1
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Carnie CJ, Götz MJ, Palma-Chaundler CS, Weickert P, Wanders A, Serrano-Benitez A, Li HY, Gupta V, Awwad SW, Blum CJ, Sczaniecka-Clift M, Cordes J, Zagnoli-Vieira G, D'Alessandro G, Richards SL, Gueorguieva N, Lam S, Beli P, Stingele J, Jackson SP. Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS. EMBO J 2024; 43:2397-2423. [PMID: 38760575 PMCID: PMC11183266 DOI: 10.1038/s44318-024-00108-2] [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: 09/19/2023] [Revised: 03/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation is cytotoxic. Combining results from a subsequent genetic screen in DCTD-deficient cells with the identification of the DNMT1-DPC-proximal proteome, we uncover the ubiquitin and SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to SUMOylated DNMT1-DPCs and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism, potentially laying the foundations for future identification of predictive biomarkers for decitabine treatment.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Amy Wanders
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hao-Yi Li
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sean L Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Nadia Gueorguieva
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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2
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Liu JCY, Ackermann L, Hoffmann S, Gál Z, Hendriks IA, Jain C, Morlot L, Tatham MH, McLelland GL, Hay RT, Nielsen ML, Brummelkamp T, Haahr P, Mailand N. Concerted SUMO-targeted ubiquitin ligase activities of TOPORS and RNF4 are essential for stress management and cell proliferation. Nat Struct Mol Biol 2024:10.1038/s41594-024-01294-7. [PMID: 38649616 DOI: 10.1038/s41594-024-01294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Protein SUMOylation provides a principal driving force for cellular stress responses, including DNA-protein crosslink (DPC) repair and arsenic-induced PML body degradation. In this study, using genome-scale screens, we identified the human E3 ligase TOPORS as a key effector of SUMO-dependent DPC resolution. We demonstrate that TOPORS promotes DPC repair by functioning as a SUMO-targeted ubiquitin ligase (STUbL), combining ubiquitin ligase activity through its RING domain with poly-SUMO binding via SUMO-interacting motifs, analogous to the STUbL RNF4. Mechanistically, TOPORS is a SUMO1-selective STUbL that complements RNF4 in generating complex ubiquitin landscapes on SUMOylated targets, including DPCs and PML, stimulating efficient p97/VCP unfoldase recruitment and proteasomal degradation. Combined loss of TOPORS and RNF4 is synthetic lethal even in unstressed cells, involving defective clearance of SUMOylated proteins from chromatin accompanied by cell cycle arrest and apoptosis. Our findings establish TOPORS as a STUbL whose parallel action with RNF4 defines a general mechanistic principle in crucial cellular processes governed by direct SUMO-ubiquitin crosstalk.
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Affiliation(s)
- Julio C Y Liu
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leena Ackermann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Saskia Hoffmann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Zita Gál
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Charu Jain
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Louise Morlot
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gian-Luca McLelland
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael Lund Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thijn Brummelkamp
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Peter Haahr
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Cellular and Molecular Medicine, Center for Gene Expression, University of Copenhagen, Copenhagen, Denmark.
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark.
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3
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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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4
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Wang Y, Liu Z, Bian X, Zhao C, Zhang X, Liu X, Wang N. Function and regulation of ubiquitin-like SUMO system in heart. Front Cell Dev Biol 2023; 11:1294717. [PMID: 38033852 PMCID: PMC10687153 DOI: 10.3389/fcell.2023.1294717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
The small ubiquitin-related modifier (SUMOylation) system is a conserved, reversible, post-translational protein modification pathway covalently attached to the lysine residues of proteins in eukaryotic cells, and SUMOylation is catalyzed by SUMO-specific activating enzyme (E1), binding enzyme (E2) and ligase (E3). Sentrin-specific proteases (SENPs) can cleave the isopeptide bond of a SUMO conjugate and catalyze the deSUMOylation reaction. SUMOylation can regulate the activity of proteins in many important cellular processes, including transcriptional regulation, cell cycle progression, signal transduction, DNA damage repair and protein stability. Biological experiments in vivo and in vitro have confirmed the key role of the SUMO conjugation/deconjugation system in energy metabolism, Ca2+ cycle homeostasis and protein quality control in cardiomyocytes. In this review, we summarized the research progress of the SUMO conjugation/deconjugation system and SUMOylation-mediated cardiac actions based on related studies published in recent years, and highlighted the further research areas to clarify the role of the SUMO system in the heart by using emerging technologies.
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Affiliation(s)
- Ying Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Zhihao Liu
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
- State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiyun Bian
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development in Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Chenxu Zhao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xin Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaozhi Liu
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development in Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin, China
| | - Nan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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5
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Strong A, Qu H, Cullina S, McManus M, Zackai EH, Glessner J, Kenny EE, Hakonarson H. TOPORS as a novel causal gene for Joubert syndrome. Am J Med Genet A 2023; 191:2156-2163. [PMID: 37227088 PMCID: PMC10449431 DOI: 10.1002/ajmg.a.63303] [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: 03/03/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
Joubert syndrome (JBTS) is a Mendelian disorder of the primary cilium defined by the clinical triad of hypotonia, developmental delay, and a distinct cerebellar malformation called the molar tooth sign. JBTS is inherited in an autosomal recessive, autosomal dominant, or X-linked recessive manner. Though over 40 genes have been identified as causal for JBTS, molecular diagnosis is not made in 30%-40% of individuals who meet clinical criteria. TOPORS encodes topoisomerase I-binding arginine/serine-rich protein, and homozygosity for a TOPORS missense variant (c.29C > A; p.(Pro10Gln)) was identified in individuals with the ciliopathy oral-facial-digital syndrome in two families of Dominican descent. Here, we report an additional proband of Dominican ancestry with JBTS found by exome sequencing to be homozygous for the identical p.(Pro10Gln) TOPORS missense variant. Query of the Mount Sinai BioMe biobank, which includes 1880 individuals of Dominican ancestry, supports a high carrier frequency of the TOPORS p.(Pro10Gln) variant in individuals of Dominican descent. Our data nominates TOPORS as a novel causal gene for JBTS and suggests that TOPORS variants should be considered in the differential of ciliopathy-spectrum disease in individuals of Dominican ancestry.
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Affiliation(s)
- Alanna Strong
- The Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Huiqi Qu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sinéad Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Morgan McManus
- The Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elaine H. Zackai
- The Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joseph Glessner
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Hakon Hakonarson
- The Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
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6
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Vidal S, Bouzaher YH, El Motiam A, Seoane R, Rivas C. Overview of the regulation of the class IA PI3K/AKT pathway by SUMO. Semin Cell Dev Biol 2022; 132:51-61. [PMID: 34753687 DOI: 10.1016/j.semcdb.2021.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022]
Abstract
The phosphatidylinositol-3-kinase (PI3K)/AKT pathway is a major regulator of metabolism, migration, survival, proliferation, and antiviral immunity. Both an overactivation and an inhibition of the PI3K/AKT pathway are related to different pathologies. Activation of this signaling pathway is tightly controlled through a multistep process and its deregulation can be associated with aberrant post-translational modifications including SUMOylation. Here, we review the complex modulation of the PI3K/AKT pathway by SUMOylation and we discuss its putative incvolvement in human disease.
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Affiliation(s)
- Santiago Vidal
- Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Instituto de Investigaciones Sanitarias (IDIS), 15706 Santiago de Compostela, Spain
| | - Yanis Hichem Bouzaher
- Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Instituto de Investigaciones Sanitarias (IDIS), 15706 Santiago de Compostela, Spain
| | - Ahmed El Motiam
- Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Instituto de Investigaciones Sanitarias (IDIS), 15706 Santiago de Compostela, Spain; Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health Systems, Department of Ophthalmology and Vision Science, and Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Rocío Seoane
- Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Instituto de Investigaciones Sanitarias (IDIS), 15706 Santiago de Compostela, Spain
| | - Carmen Rivas
- Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Instituto de Investigaciones Sanitarias (IDIS), 15706 Santiago de Compostela, Spain; Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, 28049 Madrid, Spain.
