1
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Wang X, Liu J, Mao C, Mao Y. Phase separation-mediated biomolecular condensates and their relationship to tumor. Cell Commun Signal 2024; 22:143. [PMID: 38383403 PMCID: PMC10880379 DOI: 10.1186/s12964-024-01518-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.
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Affiliation(s)
- Xi Wang
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jiameng Liu
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Chaoming Mao
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Yufei Mao
- Department of Ultrasound Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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2
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Jelinska C, Kannan S, Frosi Y, Ramlan SR, Winnerdy F, Lakshminarayanan R, Johannes CW, Brown CJ, Phan AT, Rhodes D, Verma CS. Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein. RSC Chem Biol 2023; 4:1096-1110. [PMID: 38033728 PMCID: PMC10685803 DOI: 10.1039/d3cb00149k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 12/02/2023] Open
Abstract
DAXX (Death Domain Associated Protein 6) is frequently upregulated in various common cancers, and its suppression has been linked to reduced tumor progression. Consequently, DAXX has gained significant interest as a therapeutic target in such cancers. DAXX is known to function in several critical biological pathways including chromatin remodelling, transcription regulation, and DNA repair. Leveraging structural information, we have designed and developed a novel set of stapled/stitched peptides that specifically target a surface on the N-terminal helical bundle domain of DAXX. This surface serves as the anchor point for binding to multiple interaction partners, such as Rassf1C, p53, Mdm2, and ATRX, as well as for the auto-regulation of the DAXX N-terminal SUMO interaction motif (SIM). Our experiments demonstrate that these peptides effectively bind to and inhibit DAXX with a higher affinity than the known interaction partners. Furthermore, these peptides release the auto-inhibited SIM, enabling it to interact with SUMO-1. Importantly, we have developed stitched peptides that can enter cells, maintaining their intracellular concentrations at nanomolar levels even after 24 hours, without causing any membrane perturbation. Collectively, our findings suggest that these stitched peptides not only serve as valuable tools for probing the molecular interactions of DAXX but also hold potential as precursors to the development of therapeutic interventions.
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Affiliation(s)
- Clare Jelinska
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | | | - Yuri Frosi
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Siti Radhiah Ramlan
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Fernaldo Winnerdy
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
| | - Rajamani Lakshminarayanan
- Ocular Infections and Anti-Microbials Research Group, Singapore Eye Research Institute, The Academia, 20 College Road Singapore 169856 Singapore
- Department of Pharmacy, National University of Singapore Singapore 117543 Singapore
- Academic Clinical Program in Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School 169857 Singapore
| | - Charles W Johannes
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Christopher J Brown
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Anh-Tuan Phan
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Physical and Mathematical Sciences. 21 Nanyang link 637371 Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | - Chandra S Verma
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- Bioinformatics institute (A*STAR), 30 Biopolis Street, Matrix Level 07-01 138671 Singapore
- Department of Biological Sciences, National University of Singapore Block S3 #05-01 16 Science Drive 4 117558 Singapore
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3
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Kötter A, Mootz HD, Heuer A. Conformational and Interface Variability in Multivalent SIM-SUMO Interaction. J Phys Chem B 2023; 127:3806-3815. [PMID: 37079893 DOI: 10.1021/acs.jpcb.2c08760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
SUMO targeted ubiqutin ligases (STUbLs) like RNF4 or Arkadia/RNF111 recognize SUMO chains through multiple SUMO interacting motifs (SIMs). Typically, these are contained in disordered regions of these enzymes and also the individual SUMO domains of SUMO chains move relatively freely. It is assumed that binding the SIM region significantly restricts the conformational freedom of SUMO chains. Here, we present the results of extensive molecular dynamics simulations on the complex formed by the SIM2-SIM3 region of RNF4 and diSUMO3. Though our simulations highlight the importance of typical SIM-SUMO interfaces also in the multivalent situation, we observe that frequently other regions of the peptide than the canonical SIMs establish this interface. This variability regarding the individual interfaces leads to a conformationally highly flexible complex. Comparison with previous experimental measurements clearly supports our findings and indicates that our observations can be extended to other multivalent SIM-SUMO complexes.
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Affiliation(s)
- Alex Kötter
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, D-48149 Münster, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
| | - Henning D Mootz
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 2, D-48149 Münster, Germany
| | - Andreas Heuer
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, D-48149 Münster, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, D-48149 Münster, Germany
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4
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Carraro M, Hendriks IA, Hammond CM, Solis-Mezarino V, Völker-Albert M, Elsborg JD, Weisser MB, Spanos C, Montoya G, Rappsilber J, Imhof A, Nielsen ML, Groth A. DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Mol Cell 2023; 83:1075-1092.e9. [PMID: 36868228 PMCID: PMC10114496 DOI: 10.1016/j.molcel.2023.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.
