (SUMOs) alters the function of proteins involved in diverse cellular processes. SUMO-specific enzymes conjugate SUMOs to lysine residues in target proteins. Although proteomic studies have identified hundreds of sumoylated substrates, methods to identify the modified lysines on a proteomic scale are lacking. We developed a method that enabled proteome-wide identification of sumoylated lysines that involves the expression of polyhistidine (6His)-tagged SUMO2 with Thr(90) mutated to Lys. Endoproteinase cleavage with Lys-C of 6His-SUMO2(T90K)-modified proteins from human cell lysates produced a diGly remnant on SUMO2(T90K)-conjugated lysines, enabling immunoprecipitation of SUMO2(T90K)-modified peptides and producing a unique mass-to-charge signature. Mass spectrometry analysis of SUMO-enriched peptides revealed more than 1000 sumoylated lysines in 539 proteins, including many functionally related proteins involved in cell cycle, transcription, and DNA repair. Not only can this strategy be used to study the dynamics of sumoylation and other potentially similar posttranslational modifications, but also, these data provide an unprecedented resource for future research on the role of sumoylation in cellular physiology and disease.
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Affiliation(s)
- Triin Tammsalu
- Centre for Gene Regulation and Expression, University of Dundee, Sir James Black Centre, Dow Street, Dundee DD1 5EH. UK
| | - Ivan Matic
- Centre for Gene Regulation and Expression, University of Dundee, Sir James Black Centre, Dow Street, Dundee DD1 5EH. UK
| | - Ellis G. Jaffray
- Centre for Gene Regulation and Expression, University of Dundee, Sir James Black Centre, Dow Street, Dundee DD1 5EH. UK
| | - Adel F. M. Ibrahim
- MRC Protein Phosphorylation and Ubiquitination Unit, College of Life Sciences, University of Dundee, Sir James Black Centre, Dow Street, Dundee DD1 5EH. UK
| | - Michael H. Tatham
- Centre for Gene Regulation and Expression, University of Dundee, Sir James Black Centre, Dow Street, Dundee DD1 5EH. UK
| | - Ronald T. Hay
- Centre for Gene Regulation and Expression, University of Dundee, Sir James Black Centre, Dow Street, Dundee DD1 5EH. UK
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48
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Bonacci T, Audebert S, Camoin L, Baudelet E, Bidaut G, Garcia M, Witzel II, Perkins ND, Borg JP, Iovanna JL, Soubeyran P. Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins. J Proteome Res 2014; 13:2478-94. [PMID: 24654937 DOI: 10.1021/pr401258d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a very aggressive malignancy characterized by an excessive resistance to all known anticancer therapies, a still largely elusive phenomenon. To identify original mechanisms, we have explored the role of post-translational modifications (PTMs) mediated by members of the ubiquitin family. Although alterations of these pathways have been reported in different cancers, no methodical search for these kinds of anomalies has been performed so far. Therefore, we studied the ubiquitin-, Nedd8-, and SUMO1-specific proteomes of a pancreatic cancer cell line (MiaPaCa-2) and identified changes induced by gemcitabine, the standard PDAC's chemotherapeutic drug. These PTMs profiles contained both known major substrates of all three modifiers as well as original ones. Gemcitabine treatment altered the PTM profile of proteins involved in various biological functions, some known cancer associated genes, many potentially cancer-associated genes, and several cancer-signaling networks, including canonical and noncanonical WNT and PI3K/Akt/MTOR pathways. Some of these altered PTMs formed groups of functionally and physically associated proteins. Importantly, we could validate the gemcitabine-induced PTMs variations of relevant candidates and we could demonstrate the biological significance of such altered PTMs by studying in detail the sumoylation of SNIP1, one of these new targets.
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Affiliation(s)
- Thomas Bonacci
- CRCM, INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105; CNRS, UMR7258, 163 Av de Luminy, F-13009 Marseille, France
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49
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Identification and analysis of endogenous SUMO1 and SUMO2/3 targets in mammalian cells and tissues using monoclonal antibodies. Nat Protoc 2014; 9:896-909. [PMID: 24651501 DOI: 10.1038/nprot.2014.053] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
SUMOylation is a protein modification that regulates the function of hundreds of proteins. Detecting endogenous SUMOylation is challenging: most small ubiquitin-related modifier (SUMO) targets are low in abundance, and only a fraction of a protein's cellular pool is typically SUMOylated. Here we present a step-by-step protocol for the enrichment of endogenous SUMO targets from mammalian cells and tissues (specifically, mouse liver), based on the use of monoclonal antibodies that are available to the scientific community. The protocol comprises (i) production of antibodies and affinity matrix, (ii) denaturing cell lysis, and (iii) SUMO immunoprecipitation followed by peptide elution. Production of affinity matrix and cell lysis requires ∼1 d. The immunoprecipitation with peptide elution can be performed in 2 d. As SUMO proteins are conserved, this protocol should also be applicable to other organisms, including many vertebrates and Drosophila melanogaster.
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50
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Girard BJ, Daniel AR, Lange CA, Ostrander JH. PELP1: a review of PELP1 interactions, signaling, and biology. Mol Cell Endocrinol 2014; 382:642-651. [PMID: 23933151 PMCID: PMC3844065 DOI: 10.1016/j.mce.2013.07.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/29/2013] [Accepted: 07/29/2013] [Indexed: 11/29/2022]
Abstract
Proline, glutamic acid, and leucine rich protein 1 (PELP1) is a large multi-domain protein that has been shown to modulate an increasing number of pathways and biological processes. The first reports describing the cloning and characterization of PELP1 showed that it was an estrogen receptor coactivator. PELP1 has now been shown to be a coregulator for a growing number of transcription factors. Furthermore, recent reports have shown that PELP1 is a member of chromatin remodeling complexes. In addition to PELP1 nuclear functions, it has been shown to have cytoplasmic signaling functions as well. In the cytoplasm PELP1 acts as a scaffold molecule and mediates rapid signaling from growth factor and hormone receptors. PELP1 signaling ultimately plays a role in cancer biology by increasing proliferation and metastasis, among other cellular processes. Here we will review (1) the cloning and characterization of PELP1 expression, (2) interacting proteins, (3) PELP1 signaling, and (4) PELP1-mediated biology.
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Affiliation(s)
- Brian J Girard
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, United States
| | - Andrea R Daniel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, United States
| | - Carol A Lange
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, United States
| | - Julie H Ostrander
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, United States.
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