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7
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Hariharasudhan G, Jeong SY, Kim MJ, Jung SM, Seo G, Moon JR, Lee S, Chang IY, Kee Y, You H, Lee JH. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1501-1516. [PMID: 35061896 PMCID: PMC8860612 DOI: 10.1093/nar/gkac009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/23/2021] [Accepted: 01/13/2022] [Indexed: 11/24/2022] Open
Abstract
Homologous recombination (HR) is critical for error-free repair of DNA double-strand breaks. Chromatin loading of RAD51, a key protein that mediates the recombination, is a crucial step in the execution of the HR repair. Here, we present evidence that SUMOylation of RAD51 is crucial for the RAD51 recruitment to chromatin and HR repair. We found that topoisomerase 1-binding arginine/serine-rich protein (TOPORS) induces the SUMOylation of RAD51 at lysine residues 57 and 70 in response to DNA damaging agents. The SUMOylation was facilitated by an ATM-induced phosphorylation of TOPORS at threonine 515 upon DNA damage. Knockdown of TOPORS or expression of SUMOylation-deficient RAD51 mutants caused reduction in supporting normal RAD51 functions during the HR repair, suggesting the physiological importance of the modification. We found that the SUMOylation-deficient RAD51 reduces the association with its crucial binding partner BRCA2, explaining its deficiency in supporting the HR repair. These findings altogether demonstrate a crucial role for TOPORS-mediated RAD51 SUMOylation in promoting HR repair and genomic maintenance.
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Affiliation(s)
- Gurusamy Hariharasudhan
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Seo-Yeon Jeong
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Min-Ji Kim
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Sung Mi Jung
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Gwanwoo Seo
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Ju-Ran Moon
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Sumi Lee
- Laboratory of Genomic Instability and Cancer Therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - In-Youb Chang
- Department of Anatomy, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Younghoon Kee
- Correspondence may also be addressed to Younghoon Kee. Tel: +82 53 785 1610;
| | - Ho Jin You
- Correspondence may also be addressed to Ho Jin You. Tel: +82 62 230 6337;
| | - Jung-Hee Lee
- To whom correspondence should be addressed. Tel: +82 62 230 6399;
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8
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Dodat F, Mader S, Lévesque D. Minireview: What is Known about SUMOylation Among NR4A Family Members? J Mol Biol 2021; 433:167212. [PMID: 34437889 DOI: 10.1016/j.jmb.2021.167212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/16/2021] [Accepted: 08/16/2021] [Indexed: 02/06/2023]
Abstract
NR4A receptors, including NUR77 (NR4A1), NURR1 (NR4A2) and NOR-1 (NR4A3), form a family of nuclear receptors that act as transcription factors to regulate many physiological and pathological processes such as cell cycle and apoptosis, lipid metabolism, inflammation, carcinogenesis, vascular and neuronal functions. In the absence of known endogenous ligand modulating their physiological functions, the NR4A family remains a class of orphan receptors. However, several post-translational modifications (PTMs), including SUMOylation, have been shown to regulate the expression and/or activity of these receptors. Addition of Small Ubiquitin-like MOdifier (SUMO) proteins is a dynamic and reversible enzymatic process that regulates multiple essential functions of proteins, including nuclear receptors. This review aims at summarizing what is known about the impact of SUMOylation on NR4A family member transcriptional activities and physiological functions.
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MESH Headings
- Animals
- Apoptosis/genetics
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Cell Cycle/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Eukaryotic Cells/cytology
- Eukaryotic Cells/metabolism
- Humans
- Inflammation
- Lipid Metabolism/genetics
- Multigene Family
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- Nuclear Receptor Subfamily 4, Group A, Member 2/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 2/metabolism
- Protein Processing, Post-Translational
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Small Ubiquitin-Related Modifier Proteins/genetics
- Small Ubiquitin-Related Modifier Proteins/metabolism
- Sumoylation
- Transcription, Genetic
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Affiliation(s)
- Fatéma Dodat
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, Canada; Institut de Recherche en Immunologie et Cancérologie (IRIC) and Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Sylvie Mader
- Institut de Recherche en Immunologie et Cancérologie (IRIC) and Département de biochimie et de médecine moléculaire, Faculté de médecine, Université de Montréal, Montréal, QC, Canada
| | - Daniel Lévesque
- Faculté de Pharmacie, Université de Montréal, Montréal, QC, Canada
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9
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Strong A, Simone L, Krentz A, Vaccaro C, Watson D, Ron H, Kalish JM, Pedro HF, Zackai EH, Hakonarson H. Expanding the genetic landscape of oral-facial-digital syndrome with two novel genes. Am J Med Genet A 2021; 185:2409-2416. [PMID: 34132027 PMCID: PMC8361718 DOI: 10.1002/ajmg.a.62337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022]
Abstract
Oral‐facial‐digital syndromes (OFDS) are a heterogeneous and rare group of Mendelian disorders characterized by developmental abnormalities of the oral cavity, face, and digits caused by dysfunction of the primary cilium, a mechanosensory organelle that exists atop most cell types that facilitates organ patterning and growth. OFDS is inherited both in an X‐linked dominant, X‐linked recessive, and autosomal recessive manner. Importantly, though many of the causal genes for OFDS have been identified, up to 40% of OFD syndromes are of unknown genetic basis. Here we describe three children with classical presentations of OFDS including lingual hamartomas, polydactyly, and characteristic facial features found by exome sequencing to harbor variants in causal genes not previously associated with OFDS. We describe a female with hypothalamic hamartoma, urogenital sinus, polysyndactyly, and multiple lingual hamartomas consistent with OFDVI with biallelic pathogenic variants in CEP164, a gene associated with ciliopathy‐spectrum disease, but never before with OFDS. We additionally describe two unrelated probands with postaxial polydactyly, multiple lingual hamartomas, and dysmorphic features both found to be homozygous for an identical TOPORS missense variant, c.29 C>A; (p.Pro10Gln). Heterozygous TOPORS pathogenic gene variants are associated with autosomal dominant retinitis pigmentosa, but never before with syndromic ciliopathy. Of note, both probands are of Dominican ancestry, suggesting a possible founder allele.
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Affiliation(s)
- Alanna Strong
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laurie Simone
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | | | - Courtney Vaccaro
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Deborah Watson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hayley Ron
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Helio F Pedro
- Center for Genetic and Genomic Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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10
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The role of SUMOylation during development. Biochem Soc Trans 2021; 48:463-478. [PMID: 32311032 PMCID: PMC7200636 DOI: 10.1042/bst20190390] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022]
Abstract
During the development of multicellular organisms, transcriptional regulation plays an important role in the control of cell growth, differentiation and morphogenesis. SUMOylation is a reversible post-translational process involved in transcriptional regulation through the modification of transcription factors and through chromatin remodelling (either modifying chromatin remodelers or acting as a ‘molecular glue’ by promoting recruitment of chromatin regulators). SUMO modification results in changes in the activity, stability, interactions or localization of its substrates, which affects cellular processes such as cell cycle progression, DNA maintenance and repair or nucleocytoplasmic transport. This review focuses on the role of SUMO machinery and the modification of target proteins during embryonic development and organogenesis of animals, from invertebrates to mammals.
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11
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F-box only and CUE proteins are crucial ubiquitination-associated components for conidiation and pathogenicity in the rice blast fungus, Magnaporthe oryzae. Fungal Genet Biol 2020; 144:103473. [DOI: 10.1016/j.fgb.2020.103473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 08/11/2020] [Accepted: 09/19/2020] [Indexed: 11/21/2022]
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12
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Chaubal A, Pile LA. Same agent, different messages: insight into transcriptional regulation by SIN3 isoforms. Epigenetics Chromatin 2018; 11:17. [PMID: 29665841 PMCID: PMC5902990 DOI: 10.1186/s13072-018-0188-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
SIN3 is a global transcriptional coregulator that governs expression of a large repertoire of gene targets. It is an important player in gene regulation, which can repress or activate diverse gene targets in a context-dependent manner. SIN3 is required for several vital biological processes such as cell proliferation, energy metabolism, organ development, and cellular senescence. The functional flexibility of SIN3 arises from its ability to interact with a large variety of partners through protein interaction domains that are conserved across species, ranging from yeast to mammals. Several isoforms of SIN3 are present in these different species that can perform common and specialized functions through interactions with distinct enzymes and DNA-binding partners. Although SIN3 has been well studied due to its wide-ranging functions and highly conserved interaction domains, precise roles of individual SIN3 isoforms have received less attention. In this review, we discuss the differences in structure and function of distinct SIN3 isoforms and provide possible avenues to understand the complete picture of regulation by SIN3.
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Affiliation(s)
- Ashlesha Chaubal
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA.
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13
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Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M. The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. Cell Stem Cell 2018; 22:369-383.e8. [PMID: 29499153 PMCID: PMC5836508 DOI: 10.1016/j.stem.2018.02.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 12/20/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
A permissive chromatin environment coupled to hypertranscription drives the rapid proliferation of embryonic stem cells (ESCs) and peri-implantation embryos. We carried out a genome-wide screen to systematically dissect the regulation of the euchromatic state of ESCs. The results revealed that cellular growth pathways, most prominently translation, perpetuate the euchromatic state and hypertranscription of ESCs. Acute inhibition of translation rapidly depletes euchromatic marks in mouse ESCs and blastocysts, concurrent with delocalization of RNA polymerase II and reduction in nascent transcription. Translation inhibition promotes rewiring of chromatin accessibility, which decreases at a subset of active developmental enhancers and increases at histone genes and transposable elements. Proteome-scale analyses revealed that several euchromatin regulators are unstable proteins and continuously depend on a high translational output. We propose that this mechanistic interdependence of euchromatin, transcription, and translation sets the pace of proliferation at peri-implantation and may be employed by other stem/progenitor cells.