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Affiliation(s)
- Massimo Carraro
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin M Hammond
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | | | | | - Jonas D Elsborg
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Melanie B Weisser
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Axel Imhof
- EpiQMAx GmbH, Planegg, Germany; Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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5
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SENP2 suppresses browning of white adipose tissues by de-conjugating SUMO from C/EBPβ. Cell Rep 2022; 38:110408. [PMID: 35196497 DOI: 10.1016/j.celrep.2022.110408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/26/2021] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
The adipose tissue is a key site regulating energy metabolism. One of the contributing factors behind this is browning of white adipose tissue (WAT). However, knowledge of the intracellular determinants of the browning process remains incomplete. By generating adipocyte-specific Senp2 knockout (Senp2-aKO) mice, here we show that SENP2 negatively regulates browning by de-conjugating small ubiquitin-like modifiers from C/EBPβ. Senp2-aKO mice are resistant to diet-induced obesity due to increased energy expenditure and heat production. Senp2 knockout promotes beige adipocyte accumulation in inguinal WAT by upregulation of thermogenic gene expression. In addition, SENP2 knockdown promotes thermogenic adipocyte differentiation of precursor cells isolated from inguinal and epididymal WATs. Mechanistically, sumoylated C/EBPβ, a target of SENP2, suppresses expression of HOXC10, a browning inhibitor, by recruiting a transcriptional repressor DAXX. These findings indicate that a SENP2-C/EBPβ-HOXC10 axis operates for the control of beige adipogenesis in inguinal WAT.
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González-Prieto R, Eifler-Olivi K, Claessens LA, Willemstein E, Xiao Z, Talavera Ormeno CMP, Ovaa H, Ulrich HD, Vertegaal ACO. Global non-covalent SUMO interaction networks reveal SUMO-dependent stabilization of the non-homologous end joining complex. Cell Rep 2021; 34:108691. [PMID: 33503430 DOI: 10.1016/j.celrep.2021.108691] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/11/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
In contrast to our extensive knowledge on covalent small ubiquitin-like modifier (SUMO) target proteins, we are limited in our understanding of non-covalent SUMO-binding proteins. We identify interactors of different SUMO isoforms-monomeric SUMO1, monomeric SUMO2, or linear trimeric SUMO2 chains-using a mass spectrometry-based proteomics approach. We identify 379 proteins that bind to different SUMO isoforms, mainly in a preferential manner. Interestingly, XRCC4 is the only DNA repair protein in our screen with a preference for SUMO2 trimers over mono-SUMO2, as well as the only protein in our screen that belongs to the non-homologous end joining (NHEJ) DNA double-strand break repair pathway. A SUMO interaction motif (SIM) in XRCC4 regulates its recruitment to sites of DNA damage and phosphorylation of S320 by DNA-PKcs. Our data highlight the importance of non-covalent and covalent sumoylation for DNA double-strand break repair via the NHEJ pathway and provide a resource of SUMO isoform interactors.
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Affiliation(s)
- Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Karolin Eifler-Olivi
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Laura A Claessens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Edwin Willemstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Zhenyu Xiao
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Cami M P Talavera Ormeno
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Oncode Institute, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands; Oncode Institute, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
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7
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SUMOylation Targets Adeno-associated Virus Capsids but Mainly Restricts Transduction by Cellular Mechanisms. J Virol 2020; 94:JVI.00871-20. [PMID: 32669341 DOI: 10.1128/jvi.00871-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/08/2020] [Indexed: 11/20/2022] Open
Abstract
Adeno-associated virus (AAV) has proven to be a promising candidate for gene therapy due to its nonpathogenic nature, ease of production, and broad tissue tropism. However, its transduction capabilities are not optimal due to the interaction with various host factors within the cell. In a previous study, we identified members of the small ubiquitin-like modifier (SUMO) pathway as significant restriction factors in AAV gene transduction. In the present study, we explored the scope of this restriction by focusing on the AAV capsid and host cell proteins as targets. We show that during vector production, the capsid protein VP2 becomes SUMOylated, as indicated by deletion and point mutations of VP2 or the obstruction of its N terminus via the addition of a tag. We observed that SUMOylated AAV capsids display higher stability than non-SUMOylated capsids. Prevention of capsid SUMOylation by VP2 mutations did not abolish transduction restriction by SUMOylation; however, it reduced activation of gene transduction by shutdown of the cellular SUMOylation pathway. This indicates a link between capsid SUMOylation and SUMOylation of cellular proteins in restricting gene transduction. Infection with AAV triggers general SUMOylation of cellular proteins. In particular, the DAXX protein, a putative host cell restriction factor that can become SUMOylated, is able to restrict AAV gene transduction by reducing the intracellular accumulation of AAV vectors. We also observe that the coexpression of a SUMOylation inhibitor with an AAV2 reporter gene vector increased gene transduction significantly.IMPORTANCE Host factors within the cell are the major mode of restriction of adeno-associated virus (AAV) and keep it from fulfilling its maximum potential as a gene therapy vector. A better understanding of the intricacies of restriction would enable the engineering of better vectors. Via a genome-wide short interfering RNA screen, we identified that proteins of the small ubiquitin-like modifier (SUMO) pathway play an important role in AAV restriction. In this study, we investigate whether this restriction is targeted to the AAV directly or indirectly through host cell factors. The results indicate that both targets act in concert to restrict AAV.