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Affiliation(s)
- Aydan Bulut-Karslioglu
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Trisha A Macrae
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sergio Covarrubias
- UCSF Diabetes Center, WM Keck Center for Noncoding RNAs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle Percharde
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory Ku
- UCSF Diabetes Center, WM Keck Center for Noncoding RNAs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aaron Diaz
- Department of Neurological Surgery, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- UCSF Diabetes Center, WM Keck Center for Noncoding RNAs, Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, Mass Spectrometry Facility, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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14
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Prudent J, McBride HM. The mitochondria–endoplasmic reticulum contact sites: a signalling platform for cell death. Curr Opin Cell Biol 2017; 47:52-63. [DOI: 10.1016/j.ceb.2017.03.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 01/23/2023]
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15
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Kumar S, Sharma G, Chakraborty C, Sharma AR, Kim J. Regulatory functional territory of PLK-1 and their substrates beyond mitosis. Oncotarget 2017; 8:37942-37962. [PMID: 28415805 PMCID: PMC5514964 DOI: 10.18632/oncotarget.16290] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/03/2017] [Indexed: 12/04/2022] Open
Abstract
Polo-like kinase 1 (PLK-1) is a well-known (Ser/Thr) mitotic protein kinase and is considered as a proto-oncogene. As hyper-activation of PLK-1 is broadly associated with poor prognosis and cancer progression, it is one of the most extensively studied mitotic kinases. During mitosis, PLK-1 regulates various cell cycle events, such as spindle pole maturation, chromosome segregation and cytokinesis. However, studies have demonstrated that the role of PLK-1 is not only restricted to mitosis, but PLK-1 can also regulate other vital events beyond mitosis, including transcription, translation, ciliogenesis, checkpoint adaptation and recovery, apoptosis, chromosomes dynamics etc. Recent reviews have tried to define the regulatory role of PLK-1 during mitosis progression and tumorigenesis, but its' functional role beyond mitosis is still largely unexplored. PLK-1 can regulate the activity of many proteins that work outside of its conventional territory. The dysregulation of these proteins can cause diseases such as Alzheimer's disease, tumorigenesis etc. and may also lead to drug resistance. Thus, in this review, we discussed the versatile role of PLK-1 and tried to collect data to validate its' functional role in cell cycle regulation apart from mitosis.
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Affiliation(s)
- Shiv Kumar
- Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
| | - Garima Sharma
- Institute For Skeletal Aging & Orthopedic Surgery, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Ashish Ranjan Sharma
- Institute For Skeletal Aging & Orthopedic Surgery, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
| | - Jaebong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University, College of Medicine, Chucheonsi, Gangwondo, Republic of Korea
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16
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Namuduri AV, Heras G, Mi J, Cacciani N, Hörnaeus K, Konzer A, Lind SB, Larsson L, Gastaldello S. A Proteomic Approach to Identify Alterations in the Small Ubiquitin-like Modifier (SUMO) Network during Controlled Mechanical Ventilation in Rat Diaphragm Muscle. Mol Cell Proteomics 2017; 16:1081-1097. [PMID: 28373296 DOI: 10.1074/mcp.m116.066159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/03/2017] [Indexed: 12/17/2022] Open
Abstract
The small ubiquitin-like modifier (SUMO) is as a regulator of many cellular functions by reversible conjugation to a broad number of substrates. Under endogenous or exogenous perturbations, the SUMO network becomes a fine sensor of stress conditions by alterations in the expression level of SUMO enzymes and consequently changing the status of SUMOylated proteins. The diaphragm is the major inspiratory muscle, which is continuously active under physiological conditions, but its structure and function is severely affected when passively displaced for long extents during mechanical ventilation (MV). An iatrogenic condition called Ventilator-Induced Diaphragm Dysfunction (VIDD) is a major cause of failure to wean patients from ventilator support but the molecular mechanisms underlying this dysfunction are not fully understood. Using a unique experimental Intensive Care Unit (ICU) rat model allowing long-term MV, diaphragm muscles were collected in rats control and exposed to controlled MV (CMV) for durations varying between 1 and 10 days. Endogenous SUMOylated diaphragm proteins were identified by mass spectrometry and validated with in vitro SUMOylation systems. Contractile, calcium regulator and mitochondrial proteins were of specific interest due to their putative involvement in VIDD. Differences were observed in the abundance of SUMOylated proteins between glycolytic and oxidative muscle fibers in control animals and high levels of SUMOylated proteins were present in all fibers during CMV. Finally, previously reported VIDD biomarkers and therapeutic targets were also identified in our datasets which may play an important role in response to muscle weakness seen in ICU patients. Data are available via ProteomeXchange with identifier PXD006085. Username: reviewer26663@ebi.ac.uk, Password: rwcP5W0o.
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Affiliation(s)
- Arvind Venkat Namuduri
- From the ‡Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Gabriel Heras
- From the ‡Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Jia Mi
- §Department of Chemistry-BMC, Analytical Chemistry and Science for Lab Laboratory, Uppsala University, Box 599, Uppsala, SE-75124, Sweden.,¶Medicine and Pharmacy Research Center, Binzhou Medical University, Laishan District, No. 346, Guanhai Road, Yantai, Shandong Province, 264003 China
| | - Nicola Cacciani
- From the ‡Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Katarina Hörnaeus
- §Department of Chemistry-BMC, Analytical Chemistry and Science for Lab Laboratory, Uppsala University, Box 599, Uppsala, SE-75124, Sweden
| | - Anne Konzer
- §Department of Chemistry-BMC, Analytical Chemistry and Science for Lab Laboratory, Uppsala University, Box 599, Uppsala, SE-75124, Sweden
| | - Sara Bergström Lind
- §Department of Chemistry-BMC, Analytical Chemistry and Science for Lab Laboratory, Uppsala University, Box 599, Uppsala, SE-75124, Sweden
| | - Lars Larsson
- From the ‡Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, SE-17177, Sweden.,‖Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania 16801; and.,**Department of Clinical Neuroscience, Clinical Neurophysiology, Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Stefano Gastaldello
- From the ‡Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, SE-17177, Sweden;
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17
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Chaubal A, Todi SV, Pile LA. Inter-isoform-dependent Regulation of the Drosophila Master Transcriptional Regulator SIN3. J Biol Chem 2016; 291:11566-71. [PMID: 27129248 DOI: 10.1074/jbc.c116.724799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 11/06/2022] Open
Abstract
SIN3 is a transcriptional corepressor that acts as a scaffold for a histone deacetylase (HDAC) complex. The SIN3 complex regulates various biological processes, including organ development, cell proliferation, and energy metabolism. Little is known, however, about the regulation of SIN3 itself. There are two major isoforms of Drosophila SIN3, 187 and 220, which are differentially expressed. Intrigued by the developmentally timed exchange of SIN3 isoforms, we examined whether SIN3 187 controls the fate of the 220 counterpart. Here, we show that in developing tissue, there is interplay between SIN3 isoforms: when SIN3 187 protein levels increase, SIN3 220 protein decreases concomitantly. SIN3 187 has a dual effect on SIN3 220. Expression of 187 leads to reduced 220 transcript, while also increasing the turnover of SIN3 220 protein by the proteasome. These data support the presence of a novel, inter-isoform-dependent mechanism that regulates the amount of SIN3 protein, and potentially the level of specific SIN3 complexes, during distinct developmental stages.