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8
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Insights into the Microscopic Structure of RNF4-SIM-SUMO Complexes from MD Simulations. Biophys J 2020; 119:1558-1567. [PMID: 32976759 DOI: 10.1016/j.bpj.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022] Open
Abstract
Post-translational modification with one of the isoforms of the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome. The binding of SUMO to SUMO interacting motifs (SIMs) can translate the SUMOylation event into functional consequences. The E3 ubiquitin ligase RNF4 contains multiple SIMs and connects SUMOylation to the ubiquitin pathway. SIM2 and SIM3 of RNF4 were shown to be the most important motifs to recognize SUMO chains. However, the study of SIM-SUMO complexes is complicated by their typically low affinity and variable binding of the SIMs in parallel and antiparallel orientations. We investigated properties of complexes formed by SUMO3 with peptides containing either SIM2 or SIM3 using molecular dynamics simulations. The affinities of the complexes were determined using a state-of-the-art free energy protocol and were found to be in good agreement with experimental data, thus corroborating our method. Long unrestrained simulations allowed a new interpretation of experimental results regarding the structure of the SIM-SUMO interface. We show that both SIM2 and SIM3 bind SUMO3 in parallel and antiparallel orientations and identified main interaction sites for acidic residues flanking the SIM. We noticed unusual SIM-SUMO interfaces in a previously reported NMR structure (PDB: 2mp2) of a complex formed by a SUMO3 dimer with the bivalent SIM2-SIM3 peptide. Computational determination of the individual SIM-SUMO affinities based on these structural arrangements yielded significantly higher dissociation constants. To our knowledge, our approach adds new opportunities to characterize individual SIM-SUMO complexes and suggests that further studies will be necessary to understand these interactions when occurring in multivalent form.
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9
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Mahmud I, Liao D. DAXX in cancer: phenomena, processes, mechanisms and regulation. Nucleic Acids Res 2019; 47:7734-7752. [PMID: 31350900 PMCID: PMC6735914 DOI: 10.1093/nar/gkz634] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ATRX). DAXX's central region folds with the H3.3/H4 dimer, providing a H3.3-specific chaperoning function. DAXX has two functionally critical SUMO-interacting motifs. These modules are connected by disordered regions. DAXX's structural features provide a framework for deciphering how DAXX mechanistically imparts its functions and how its activity is regulated. DAXX modulates transcription through binding to transcription factors, epigenetic modifiers, and chromatin remodelers. DAXX's localization in the PML nuclear bodies also plays roles in transcriptional regulation. DAXX-regulated genes are likely important effectors of its biological functions. Deposition of H3.3 and its interactions with epigenetic modifiers are likely key events for DAXX to regulate transcription, DNA repair, and viral infection. Interactions between DAXX and its partners directly impact apoptosis and cell signaling. DAXX's activity is regulated by posttranslational modifications and ubiquitin-dependent degradation. Notably, the tumor suppressor SPOP promotes DAXX degradation in phase-separated droplets. We summarize here our current understanding of DAXX's complex functions with a focus on how it promotes oncogenesis.
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Affiliation(s)
- Iqbal Mahmud
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, 1333 Center Drive, Gainesville, FL 32610-0235, USA
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10
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Mason-Osann E, Dai A, Floro J, Lock YJ, Reiss M, Gali H, Matschulat A, Labadorf A, Flynn RL. Identification of a novel gene fusion in ALT positive osteosarcoma. Oncotarget 2018; 9:32868-32880. [PMID: 30214690 PMCID: PMC6132345 DOI: 10.18632/oncotarget.26029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/15/2018] [Indexed: 01/13/2023] Open
Abstract
The Alternative Lengthening of Telomeres (ALT) pathway stimulates telomere elongation and prevents cellular senescence in approximately 60% of osteosarcoma. While the precise mechanism underlying activation of the ALT pathway is unclear, mutations in the chromatin remodeling protein ATRX, histone chaperone DAXX, and the histone variant H3.3 correlate with ALT status. ATRX and DAXX facilitate deposition of the histone variant H3.3 within heterochromatic regions suggesting that loss of ATRX, DAXX, and/or H3.3 lead to defects in the stability of telomeric heterochromatin. Genetic mutations in ATRX, DAXX, and H3.3 have been detected in ALT positive cancers, however, a subset of ALT samples show loss of ATRX or DAXX protein expression or localization without evidence of genetic alterations suggesting additional uncharacterized defects in ATRX/DAXX/H3.3 function. Here, using Next Generation Sequencing we identified a novel gene fusion event between DAXX and the kinesin motor protein, KIFC3, leading to the translation of a chimeric DAXX-KIFC3 fusion protein. Moreover, we demonstrate that the fusion of KIFC3 to DAXX causes defects in DAXX function likely promoting ALT activity. These data highlight a potentially unrecognized mechanism of DAXX inactivation in ALT positive osteosarcoma and provide rationale for thorough and comprehensive analyses of ATRX/DAXX/H3.3 proteins in ALT positive cancers.