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Affiliation(s)
- Ashlesha Chaubal
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
| | - Sokol V Todi
- the Department of Pharmacology, Wayne State University, Detroit, Michigan 48201
| | - Lori A Pile
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
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18
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TOPORS, a Dual E3 Ubiquitin and Sumo1 Ligase, Interacts with 26 S Protease Regulatory Subunit 4, Encoded by the PSMC1 Gene. PLoS One 2016; 11:e0148678. [PMID: 26872363 PMCID: PMC4752349 DOI: 10.1371/journal.pone.0148678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
The significance of the ubiquitin-proteasome system (UPS) for protein degradation has been highlighted in the context of neurodegenerative diseases, including retinal dystrophies. TOPORS, a dual E3 ubiquitin and SUMO1 ligase, forms a component of the UPS and selected substrates for its enzymatic activities, such as DJ-1/PARK7 and APOBEC2, are important for neuronal as well as retinal homeostasis, respectively. TOPORS is ubiquitously expressed, yet its mutations are only known to result in autosomal dominant retinitis pigmentosa. We performed a yeast two-hybrid (Y2H) screen of a human retinal cDNA library in order to identify interacting protein partners of TOPORS from the retina, and thus begin delineating the putative disease mechanism(s) associated with the retina-specific phenotype resulting from mutations in TOPORS. The screen led to isolation of the 26 S protease regulatory subunit 4 (P26s4/ PSMC1), an ATPase indispensable for correct functioning of UPS-mediated proteostasis. The interaction between endogenous TOPORS and P26s4 proteins was validated by co-immuno-precipitation from mammalian cell extracts and further characterised by immunofluorescent co-localisation studies in cell lines and retinal sections. Findings from hTERT-RPE1 and 661W cells demonstrated that TOPORS and P26s4 co-localise at the centrosome in cultured cells. Immunofluorescent staining of mouse retinae revealed a strong P26s4 reactivity at the interface between retinal pigmented epithelium (RPE) layer and the photoreceptors outer segments (OS). This finding leads us to speculate that P26s4, along with TOPORS, may have a role(s) in RPE phagocytosis, in addition to contributing to the overall photoreceptor and retinal homeostasis via the UPS.
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19
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Gan J, Wang C, Jin Y, Guo Y, Xu F, Zhu Q, Ding L, Shang H, Wang J, Wei F, Cai Q, Robertson ES. Proteomic profiling identifies the SIM-associated complex of KSHV-encoded LANA. Proteomics 2015; 15:2023-37. [PMID: 25894481 PMCID: PMC5868752 DOI: 10.1002/pmic.201400624] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 02/11/2015] [Accepted: 04/17/2015] [Indexed: 11/08/2022]
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) encoded latent nuclear antigen latency-associated nuclear antigen (LANA) plays an essential role in viral episome maintenance. LANA also contributes to DNA replication and tumorigenesis during latency. Recent studies suggested that LANA was involved in regulation of SUMOylation, which results in chromatin silencing. To examine the pleiotropic effects of LANA protein on host cell gene expression, we utilized MS analysis to identify cellular proteins associated with the small ubiquitin related modifier (SUMO) interacting motif of LANA (LANA(SIM)). In addition to the six bands identified as substantially associated with LANA(SIM), 151 proteins were positively identified by MS/MS analysis. Compared with previous proteomic analysis of the N- and C-truncated mutants of LANA (LANA(NC)), our results revealed that a complex of specific proteins with relatively high SUMOylation and SIM motifs is associated with LANA(SIM). Intriguingly, consistent with our previous report that identified KAP1 as a key component, the in vitro SUMO-2-modified isoform has a substantially higher affinity with LANA(SIM) than the SUMO-1-modified isoform. Moreover, via cluster and pathway analysis, we proposed a hypothetical model for the LANA(SIM) regulatory circuit involving aberrant SUMOylation of cell cycle (particular mitotic), DNA unwinding and replication, and pre-mRNA/mRNA processing related proteins. This study provides a SUMOylated and non-SUMOylated proteome profile of LANA(SIM) -associated complex and facilitates our understanding that viral-mediated gene regulation through SUMOylation is important for Kaposi's sarcoma-associated herpesvirus persistence and pathogenesis.
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Affiliation(s)
- Jin Gan
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Chong Wang
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Yanling Jin
- ShengYushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yi Guo
- Department of Gynecology, Key laboratory of AIDS immunology of Ministry of Health, First Affiliated Hospital of China Medical University, Shenyang 110000, P. R. China
| | - Feng Xu
- Department of Biochemistry and Center for Genome Science, The University of Hong Kong, Hong Kong, P. R. China
| | - Qing Zhu
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Ling Ding
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Hong Shang
- Department of Gynecology, Key laboratory of AIDS immunology of Ministry of Health, First Affiliated Hospital of China Medical University, Shenyang 110000, P. R. China
| | - Junwen Wang
- Department of Biochemistry and Center for Genome Science, The University of Hong Kong, Hong Kong, P. R. China
| | - Fang Wei
- ShengYushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Qiliang Cai
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Erle S Robertson
- Department of Microbiology and Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia 19104, USA
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20
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Abstract
Meiosis entails sorting and separating both homologous and sister chromatids. The mechanisms for connecting sister chromatids and homologs during meiosis are highly conserved and include specialized forms of the cohesin complex and a tightly regulated homolog synapsis/recombination pathway designed to yield regular crossovers between homologous chromatids. Drosophila male meiosis is of special interest because it dispenses with large segments of the standard meiotic script, particularly recombination, synapsis and the associated structures. Instead, Drosophila relies on a unique protein complex composed of at least two novel proteins, SNM and MNM, to provide stable connections between homologs during meiosis I. Sister chromatid cohesion in Drosophila is mediated by cohesins, ring-shaped complexes that entrap sister chromatids. However, unlike other eukaryotes Drosophila does not rely on the highly conserved Rec8 cohesin in meiosis, but instead utilizes two novel cohesion proteins, ORD and SOLO, which interact with the SMC1/3 cohesin components in providing meiotic cohesion.
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Affiliation(s)
- Bruce D McKee
- Department of Biochemistry, Cellular & Molecular Biology; University of Tennessee; Knoxville TN USA ; Genome Science and Technology Program; University of Tennessee; Knoxville TN USA
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21
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SIM-dependent enhancement of substrate-specific SUMOylation by a ubiquitin ligase in vitro. Biochem J 2014; 457:435-40. [DOI: 10.1042/bj20131381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The present study demonstrates that the Saccharomyces cerevisiae ubiquitin ligase Rad18 can unexpectedly catalyse conjugation of SUMO to its target, PCNA, with high selectivity under in vitro conditions by means of a SUMO-interacting motif that is normally involved in substrate recognition.
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22
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A unique SUMO-2-interacting motif within LANA is essential for KSHV latency. PLoS Pathog 2013; 9:e1003750. [PMID: 24278015 PMCID: PMC3836728 DOI: 10.1371/journal.ppat.1003750] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/23/2013] [Indexed: 12/02/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) stabilizes hypoxia-inducible factor α (HIF-1α) during latent infection, and HIF-1α reactivates lytic replication under hypoxic stress. However, the mechanism utilized by KSHV to block lytic reactivation with the accumulation of HIF-1α in latency remains unclear. Here, we report that LANA encoded by KSHV contains a unique SUMO-interacting motif (LANASIM) which is specific for interaction with SUMO-2 and facilitates LANA SUMOylation at lysine 1140. Proteomic and co-immunoprecipitation analysis further reveal that the SUMO-2 modified transcription repressor KAP1 is a critical factor recruited by LANASIM. Deletion of LANASIM led to functional loss of both LANA-mediated viral episome maintenance and lytic gene silencing. Moreover, hypoxia reduced KAP1 SUMOylation and resulted in dissociation of both KAP1 and Sin3A repressors from LANASIM-associated complex. Therefore, the LANASIM motif plays an essential role in KSHV latency and is a potential drug target against KSHV-associated cancers. Hypoxia stress is a common feature of tumor microenvironment and is widely associated with pathogenesis linked to many oncogenic viruses. Kaposi's sarcoma-associated herpesvirus (KSHV), the etiological cause of Kaposi's sarcoma and primary effusion lymphoma, has been reported to encode several proteins that usurp hypoxia signaling during infection. One encoded protein LANA is a latent protein important for regulation of KSHV life cycle and cell transformation. The molecular mechanisms of how KSHV controls life cycle in normoxia and hypoxia is not fully understood. In this study, we show that LANA contains a unique SUMO-interacting motif (LANASIM) which is specific for SUMO-2 binding. Importantly, SUMO-2 modified KAP1, a chromatin remodeling factor recruited by LANASIM is hypoxia sensitive, and plays a critical role in silencing viral gene expression. This discovery not only adds to our understanding of hypoxia-mediated remodeling of the viral episome in a SUMO dependent manner, but also provides a new dimension to development of therapeutic strategies against KSHV-associated cancers.