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Affiliation(s)
- Emily Mason-Osann
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anqi Dai
- BU Bioinformatics Hub, Boston University, Boston, MA 02118, USA
| | - Jess Floro
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ying Jie Lock
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Matthew Reiss
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Himabindu Gali
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adeline Matschulat
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam Labadorf
- BU Bioinformatics Hub, Boston University, Boston, MA 02118, USA
| | - Rachel Litman Flynn
- Departments of Pharmacology and Experimental Therapeutics, and Medicine Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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11
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Chen H, Xu Z, Li X, Yang Y, Li B, Li Y, Xia K, Wang J, Li S, Wang M, Wu H. α-catenin SUMOylation increases IκBα stability and inhibits breast cancer progression. Oncogenesis 2018. [PMID: 29540699 PMCID: PMC5852976 DOI: 10.1038/s41389-018-0037-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
α-catenin has been demonstrated to suppress several different types of cancers. Here we demonstrate that α-catenin is modified by SUMO protein, which covalently binds α-catenin at the carboxy terminus at lysine 870. Substitution of lysine 870 with arginine completely abolishes α-catenin SUMOylation. This modification can be removed by SENP1. However, α-catenin SUMOylation does not affect its stability and subcellular localization. In addition, we observed that the SUMOylation-deficient α-catenin mutant has a reduced interaction with IκBα which prevents subsequent ubiquitination of IκBα, and therefore a reduced suppression of expression of the NF-κB target genes TNF-α, IL-8, VEGF, and uPA. In addition, the α-catenin SUMOylation mutant shows impaired suppression of tumor growth. These results demonstrate that SUMOylation at lysine 870 of α-catenin plays a key role in the suppression of the NF-κB pathway, which inhibits breast cancer tumor growth and migration.
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Affiliation(s)
- Huan Chen
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Zhaowei Xu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xiahui Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yangyang Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Bowen Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yanan Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Kangkai Xia
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Jian Wang
- School of Life Science and Medicine, Dalian University of Technology, Panjin, China
| | - Shujing Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Miao Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
| | - Huijian Wu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China. .,School of Life Science and Medicine, Dalian University of Technology, Panjin, China.
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12
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Morozov VM, Giovinazzi S, Ishov AM. CENP-B protects centromere chromatin integrity by facilitating histone deposition via the H3.3-specific chaperone Daxx. Epigenetics Chromatin 2017; 10:63. [PMID: 29273057 PMCID: PMC5741900 DOI: 10.1186/s13072-017-0164-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/24/2017] [Indexed: 12/27/2022] Open
Abstract
Background The main chromatin unit, the nucleosome, can be modulated by the incorporation of histone variants that, in combination with posttranslational histones modifications, determine epigenetics properties of chromatin. Understanding the mechanism that creates a histone variants landscape at different genomic elements is expected to elevate our comprehension of chromatin assembly and function. The Daxx chaperone deposits transcription-associated histone H3.3 at centromeres, but mechanism of centromere-specific Daxx targeting remains unclear. Results In this study, we identified an unexpected function of the constitutive centromeric protein CENP-B that serves as a “beacon” for H3.3 incorporation. CENP-B depletion reduces Daxx association and H3.3 incorporation at centromeres. Daxx/CENP-B interaction and Daxx centromeric association are SUMO dependent and requires SIMs of Daxx. Depletion of SUMO-2, but not SUMO-1, decreases Daxx/CENP-B interaction and reduces centromeric accumulation of Daxx and H3.3, demonstrating distinct functions of SUMO paralogs in H3.3 chaperoning. Finally, disruption of CENP-B/Daxx-dependent H3.3 pathway deregulates heterochromatin marks H3K9me3, ATRX and HP1α at centromeres and elevates chromosome instability. Conclusion The demonstrated roles of CENP-B and SUMO-2 in H3.3 loading reveal a novel mechanism controlling chromatin maintenance and genome stability. Given that CENP-B is the only centromere protein that binds centromere-specific DNA elements, our study provides a new link between centromere DNA and unique epigenetic landscape of centromere chromatin. Electronic supplementary material The online version of this article (10.1186/s13072-017-0164-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viacheslav M Morozov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA
| | - Serena Giovinazzi
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA.,Division of Food Safety, Florida Department of Agriculture and Consumer Services, Tallahassee, FL, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, 2033 Mowry Road, Room 358, Gainesville, FL, 32610, USA.
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13
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Lee BL, Singh A, Mark Glover JN, Hendzel MJ, Spyracopoulos L. Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics. J Mol Biol 2017; 429:3409-3429. [PMID: 28587922 DOI: 10.1016/j.jmb.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022]
Abstract
Cells are exposed to thousands of DNA damage events on a daily basis. This damage must be repaired to preserve genetic information and prevent development of disease. The most deleterious damage is a double-strand break (DSB), which is detected and repaired by mechanisms known as non-homologous end-joining (NHEJ) and homologous recombination (HR), which are components of the DNA damage response system. NHEJ is an error-prone first line of defense, whereas HR invokes error-free repair and is the focus of this review. The functions of the protein components of HR-driven DNA repair are regulated by the coordinated action of post-translational modifications including lysine acetylation, phosphorylation, ubiquitination, and SUMOylation. The latter two mechanisms are fundamental for recognition of DSBs and reorganizing chromatin to facilitate repair. We focus on the structures and molecular mechanisms for the protein components underlying synthesis, recognition, and cleavage of K63-linked ubiquitin chains, which are abundant at damage sites and obligatory for DSB repair. The forward flux of the K63-linked ubiquitination cascade is driven by the combined activity of E1 enzyme, the heterodimeric E2 Mms2-Ubc13, and its cognate E3 ligases RNF8 and RNF168, which is balanced through the binding and cleavage of chains by the deubiquitinase BRCC36, and the proteasome, and through the binding of chains by recognition modules on repair proteins such as RAP80. We highlight a number of aspects regarding our current understanding for the role of kinetics and dynamics in determining the function of the enzymes and chain recognition modules that drive K63 ubiquitination.