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23
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Ijaz A. SUMOhunt: Combining Spatial Staging between Lysine and SUMO with Random Forests to Predict SUMOylation. ISRN BIOINFORMATICS 2013; 2013:671269. [PMID: 25937950 PMCID: PMC4393069 DOI: 10.1155/2013/671269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 05/28/2013] [Indexed: 11/20/2022]
Abstract
Modification with SUMO protein has many key roles in eukaryotic systems which renders the identification of its target proteins and sites of considerable importance. Information regarding the SUMOylation of a protein may tell us about its subcellular localization, function, and spatial orientation. This modification occurs at particular and not all lysine residues in a given protein. In competition with biochemical means of modified-site recognition, computational methods are strong contenders in the prediction of SUMOylation-undergoing sites on proteins. In this research, physicochemical properties of amino acids retrieved from AAIndex, especially those involved in docking of modifier and target proteins and optimal presentation of target lysine, in combination with sequence information and random forest-based classifier presented in WEKA have been used to develop a prediction model, SUMOhunt, with statistics significantly better than all previous predictors. In this model 97.56% accuracy, 100% sensitivity, 94% specificity, and 0.95 MCC have been achieved which shows that proposed amino acid properties have a significant role in SUMO attachment. SUMOhunt will hence bring great reliability and efficiency in SUMOylation prediction.
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Affiliation(s)
- Amna Ijaz
- National Institute of Biotechnology and Genetic Engineering, P.O. Box 577, Jhang Road, Faisalabad, Pakistan
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24
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Multiple crosstalks between mRNA biogenesis and SUMO. Chromosoma 2013; 122:387-99. [PMID: 23584125 DOI: 10.1007/s00412-013-0408-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/10/2013] [Accepted: 03/13/2013] [Indexed: 12/26/2022]
Abstract
mRNA metabolism involves the orchestration of multiple nuclear events, including transcription, processing (e.g., capping, splicing, polyadenylation), and quality control. This leads to the accurate formation of messenger ribonucleoparticles (mRNPs) that are finally exported to the cytoplasm for translation. The production of defined sets of mRNAs in given environmental or physiological situations relies on multiple regulatory mechanisms that target the mRNA biogenesis machineries. Among other regulations, post-translational modification by the small ubiquitin-like modifier SUMO, whose prominence in several cellular processes has been largely demonstrated, also plays a key role in mRNA biogenesis. Analysis of the multiple available SUMO proteomes and functional validations of an increasing number of sumoylated targets have revealed the key contribution of SUMO-dependent regulation in nuclear mRNA metabolism. While sumoylation of transcriptional activators and repressors is so far best documented, SUMO contribution to other stages of mRNA biogenesis is also emerging. Modification of mRNA metabolism factors by SUMO determine their subnuclear targeting and biological activity, notably by regulating their molecular interactions with nucleic acids or protein partners. In particular, sumoylation of DNA-bound transcriptional regulators interfere with their association to target sequences or chromatin modifiers. In addition, the recent identification of enzymes of the SUMO pathway within specialized mRNA biogenesis machineries may provide a further level of regulation to their specificity. These multiple crosstalks between mRNA metabolism and SUMO appear therefore as important players in cellular regulatory networks.
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Wan J, Subramonian D, Zhang XD. SUMOylation in control of accurate chromosome segregation during mitosis. Curr Protein Pept Sci 2013; 13:467-81. [PMID: 22812528 PMCID: PMC3474960 DOI: 10.2174/138920312802430563] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/26/2012] [Accepted: 06/11/2012] [Indexed: 12/15/2022]
Abstract
Posttranslational protein modification by small ubiquitin-related modifier (SUMO) has emerged as an important regulatory mechanism for chromosome segregation during mitosis. This review focuses on how SUMOylation regulates the centromere and kinetochore activities to achieve accurate chromosome segregation during mitosis. Kinetochores are assembled on the specialized chromatin domains called centromeres and serve as the sites for attaching spindle microtubule to segregate sister chromatids to daughter cells. Many proteins associated with mitotic centromeres and kinetochores have been recently found to be modified by SUMO. Although we are still at the early stage of elucidating how SUMOylation controls chromosome segregation during mitosis, a substantial progress has been achieved over the past decade. Furthermore, a major theme that has emerged from the recent studies of SUMOylation in mitosis is that both SUMO conjugation and deconjugation are critical for kinetochore assembly and disassembly. Lastly, we propose a model that SUMOylation coordinates multiple centromere and kinetochore activities to ensure accurate chromosome segregation.
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Affiliation(s)
- Jun Wan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, USA
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Seong KM, Nam SY, Kim JY, Yang KH, An S, Jin YW, Kim CS. TOPORS modulates H2AX discriminating genotoxic stresses. J Biochem Mol Toxicol 2012; 26:429-38. [PMID: 22972498 DOI: 10.1002/jbt.21438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/26/2012] [Accepted: 08/11/2012] [Indexed: 11/07/2022]
Abstract
H2AX plays an important role in chromatin reorganization implicated in DNA repair and apoptosis under various DNA damaging conditions. In this study, the interaction between TOPORS (topoisomerase I-binding protein) and H2AX was verified using mammalian cell extracts exposed to diverse DNA damaging stresses such as ionizing radiation, doxorubicin, camptothecin, and hydrogen peroxide. In vitro assays for ubiquitination revealed that TOPORS functions as a novel E3 ligase for H2AX ubiquitination. TOPORS was found to be dissociated from H2AX proteins when cells were exposed to oxidative stress, but not replication-inducing DNA damaging stress. The protein stability of H2AX was decreased when TOPORS was ectopically expressed in cells, and oxidative stresses such as hydrogen peroxide and ionizing radiation induced recovery of the H2AX protein level. Therefore, these biochemical data suggest that TOPORS plays a key role in the turnover of H2AX protein, discriminating the type of DNA damaging stress.
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Affiliation(s)
- Ki Moon Seong
- Division of Radiation Effect Research, Radiation Health Research Institute, Korea Hydro & Nuclear Power Co., Ltd., 132-703, Seoul, Korea.
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Braun KR, DeWispelaere AM, Bressler SL, Fukai N, Kenagy RD, Chen L, Clowes AW, Kinsella MG. Inhibition of PDGF-B induction and cell growth by syndecan-1 involves the ubiquitin and SUMO-1 ligase, Topors. PLoS One 2012; 7:e43701. [PMID: 22912899 PMCID: PMC3422340 DOI: 10.1371/journal.pone.0043701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 07/23/2012] [Indexed: 01/14/2023] Open
Abstract
Syndecans are receptors for soluble ligands, including heparin-binding growth factors, and matrix proteins. However, intracellular targets of syndecan-1 (Sdc-1)-mediated signaling are not fully understood. A yeast two-hybrid protein interaction screening of a mouse embryo library identified the ubiquitin and SUMO-1 E3 ligase, Topors, as a novel ligand of the Sdc-1 cytoplasmic domain (S1CD), a finding confirmed by ligand blotting and co-precipitation with Sdc-1 from cell lysates. Deletion mutagenesis identified an 18-amino acid sequence of Topors required for the interaction with the S1CD. By immunohistochemistry, Topors and Sdc-1 co-localized near the cell periphery in normal murine mammary gland (NMuMG) cells in vitro and in mouse embryonic epithelia in vivo. Finally, siRNA-mediated knockdown of Topors demonstrated that Topors is a growth promoter for murine arterial smooth muscle cells and is required for the inhibitory effect of Sdc-1 on cell growth and platelet-derived growth factor-B induction. These data suggest a novel mechanism for the inhibitory effects of Sdc-1 on cell growth that involves the interaction between the cytoplasmic domain of Sdc-1 and the SUMO-1 E3 ligase, Topors.
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Affiliation(s)
- Kathleen R. Braun
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Allison M. DeWispelaere
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Steven L. Bressler
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Nozomi Fukai
- Department of Surgery, University of Washington, Seattle, Washington, United States of America
| | - Richard D. Kenagy
- Department of Surgery, University of Washington, Seattle, Washington, United States of America
| | - Lihua Chen
- Department of Surgery, University of Washington, Seattle, Washington, United States of America
| | - Alexander W. Clowes
- Department of Surgery, University of Washington, Seattle, Washington, United States of America
| | - Michael G. Kinsella
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
- * E-mail:
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Praefcke GJK, Hofmann K, Dohmen RJ. SUMO playing tag with ubiquitin. Trends Biochem Sci 2011; 37:23-31. [PMID: 22018829 DOI: 10.1016/j.tibs.2011.09.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/13/2011] [Accepted: 09/15/2011] [Indexed: 10/16/2022]
Abstract
In addition to being structurally related, the protein modifiers ubiquitin and SUMO (small ubiquitin-related modifier), share a multitude of functional interrelations. These include the targeting of the same attachment sites in certain substrates, and SUMO-dependent ubiquitylation in others. Notably, several cellular processes, including the targeting of repair machinery to DNA damage sites, require the sequential sumoylation and ubiquitylation of distinct substrates. Some proteins promote both modifications. By contrast, the activity of some enzymes that control either sumoylation or ubiquitylation is regulated by the respective other modification. In this review, we summarize recent findings regarding intersections between SUMO and ubiquitin that influence genome stability and cell growth and which are relevant in pathogen resistance and cancer treatment.
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Affiliation(s)
- Gerrit J K Praefcke
- Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, Cologne Biocenter, Zülpicher Straße 47a, D-50674 Cologne, Germany
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Nuclear structure and chromosome segregation in Drosophila male meiosis depend on the ubiquitin ligase dTopors. Genetics 2011; 189:779-93. [PMID: 21900273 DOI: 10.1534/genetics.111.133819] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many organisms, homolog pairing and synapsis at meiotic prophase depend on interactions between chromosomes and the nuclear membrane. Male Drosophila lack synapsis, but nonetheless, their chromosomes closely associate with the nuclear periphery at prophase I. To explore the functional significance of this association, we characterize mutations in nuclear blebber (nbl), a gene required for both spermatocyte nuclear shape and meiotic chromosome transmission. We demonstrate that nbl corresponds to dtopors, the Drosophila homolog of the mammalian dual ubiquitin/small ubiquitin-related modifier (SUMO) ligase Topors. We show that mutations in dtopors cause abnormalities in lamin localizations, centriole separation, and prophase I chromatin condensation and also cause anaphase I bridges that likely result from unresolved homolog connections. Bridge formation does not require mod(mdg4) in meiosis, suggesting that bridges do not result from misregulation of the male homolog conjunction complex. At the ultrastructural level, we observe disruption of nuclear shape, an uneven perinuclear space, and excess membranous structures. We show that dTopors localizes to the nuclear lamina at prophase, and also transiently to intranuclear foci. As a role of dtopors at gypsy insulator has been reported, we also asked whether these new alleles affected expression of the gypsy-induced mutation ct(6) and found that it was unaltered in dtopors homozygotes. Our results indicate that dTopors is required for germline nuclear structure and meiotic chromosome segregation, but in contrast, is not necessary for gypsy insulator function. We suggest that dtopors plays a structural role in spermatocyte lamina that is critical for multiple aspects of meiotic chromosome transmission.
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Wang J. Cardiac function and disease: emerging role of small ubiquitin-related modifier. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2011; 3:446-57. [PMID: 21197655 PMCID: PMC3110591 DOI: 10.1002/wsbm.130] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Small ubiquitin-related modifiers, or SUMOs, have emerged as versatile regulators of many biological functions that do so by covalent attachment to a variety of substrates via enzymatic reactions. SUMO conjugation has also been shown to be involved in a number of human pathogenic processes. More recent advances in the SUMO field have indicated a potential role for SUMO conjugation pathway in cardiogenesis. This advanced review will describe the basic features of the SUMO conjugation pathway and will summarize the most recent studies implicating the influence of the sumoylation pathway in cardiac function under both physiological and pathological conditions. WIREs Syst Biol Med 2011 3 446-457 DOI: 10.1002/wsbm.130
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Affiliation(s)
- Jun Wang
- Center for Stem Cell Engineering, Department of Basic Research Laboratories, Texas Heart Institute, Houston, TX, USA.
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Lugthart S, Figueroa ME, Bindels E, Skrabanek L, Valk PJM, Li Y, Meyer S, Erpelinck-Verschueren C, Greally J, Löwenberg B, Melnick A, Delwel R. Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1. Blood 2011; 117:234-41. [PMID: 20855866 PMCID: PMC3037746 DOI: 10.1182/blood-2010-04-281337] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 08/31/2010] [Indexed: 12/20/2022] Open
Abstract
DNA methylation patterns are frequently dysregulated in cancer, although little is known of the mechanisms through which specific gene sets become aberrantly methylated. The ecotropic viral integration site 1 (EVI1) locus encodes a DNA binding zinc-finger transcription factor that is aberrantly expressed in a subset of acute myeloid leukemia (AML) patients with poor outcome. We find that the promoter DNA methylation signature of EVI1 AML blast cells differs from those of normal CD34(+) bone marrow cells and other AMLs. This signature contained 294 differentially methylated genes, of which 238 (81%) were coordinately hypermethylated. An unbiased motif analysis revealed an overrepresentation of EVI1 binding sites among these aberrantly hypermethylated loci. EVI1 was capable of binding to these promoters in 2 different EVI1-expressing cell lines, whereas no binding was observed in an EVI1-negative cell line. Furthermore, EVI1 was observed to interact with DNA methyl transferases 3A and 3B. Among the EVI1 AML cases, 2 subgroups were recognized, of which 1 contained AMLs with many more methylated genes, which was associated with significantly higher levels of EVI1 than in the cases of the other subgroup. Our data point to a role for EVI1 in directing aberrant promoter DNA methylation patterning in EVI1 AMLs.
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Affiliation(s)
- Sanne Lugthart
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
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The program for processing newly synthesized histones H3.1 and H4. Nat Struct Mol Biol 2010; 17:1343-51. [PMID: 20953179 PMCID: PMC2988979 DOI: 10.1038/nsmb.1911] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 08/17/2010] [Indexed: 12/31/2022]
Abstract
The mechanism by which newly synthesized histones are imported into the nucleus and deposited onto replicating chromatin alongside segregating nucleosomal counterparts is poorly understood, yet this program is expected to bear on the putative epigenetic nature of histone posttranslational modifications. In order to define the events by which naïve pre-deposition histones are imported into the nucleus, we biochemically purified and characterized the gamut of histone H3.1-containing complexes from human cytoplasmic fractions and identified their associated histone PTMs. Through reconstitution assays, biophysical analyses, and live cell manipulations, we describe in detail this series of events, namely the assembly of H3-H4 dimers, the acetylation of histones by the HAT1 holoenzyme, and the transfer of histones between chaperones that culminates with their karyopherin-mediated nuclear import. We further demonstrate the high degree of conservation for this pathway between higher and lower eukaryotes.
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Ellison-Zelski SJ, Alarid ET. Maximum growth and survival of estrogen receptor-alpha positive breast cancer cells requires the Sin3A transcriptional repressor. Mol Cancer 2010; 9:263. [PMID: 20920219 PMCID: PMC2956731 DOI: 10.1186/1476-4598-9-263] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 09/29/2010] [Indexed: 11/16/2022] Open
Abstract
Background Sin3A is an evolutionarily conserved transcriptional repressor which regulates gene expression as part of the multi-protein Sin3 repressive complex. It functions as a scaffold upon which proteins with enzymatic activity dock, including chromatin modifying histone deacetylases. Although regulation of transcription by Sin3A has been studied in detail, little is understood about the function of Sin3A in cancer cells. We previously showed that Sin3A is expressed in breast cancer cells and is a repressor of estrogen receptor-alpha (ERα, ESR1) gene expression. Here, we expand our previous studies to elucidate the function of Sin3A in the control of gene expression and growth of breast cancer cells. Results Analysis of gene expression following knockdown of Sin3A revealed changes in both basal and regulated gene transcription. Genes of known importance in breast cancer and estrogen signaling, including ERBB2, PGR, MYC, CLU, and NCOA2, were among those identified as Sin3A-responsive. The mechanism of Sin3A action varied among genes and was found to be mediated through both HDAC1/2 -dependent and -independent activities. Loss of Sin3A inhibited breast cancer cell growth by increasing apoptosis without affecting cell cycle progression. Analysis of both ERα-positive and ERα-negative cell lines revealed that the effects of Sin3A on growth were cell-type specific, as Sin3A expression promoted maximum growth of only the ERα-positive cells, and, notably, Sin3A protein itself was increased by estrogen. Further gene expression experiments revealed that Sin3A repressed expression of key apoptotic genes, including TRAIL, TRAILR1, CASP10, and APAF1, in ERα-positive, but not ERα-negative, cell lines, which could provide a mechanistic explanation for cell-type differences in growth. Conclusions This study identifies Sin3A as a regulator of gene expression, survival, and growth in ERα-positive breast cancer cells. Sin3A regulates the transcription of genes involved in breast cancer and apoptosis and acts through multiple mechanisms not limited to histone deacetylase function. These findings reveal previously undescribed functions of Sin3A in breast cancer and provide evidence for an important role of this transcriptional repressor in ERα-positive tumor cell growth.