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Affiliation(s)
- Brian L Lee
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Anamika Singh
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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14
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Abstract
Ubiquitin-like proteins (Ubl's) are conjugated to target proteins or lipids to regulate their activity, stability, subcellular localization, or macromolecular interactions. Similar to ubiquitin, conjugation is achieved through a cascade of activities that are catalyzed by E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. In this review, we will summarize structural and mechanistic details of enzymes and protein cofactors that participate in Ubl conjugation cascades. Precisely, we will focus on conjugation machinery in the SUMO, NEDD8, ATG8, ATG12, URM1, UFM1, FAT10, and ISG15 pathways while referring to the ubiquitin pathway to highlight common or contrasting themes. We will also review various strategies used to trap intermediates during Ubl activation and conjugation.
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Affiliation(s)
- Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States.,Howard Hughes Medical Institute, Sloan Kettering Institute , New York, New York 10021, United States
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15
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Cai J, Zuo Y, Wang T, Cao Y, Cai R, Chen FL, Cheng J, Mu J. A crucial role of SUMOylation in modulating Sirt6 deacetylation of H3 at lysine 56 and its tumor suppressive activity. Oncogene 2016; 35:4949-56. [PMID: 26898756 DOI: 10.1038/onc.2016.24] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/18/2015] [Accepted: 11/06/2015] [Indexed: 02/07/2023]
Abstract
Sirt6 is a histone deacetylase with NAD(+)-dependent activity. Sirt6 has been shown as a tumor suppressor partially via inhibiting the expression of c-Myc target genes and ribosome biogenesis. However, how to regulate Sirt6 activity is largely unknown. In this study, we identify that Sirt6 can be modified by small ubiquitin-like modifier. Sirt6 SUMOylation deficiency specifically decreases its deacetylation of H3K56 but not H3K9 in vivo. Mechanistically, we find that SUMOylation deficiency decreases Sirt6 binding with c-Myc, decreasing Sirt6 occupancy on the locus of c-Myc target genes. Therefore, Sirt6 SUMOylation deficiency reduces its deacetylation of H3k56 and its repression of c-Myc target genes. Moreover, Sirt6 SUMOylation deficiency reduces its suppression of cell proliferation and tumorigenesis. Thus, these results reveal that SUMOylation has an important role in regulation of Sirt6 deacetylation on H3K56, as well as its tumor suppressive activity.
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Affiliation(s)
- J Cai
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Zuo
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - T Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Cao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - R Cai
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - F-L Chen
- Shanghai Third People's Hospital Affiliated Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J Cheng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J Mu
- Department of Thoracic Surgery, Cancer Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
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16
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Anamika, Spyracopoulos L. Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80. J Biol Chem 2015; 291:4417-28. [PMID: 26719330 DOI: 10.1074/jbc.m115.705061] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/04/2023] Open
Abstract
Recognition and repair of double-stranded DNA breaks (DSB) involves the targeted recruitment of BRCA tumor suppressors to damage foci through binding of both ubiquitin (Ub) and the Ub-like modifier SUMO. RAP80 is a component of the BRCA1 A complex, and plays a key role in the recruitment process through the binding of Lys(63)-linked poly-Ub chains by tandem Ub interacting motifs (UIM). RAP80 also contains a SUMO interacting motif (SIM) just upstream of the tandem UIMs that has been shown to specifically bind the SUMO-2 isoform. The RAP80 tandem UIMs and SIM function collectively for optimal recruitment of BRCA1 to DSBs, although the molecular basis of this process is not well understood. Using NMR spectroscopy, we demonstrate that the RAP80 SIM binds SUMO-2, and that both specificity and affinity are enhanced through phosphorylation of the canonical CK2 site within the SIM. The affinity increase results from an enhancement of electrostatic interactions between the phosphoserines of RAP80 and the SIM recognition module within SUMO-2. The NMR structure of the SUMO-2·phospho-RAP80 complex reveals that the molecular basis for SUMO-2 specificity is due to isoform-specific sequence differences in electrostatic SIM recognition modules.
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Affiliation(s)
- Anamika
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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17
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van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2015; 428:720-725. [PMID: 26410586 DOI: 10.1016/j.jmb.2015.09.014] [Citation(s) in RCA: 1699] [Impact Index Per Article: 188.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022]
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - J P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - M Trellet
- Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France
| | - C Schmitz
- Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia
| | - P L Kastritis
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - E Karaca
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - A S J Melquiond
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M van Dijk
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - S J de Vries
- Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
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18
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Binding properties of SUMO-interacting motifs (SIMs) in yeast. J Mol Model 2015; 21:50. [PMID: 25690366 DOI: 10.1007/s00894-015-2597-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/26/2015] [Indexed: 11/27/2022]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.
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19
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Abstract
The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.