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Westman BJ, Verheggen C, Hutten S, Lam YW, Bertrand E, Lamond AI. A proteomic screen for nucleolar SUMO targets shows SUMOylation modulates the function of Nop5/Nop58. Mol Cell 2010; 39:618-31. [PMID: 20797632 PMCID: PMC2938476 DOI: 10.1016/j.molcel.2010.07.025] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 04/30/2010] [Accepted: 06/08/2010] [Indexed: 11/23/2022]
Abstract
Posttranslational SUMO modification is an important mechanism of regulating protein function, especially in the cell nucleus. The nucleolus is the subnuclear organelle responsible for rRNA synthesis, processing, and assembly of the large and small ribosome subunits. Here, we have used SILAC-based quantitative proteomics to identify nucleolar SUMOylated proteins. This reveals a role for SUMOylation in the biogenesis and/or function of small nucleolar ribonucleoprotein complexes (snoRNPs) via the targeting of Nhp2 and Nop58. Using combined in vitro and in vivo approaches, both Nhp2 and Nop58 (also known as Nop5) are shown to be substrates for SUMOylation. Mutational analyses revealed the sites of modification on Nhp2 as K5, and on Nop58 as K467 and K497. Unlike Nop58 and Nhp2, the closely related Nop56 and 15.5K proteins appear not to be SUMO targets. SUMOylation is essential for high-affinity Nop58 binding to snoRNAs. This study provides direct evidence linking SUMO modification with snoRNP function.
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Affiliation(s)
- Belinda J Westman
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD15EH, UK
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The serine/arginine-rich protein SF2/ASF regulates protein sumoylation. Proc Natl Acad Sci U S A 2010; 107:16119-24. [PMID: 20805487 DOI: 10.1073/pnas.1004653107] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein modification by conjugation of small ubiquitin-related modifier (SUMO) is involved in diverse biological functions, such as transcription regulation, subcellular partitioning, stress response, DNA damage repair, and chromatin remodeling. Here, we show that the serine/arginine-rich protein SF2/ASF, a factor involved in splicing regulation and other RNA metabolism-related processes, is a regulator of the sumoylation pathway. The overexpression of this protein stimulates, but its knockdown inhibits SUMO conjugation. SF2/ASF interacts with Ubc9 and enhances sumoylation of specific substrates, sharing characteristics with already described SUMO E3 ligases. In addition, SF2/ASF interacts with the SUMO E3 ligase PIAS1 (protein inhibitor of activated STAT-1), regulating PIAS1-induced overall protein sumoylation. The RNA recognition motif 2 of SF2/ASF is necessary and sufficient for sumoylation enhancement. Moreover, SF2/ASF has a role in heat shock-induced sumoylation and promotes SUMO conjugation to RNA processing factors. These results add a component to the sumoylation pathway and a previously unexplored role for the multifunctional SR protein SF2/ASF.
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Abstract
Sumoylation is a posttranslational modification process in which SUMO proteins are covalently and reversibly conjugated to their targets via enzymatic cascade reactions. Since the discovery of SUMO-1 in 1996, the SUMO pathway has garnered increased attention due to its role in a number of important biological activities such as cell cycle progression, epigenetic modulation, signal transduction, and DNA replication/repair, as well as its potential implication in human pathogenesis such as in cancer development and metastasis, neurodegenerative disorders and craniofacial defects. The role of the SUMO pathway in regulating cardiogenic gene activity, development and/or disorders is just emerging. Our review is based on recent advances that highlight the regulation of cardiac gene activity in cardiac development and disease by the SUMO conjugation pathway.
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Affiliation(s)
- Jun Wang
- Center for Stem Cell Engineering, Department of Basic Research Laboratories, Texas Heart Institute, Houston, TX 77030
| | - Robert J Schwartz
- Center for Stem Cell Engineering, Department of Basic Research Laboratories, Texas Heart Institute, Houston, TX 77030
- Department of Biology and Biochemistry, University of Houston, Houston, TX
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Marshall H, Bhaumik M, Aviv H, Moore D, Yao M, Dutta J, Rahim H, Gounder M, Ganesan S, Saleem A, Rubin E. Deficiency of the dual ubiquitin/SUMO ligase Topors results in genetic instability and an increased rate of malignancy in mice. BMC Mol Biol 2010; 11:31. [PMID: 20429939 PMCID: PMC2873312 DOI: 10.1186/1471-2199-11-31] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 04/29/2010] [Indexed: 01/07/2023] Open
Abstract
Background Topors is a nuclear protein that co-localizes with promyelocytic leukemia bodies and has both ubiquitin and SUMO E3 ligase activity. Expression studies implicated Topors as a tumor suppressor in various malignancies. To gain insight into the function of Topors, we generated a Topors-deficient mouse strain. Results Mice homozygous for a mutant Topors allele exhibited a high rate of perinatal mortality and decreased lifespan. In addition, heterozygotes were found to have an increased incidence of malignancy, involving a variety of tissues. Consistent with this finding, primary embryonic fibroblasts lacking Topors exhibited an increased rate of malignant transformation, associated with aneuploidy and defective chromosomal segregation. While loss of Topors did not alter sensitivity to DNA-damaging or microtubule-targeting agents, cells lacking Topors exhibited altered pericentric heterochromatin, manifested by mislocalization of HP1α and an increase in transcription from pericentric major satellite DNA. Topors-deficient cells exhibited a transcriptional profile similar to that of cells treated with histone deacetylase inhibitors, and were resistant to the anti-proliferative effects of the histone deacetylase inhibitor trichostatin A. Conclusion These results indicate a unique role for Topors in the maintenance of genomic stability and pericentric heterochromatin, as well as in cellular sensitivity to histone deacetylase inhibitors.
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Affiliation(s)
- Henderson Marshall
- Department of Pharmacology, Cancer Institute of New Jersey, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08901, USA
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Shan J, Lopez MC, Baker HV, Kilberg MS. Expression profiling after activation of amino acid deprivation response in HepG2 human hepatoma cells. Physiol Genomics 2010; 41:315-27. [PMID: 20215415 DOI: 10.1152/physiolgenomics.00217.2009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dietary protein malnutrition is manifested as amino acid deprivation of individual cells, which activates an amino acid response (AAR) that alters cellular functions, in part, by regulating transcriptional and posttranscriptional mechanisms. The AAR was activated in HepG2 human hepatoma cells, and the changes in mRNA content were analyzed by microarray expression profiling. The results documented that 1,507 genes were differentially regulated by P < 0.001 and by more than twofold in response to the AAR, 250 downregulated and 1,257 upregulated. The spectrum of altered genes reveals that amino acid deprivation has far-reaching implications for gene expression and cellular function. Among those cellular functions with the largest numbers of altered genes were cell growth and proliferation, cell cycle, gene expression, cell death, and development. Potential biological relationships between the differentially expressed genes were analyzed by computer software that generates gene networks. Proteins that were central to the most significant of these networks included c-myc, polycomb group proteins, transforming growth factor β1, nuclear factor (erythroid-derived 2)-like 2-related factor 2, FOS/JUN family members, and many members of the basic leucine zipper superfamily of transcription factors. Although most of these networks contained some genes that were known to be amino acid responsive, many new relationships were identified that underscored the broad impact that amino acid stress has on cellular function.
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Affiliation(s)
- Jixiu Shan
- Department of Biochemistry and Molecular Biology and
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Van Damme E, Laukens K, Dang TH, Van Ostade X. A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int J Biol Sci 2010; 6:51-67. [PMID: 20087442 PMCID: PMC2808052 DOI: 10.7150/ijbs.6.51] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 01/09/2010] [Indexed: 12/22/2022] Open
Abstract
Promyelocytic Leukaemia Protein nuclear bodies (PML-NBs) are dynamic nuclear protein aggregates. To gain insight in PML-NB function, reductionist and high throughput techniques have been employed to identify PML-NB proteins. Here we present a manually curated network of the PML-NB interactome based on extensive literature review including database information. By compiling 'the PML-ome', we highlighted the presence of interactors in the Small Ubiquitin Like Modifier (SUMO) conjugation pathway. Additionally, we show an enrichment of SUMOylatable proteins in the PML-NBs through an in-house prediction algorithm. Therefore, based on the PML network, we hypothesize that PML-NBs may function as a nuclear SUMOylation hotspot.
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Affiliation(s)
- Ellen Van Damme
- Laboratory of Protein Chemistry, Proteomics and Signal Transduction, Department of Biomedical Sciences, University of Antwerp (Campus Drie Eiken), Universiteitsplein 1 - Building T, Wilrijk, Belgium.
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Rytinki MM, Kaikkonen S, Pehkonen P, Jääskeläinen T, Palvimo JJ. PIAS proteins: pleiotropic interactors associated with SUMO. Cell Mol Life Sci 2009; 66:3029-41. [PMID: 19526197 PMCID: PMC11115825 DOI: 10.1007/s00018-009-0061-z] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 05/05/2009] [Accepted: 05/27/2009] [Indexed: 01/02/2023]
Abstract
The interactions and functions of protein inhibitors of activated STAT (PIAS) proteins are not restricted to the signal transducers and activators of transcription (STATs), but PIAS1, -2, -3 and -4 interact with and regulate a variety of distinct proteins, especially transcription factors. Although the majority of PIAS-interacting proteins are prone to modification by small ubiquitin-related modifier (SUMO) proteins and the PIAS proteins have the capacity to promote the modification as RING-type SUMO ligases, they do not function solely as SUMO E3 ligases. Instead, their effects are often independent of their Siz/PIAS (SP)-RING finger, but dependent on their capability to noncovalently interact with SUMOs or DNA through their SUMO-interacting motif and scaffold attachment factor-A/B, acinus and PIAS domain, respectively. Here, we present an overview of the cellular regulation by PIAS proteins and propose that many of their functions are due to their capability to mediate and facilitate SUMO-linked protein assemblies.