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20
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Erlendsson S, Rathje M, Heidarsson PO, Poulsen FM, Madsen KL, Teilum K, Gether U. Protein interacting with C-kinase 1 (PICK1) binding promiscuity relies on unconventional PSD-95/discs-large/ZO-1 homology (PDZ) binding modes for nonclass II PDZ ligands. J Biol Chem 2014; 289:25327-40. [PMID: 25023278 DOI: 10.1074/jbc.m114.548743] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PDZ domain proteins control multiple cellular functions by governing assembly of protein complexes. It remains unknown why individual PDZ domains can bind the extreme C terminus of very diverse binding partners and maintain selectivity. By employing NMR spectroscopy, together with molecular modeling, mutational analysis, and fluorescent polarization binding experiments, we identify here three structural mechanisms explaining why the PDZ domain of PICK1 selectively binds >30 receptors, transporters, and kinases. Class II ligands, including the dopamine transporter, adopt a canonical binding mode with promiscuity obtained via differential packing in the binding groove. Class I ligands, such as protein kinase Cα, depend on residues upstream from the canonical binding sequence that are likely to interact with flexible loop residues of the PDZ domain. Finally, we obtain evidence that the unconventional ligand ASIC1a has a dual binding mode involving a canonical insertion and a noncanonical internal insertion with the two C-terminal residues forming interactions outside the groove. Together with an evolutionary analysis, the data show how unconventional binding modes might evolve for a protein recognition domain to expand the repertoire of functionally important interactions.
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Affiliation(s)
- Simon Erlendsson
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Mette Rathje
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and
| | - Pétur O Heidarsson
- the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Flemming M Poulsen
- the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kenneth L Madsen
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and
| | - Kaare Teilum
- the Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ulrik Gether
- From the Molecular Neuropharmacology Laboratory, Lundbeck Foundation Center for Biomembranes in Nanomedicine, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute 18.6, University of Copenhagen, 2200 Copenhagen N and
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21
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Xu Y, Plechanovová A, Simpson P, Marchant J, Leidecker O, Kraatz S, Hay RT, Matthews SJ. Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4. Nat Commun 2014; 5:4217. [PMID: 24969970 PMCID: PMC4083429 DOI: 10.1038/ncomms5217] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023] Open
Abstract
The small ubiquitin-like modifier (SUMO) can form polymeric chains that are important signals in cellular processes such as meiosis, genome maintenance and stress response. The SUMO-targeted ubiquitin ligase RNF4 engages with SUMO chains on linked substrates and catalyses their ubiquitination, which targets substrates for proteasomal degradation. Here we use a segmental labelling approach combined with solution nuclear magnetic resonance (NMR) spectroscopy and biochemical characterization to reveal how RNF4 manipulates the conformation of the SUMO chain, thereby facilitating optimal delivery of the distal SUMO domain for ubiquitin transfer. SUMO forms flexible polymeric chains that can interact with ubiquitin ligases, such as RNF4. Here Xu et al. have used NMR spectroscopy and biochemical experiments to investigate the interaction between SUMO and RNF4, and propose a mechanism for delivery of substrates to the ubiquitination machinery.
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Affiliation(s)
- Yingqi Xu
- 1] Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK [2]
| | - Anna Plechanovová
- 1] Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK [2]
| | - Peter Simpson
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Jan Marchant
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Orsolya Leidecker
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sebastian Kraatz
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Steve J Matthews
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
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Multivalent interactions of the SUMO-interaction motifs in RING finger protein 4 determine the specificity for chains of the SUMO. Biochem J 2014; 457:207-14. [PMID: 24151981 PMCID: PMC3901395 DOI: 10.1042/bj20130753] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNF4 (RING finger protein 4) is a STUbL [SUMO (small ubiquitin-related modifier)-targeted ubiquitin ligase] controlling PML (promyelocytic leukaemia) nuclear bodies, DNA double strand break repair and other nuclear functions. In the present paper, we describe that the sequence and spacing of the SIMs (SUMO-interaction motifs) in RNF4 regulate the avidity-driven recognition of substrate proteins carrying SUMO chains of variable length. The ubiquitin ligase RNF4 targets proteins for proteasomal degradation if they are modified with SUMO chains. RNF4 recognizes its substrates by using short peptide motifs that interact non-covalently with SUMO chains if they contain at least two SUMO moieties.
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Abstract
Parkinson's disease (PD) is one of the most common degenerative disorders of the central nervous system that produces motor and non-motor symptoms. The majority of cases are idiopathic and characterized by the presence of Lewy bodies containing fibrillar α-synuclein. Small ubiquitin-related modifier (SUMO) immunoreactivity was observed among others in cases with PD. Key disease-associated proteins are SUMO-modified, linking this posttranslational modification to neurodegeneration. SUMOylation and SUMO-mediated mechanisms have been intensively studied in recent years, revealing nuclear and extranuclear functions for SUMO in a variety of cellular processes, including the regulation of transcriptional activity, modulation of signal transduction pathways, and response to cellular stress. This points to a role for SUMO more than just an antagonist to ubiquitin and proteasomal degradation. The identification of risk and age-at-onset gene loci was a breakthrough in PD and promoted the understanding of molecular mechanisms in the pathology. PD has been increasingly linked with mitochondrial dysfunction and impaired mitochondrial quality control. Interestingly, SUMO is involved in many of these processes and up-regulated in response to cellular stress, further emphasizing the importance of SUMOylation in physiology and disease.
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Affiliation(s)
- Katrin Eckermann
- Department of Neurology, University Medical Center Goettingen, Waldweg 33, 37073, Goettingen, Germany,
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24
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Review of Ets1 structure, function, and roles in immunity. Cell Mol Life Sci 2013; 70:3375-90. [PMID: 23288305 DOI: 10.1007/s00018-012-1243-7] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 11/20/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Abstract
The Ets1 transcription factor is a member of the Ets gene family and is highly conserved throughout evolution. Ets1 is known to regulate a number of important biological processes in normal cells and in tumors. In particular, Ets1 has been associated with regulation of immune cell function and with an aggressive behavior in tumors that express it at high levels. Here we review and summarize the general features of Ets1 and describe its roles in immunity and autoimmunity, with a focus on its roles in B lymphocytes. We also review evidence that suggests that Ets1 may play a role in malignant transformation of hematopoietic malignancies including B cell malignancies.
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New insights into the role of the small ubiquitin-like modifier (SUMO) in plants. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 300:161-209. [PMID: 23273862 DOI: 10.1016/b978-0-12-405210-9.00005-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small ubiquitin-like modifier (SUMO) is a small (∼12kDa) protein that occurs in all eukaryotes and participates in the reversible posttranslational modification of target cellular proteins. The three-dimensional structure of SUMO and ubiquitin (Ub) are superimposable although there is very little similarity in their primary amino acid sequences. In all organisms, conjugation and deconjugation of Ub and SUMO proceed by the same reactions while using pathway-specific enzymes. SUMO conjugation in plants is a part of the controls governing important biological processes such as growth, development, flowering, environmental (abiotic) stress responses, and response to pathogen infection. Most of the evidence for this comes from genetic analyses. Recent efforts to dissect the function of sumoylation have focused on uncovering targets of SUMO conjugation by using either a yeast two-hybrid screen employing components of the SUMO cycle as bait or by using affinity purification of SUMO-conjugated proteins followed by identification of these proteins by mass spectrometry. This chapter reviews the current knowledge regarding sumoylation in plants, with special focus on the model plant Arabidopsis thaliana.
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Maroui MA, Kheddache-Atmane S, El Asmi F, Dianoux L, Aubry M, Chelbi-Alix MK. Requirement of PML SUMO interacting motif for RNF4- or arsenic trioxide-induced degradation of nuclear PML isoforms. PLoS One 2012; 7:e44949. [PMID: 23028697 PMCID: PMC3445614 DOI: 10.1371/journal.pone.0044949] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 08/14/2012] [Indexed: 11/18/2022] Open
Abstract
PML, the organizer of nuclear bodies (NBs), is expressed in several isoforms designated PMLI to VII which differ in their C-terminal region due to alternative splicing of a single gene. This variability is important for the function of the different PML isoforms. PML NB formation requires the covalent linkage of SUMO to PML. Arsenic trioxide (As2O3) enhances PML SUMOylation leading to an increase in PML NB size and promotes its interaction with RNF4, a poly-SUMO-dependent ubiquitin E3 ligase responsible for proteasome-mediated PML degradation. Furthermore, the presence of a bona fide SUMO Interacting Motif (SIM) within the C-terminal region of PML seems to be required for recruitment of other SUMOylated proteins within PML NBs. This motif is present in all PML isoforms, except in the nuclear PMLVI and in the cytoplasmic PMLVII. Using a bioluminescence resonance energy transfer (BRET) assay in living cells, we found that As2O3 enhanced the SUMOylation and interaction with RNF4 of nuclear PML isoforms (I to VI). In addition, among the nuclear PML isoforms, only the one lacking the SIM sequence, PMLVI, was resistant to As2O3-induced PML degradation. Similarly, mutation of the SIM in PMLIII abrogated its sensitivity to As2O3-induced degradation. PMLVI and PMLIII-SIM mutant still interacted with RNF4. However, their resistance to the degradation process was due to their inability to be polyubiquitinated and to recruit efficiently the 20S core and the β regulatory subunit of the 11S complex of the proteasome in PML NBs. Such resistance of PMLVI to As2O3-induced degradation was alleviated by overexpression of RNF4. Our results demonstrate that the SIM of PML is dispensable for PML SUMOylation and interaction with RNF4 but is required for efficient PML ubiquitination, recruitment of proteasome components within NBs and proteasome-dependent degradation of PML in response to As2O3.
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Affiliation(s)
| | | | - Faten El Asmi
- CNRS, FRE 3235, Université Paris Descartes, Paris, France
| | | | - Muriel Aubry
- Département de Biochimie, Université de Montréal, Montréal, Canada
- * E-mail: (MKC); (MA)
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Sudharsan R, Azuma Y. The SUMO ligase PIAS1 regulates UV-induced apoptosis by recruiting Daxx to SUMOylated foci. J Cell Sci 2012; 125:5819-29. [PMID: 22976298 DOI: 10.1242/jcs.110825] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The small ubiquitin-like modifier (SUMO) ligase PIAS1 (Protein Inhibitor of Activated Stat-1) has been shown to play a role in cellular stress response by SUMOylating several proteins that are involved in DNA repair, apoptosis and transcription. In this paper, we show that PIAS1 regulates ultraviolet (UV)-induced apoptosis by recruiting Death-associated protein 6 (Daxx) to PIAS1-generated SUMO-foci. Cells that ectopically express PIAS1, but not other PIASes, show increased sensitivity to UV irradiation, suggesting that PIAS1 has a distinct function in UV-dependent apoptosis. Domain analysis of PIAS1 indicates that both PIAS1 SUMO-ligase activity and the specific localization of PIAS1 through its N-terminal and C-terminal domains are essential for UV-induced cell death. Daxx colocalizes with PIAS1-generated SUMOylated foci, and the reduction of Daxx using RNAi alleviates UV-induced apoptosis in PIAS1-expressing cells. PIAS1-mediated recruitment of Daxx and apoptosis following UV irradiation are dependent upon the Daxx C-terminal SUMO-interacting motif (SIM). Overall, our data suggest that the pro-apoptotic protein Daxx specifically interacts with one or more substrates SUMOylated by PIAS1 and this interaction leads to apoptosis following UV irradiation.