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Affiliation(s)
- Miia M. Rytinki
- Institute of Biomedicine/Medical Biochemistry, University of Kuopio, Kuopio, Finland
| | - Sanna Kaikkonen
- Institute of Biomedicine/Medical Biochemistry, University of Kuopio, Kuopio, Finland
| | - Petri Pehkonen
- Department of Biosciences, University of Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine/Medical Biochemistry, University of Kuopio, Kuopio, Finland
| | - Jorma J. Palvimo
- Institute of Biomedicine/Medical Biochemistry, University of Kuopio, Kuopio, Finland
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Zunino R, Braschi E, Xu L, McBride HM. Translocation of SenP5 from the nucleoli to the mitochondria modulates DRP1-dependent fission during mitosis. J Biol Chem 2009; 284:17783-95. [PMID: 19411255 DOI: 10.1074/jbc.m901902200] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The mechanisms that ensure an equal inheritance of cellular organelles during mitosis are an important area of study in cell biology. For the mitochondria fragment during mitosis, however, the cellular links that signal these changes are largely unknown. We recently identified a SUMO protease, SenP5, that deSUMOylates a number of mitochondrial targets, including the dynamin-related fission GTPase, DRP1. In interphase, SenP5 resides primarily within the nucleoli, in addition to a cytosolic pool. Here we report the relocalization of SenP5 from the nucleoli to the mitochondrial surface at G2/M transition prior to nuclear envelope breakdown. The recruitment of SenP5 results in a significant loss in mitochondrial SUMOylation, and a concomitant increase in the labile pool of DRP1 that drives mitochondrial fragmentation. Importantly, silencing of SenP5 leads to an arrest in the cell cycle precisely at the time when the protease is translocated to the mitochondria. These data indicate that transition of SenP5 to the mitochondria plays an important role in mitochondrial fragmentation during mitosis. The altered intracellular localization of SenP5 represents the first example of the mitochondrial recruitment of a SUMO protease and provides new insights into the mechanisms of interorganellar communication during the cell cycle.
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Affiliation(s)
- Rodolfo Zunino
- University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
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Kim KI, Baek SH. Small ubiquitin-like modifiers in cellular malignancy and metastasis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 273:265-311. [PMID: 19215907 DOI: 10.1016/s1937-6448(08)01807-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Small ubiquitin-like modifiers (SUMOs) mediate a variety of cellular functions of protein targets mainly in the nucleus but in other cellular compartments as well, and thereby participate in maintaining cellular homeostasis. SUMO system plays important roles in transcriptional regulation, DNA damage responses, maintaining genome integrity, and signaling pathways. Thus, in some cases, loss of regulated control on SUMOylation/deSUMOylation processes causes a defect in maintaining homeostasis and hence gives a cue to cancer development and progression. Furthermore, recent studies have revealed that SUMO system is involved in cancer metastasis. In this review, we will summarize the possible role of SUMO system in cancer development, progression, and metastasis and discuss future directions.
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Affiliation(s)
- Keun Il Kim
- Department of Biological Sciences, Research Center for Women's Disease, Sookmyung Women's University, Seoul, Korea
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A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem Sci 2008; 33:201-8. [PMID: 18403209 DOI: 10.1016/j.tibs.2008.02.001] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/08/2008] [Accepted: 02/12/2008] [Indexed: 11/22/2022]
Abstract
Ubiquitin and ubiquitin-like proteins (Ubls) share a beta-GRASP fold and have key roles in cellular growth and suppression of genome instability. Despite their common fold, SUMO and ubiquitin are classically portrayed as distinct, and they can have antagonistic roles. Recently, a new family of proteins, the small ubiquitin-related modifier (SUMO)-targeted ubiquitin ligases (STUbLs), which directly connect sumoylation and ubiquitylation, has been discovered. Uniquely, STUbLs use SUMO-interaction motifs (SIMs) to recognize their sumoylated targets. STUbLs are global regulators of protein sumoylation levels, and cells lacking STUbLs display genomic instability and hypersensitivity to genotoxic stress. The human STUbL, RNF4, is implicated in several diseases including cancer, highlighting the importance of characterizing the cellular functions of STUbLs.
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Abstract
The small ubiquitin-like modifier proteins (Smt3 in yeast and SUMOs 1-4 in vertebrates) are members of the ubiquitin super family. Like ubiquitin, the SUMOs are protein modifiers that are covalently attached to the epsilon-amino group of lysine residues in the substrates. The application of proteomics to the SUMO field has greatly expanded both the number of known targets and the number of identified target lysines. As new refinements of proteomic techniques are developed and applied to sumoylation, an explosion of novel data is likely in the next 5 years. This ability to examine sumoylated proteins globally, rather than individually, will lead to new insights into both the functions of the individual SUMO types, and how dynamic changes in overall sumoylation occur in response to alterations in cellular environment. In addition, there is a growing appreciation for the existence of cross-talk mechanisms between the sumoylation and ubiquitinylation processes. Rather than being strictly parallel, these two systems have many points of intersection, and it is likely that the coordination of these two systems is a critical contributor to the regulation of many fundamental cellular events.
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Affiliation(s)
- Van G Wilson
- Department of Microbial & Molecular Pathogenesis, College of Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USA.
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Schwamborn K, Knipscheer P, van Dijk E, van Dijk WJ, Sixma TK, Meloen RH, Langedijk JPM. SUMO assay with peptide arrays on solid support: insights into SUMO target sites. J Biochem 2008; 144:39-49. [PMID: 18344540 DOI: 10.1093/jb/mvn039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The modification of proteins by SUMO (small ubiquitin-like modifier) regulates various cellular processes. Sumoylation often occurs on a specific lysine residue within the consensus motif psiKxE/D. However, little is known about the specificity and selectivity of SUMO target sites. We describe here a SUMO assay with peptide array on solid support for the simultaneous characterization of hundreds of different SUMO target sites. This approach was used to characterize known SUMO substrates. The position of the motif within the peptide and the amino acids flanking the acceptor site affected the efficiency of SUMO modification. Interestingly, a sequence of only four amino acids, corresponding to the SUMO consensus motif without flanking amino acids, was a bona fide target site. Analysis of a peptide library for all variants of the psiKxE/D consensus motif revealed that the first and third positions in the tetrapeptide preferably contain aromatic amino acid residues. Furthermore, by adding the SUMO E3 ligase PIAS1 to the reaction mixture, we show specific enhancement of the modification of a PIAS1-dependent SUMO substrate in this system. Overall, our results demonstrate that the sumoylation assay with peptide array on solid support can be used for the high-throughput characterization of SUMO target sites, and provide new insights into the composition, selectivity and specificity of SUMO target sites.
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Affiliation(s)
- Klaus Schwamborn
- Pepscan Therapeutics BV, Zuidersluisweg 2, 8243 RC Lelystad, the Netherlands.
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Guan B, Pungaliya P, Li X, Uquillas C, Mutton LN, Rubin EH, Bieberich CJ. Ubiquitination by TOPORS regulates the prostate tumor suppressor NKX3.1. J Biol Chem 2007; 283:4834-40. [PMID: 18077445 DOI: 10.1074/jbc.m708630200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The NKX3.1 gene located at 8p21.2 encodes a homeodomain-containing transcription factor that acts as a haploinsufficient tumor suppressor in prostate cancer. Diminished protein expression of NKX3.1 has been observed in prostate cancer precursors and carcinomas. TOPORS is a ubiquitously expressed E3 ubiquitin ligase that can ubiquitinate tumor suppressor p53. Here we report interaction between NKX3.1 and TOPORS. NKX3.1 can be ubiquitinated by TOPORS in vitro and in vivo, and overexpression of TOPORS leads to NKX3.1 proteasomal degradation in prostate cancer cells. Conversely, small interfering RNA-mediated knockdown of TOPORS leads to an increased steady-state level and prolonged half-life of NKX3.1. These data establish TOPORS as a negative regulator of NKX3.1 and implicate TOPORS in prostate cancer progression.
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Affiliation(s)
- Bin Guan
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
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