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Affiliation(s)
- Raghavi Sudharsan
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave., Haworth Hall, Rm. 3037, Lawrence, KS 66045, USA
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28
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Wimmer P, Blanchette P, Schreiner S, Ching W, Groitl P, Berscheminski J, Branton PE, Will H, Dobner T. Cross-talk between phosphorylation and SUMOylation regulates transforming activities of an adenoviral oncoprotein. Oncogene 2012; 32:1626-37. [PMID: 22614022 DOI: 10.1038/onc.2012.187] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since the discovery of post-translational modification (PTM) by the small ubiquitin-related modifiers (SUMOs), a multitude of proteins have been described to be reversibly modified, resulting in the alteration of several cellular pathways. Interestingly, various pathogens gain access to this modification system, although the molecular mechanisms and functional consequences are barely understood. We show here that the adenoviral oncoprotein E1B-55K is a substrate of the SUMO conjugation system, which is directly linked to its C-terminal phosphorylation. This regulative connection is indispensable for modulation of the tumor suppressor p53/chromatin-remodeling factor Daxx by E1B-55K and, consequently, its oncogenic potential in primary mammalian cells. In virus infection, E1B-55K PTMs are necessary for localization to viral transcription/replication sites. Furthermore, we identify the E2 enzyme Ubc9 as an interaction partner of E1B-55K, providing a possible molecular explanation for SUMO-dependent modulation of cellular target proteins. In conclusion, these results for the first time provide evidence how E1B-55K PTMs are regulated and subsequently facilitate exploitation of the host cell SUMOylation machinery.
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Affiliation(s)
- P Wimmer
- Department of Molecular Virology, Heinrich-Pette-Institute-Leibniz-Institute for Experimental Virology, Hamburg, Germany
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29
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Vogt B, Hofmann K. Bioinformatical detection of recognition factors for ubiquitin and SUMO. Methods Mol Biol 2012; 832:249-61. [PMID: 22350891 DOI: 10.1007/978-1-61779-474-2_18] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The specific recognition of ubiquitin, small ubiquitin-like modifier (SUMO), and related proteins is absolutely crucial for the signaling capacity of these modifiers. Most ubiquitin receptor proteins employ dedicated ubiquitin binding domains (UBDs), of which about 15 families have been described. By contrast, SUMO is recognized by short linear motifs that comprise only a few residues and do not require a defined tertiary structure. At the moment, three classes of SUMO-interacting motifs (SIMs) have been described. The recognition modes of most other modifiers remain poorly understood. When working with ubiquitin-family modifiers, a frequently occurring task is to assess a given protein sequence for the presence of known ubiquitin- or SUMO-binding elements. Due to the different nature of UBDs and SIMs, completely different approaches have to be used. This chapter addresses the bioinformatical detection of UBDs and SIMs through Web-based methods that are freely accessible and do not require a particular bioinformatics infrastructure.
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Affiliation(s)
- Benjamin Vogt
- Institute for Genetics, University of Cologne, Cologne, Germany
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30
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Namanja AT, Li YJ, Su Y, Wong S, Lu J, Colson LT, Wu C, Li SSC, Chen Y. Insights into high affinity small ubiquitin-like modifier (SUMO) recognition by SUMO-interacting motifs (SIMs) revealed by a combination of NMR and peptide array analysis. J Biol Chem 2011; 287:3231-40. [PMID: 22147707 DOI: 10.1074/jbc.m111.293118] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The small ubiquitin-like modifiers (SUMOs) regulate many essential cellular functions. Only one type of SUMO-interacting motif (SIM) has been identified that can extend the β-sheet of SUMO as either a parallel or an antiparallel strand. The molecular determinants of the bound orientation and paralogue specificity of a SIM are unclear. To address this question, we have conducted structural studies of SUMO1 in complex with a SUMO1-specific SIM that binds to SUMO1 with high affinity without post-translational modifications using nuclear magnetic resonance methods. In addition, the SIM sequence requirements have been investigated by peptide arrays in comparison with another high affinity SIM that binds in the opposing orientation. We found that antiparallel binding SIMs tolerate more diverse sequences, whereas the parallel binding SIMs prefer the more strict sequences consisting of (I/V)DLT that have a preference in high affinity SUMO2 and -3 binding. Comparison of two high affinity SUMO1-binding SIMs that bind in opposing orientations has revealed common SUMO1-specific interactions needed for high affinity binding. This study has significantly advanced our understanding of the molecular determinants underlining SUMO-SIM recognition.
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Affiliation(s)
- Andrew T Namanja
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
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