1
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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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2
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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3
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Ma L, Herren AW, Espinal G, Randol J, McLaughlin B, Martinez-Cerdeño V, Pessah IN, Hagerman RJ, Hagerman PJ. Composition of the Intranuclear Inclusions of Fragile X-associated Tremor/Ataxia Syndrome. Acta Neuropathol Commun 2019; 7:143. [PMID: 31481131 PMCID: PMC6720097 DOI: 10.1186/s40478-019-0796-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 12/11/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder associated with a premutation repeat expansion (55-200 CGG repeats) in the 5' noncoding region of the FMR1 gene. Solitary intranuclear inclusions within FXTAS neurons and astrocytes constitute a hallmark of the disorder, yet our understanding of how and why these bodies form is limited. Here, we have discovered that FXTAS inclusions emit a distinct autofluorescence spectrum, which forms the basis of a novel, unbiased method for isolating FXTAS inclusions by preparative fluorescence-activated cell sorting (FACS). Using a combination of autofluorescence-based FACS and liquid chromatography/tandem mass spectrometry (LC-MS/MS)-based proteomics, we have identified more than two hundred proteins that are enriched within the inclusions relative to FXTAS whole nuclei. Whereas no single protein species dominates inclusion composition, highly enriched levels of conjugated small ubiquitin-related modifier 2 (SUMO 2) protein and p62/sequestosome-1 (p62/SQSTM1) protein were found within the inclusions. Many additional proteins involved with RNA binding, protein turnover, and DNA damage repair were enriched within inclusions relative to total nuclear protein. The current analysis has also allowed the first direct detection, through peptide sequencing, of endogenous FMRpolyG peptide, the product of repeat-associated non-ATG (RAN) translation of the FMR1 mRNA. However, this peptide was found only at extremely low levels and not within whole FXTAS nuclear preparations, raising the question whether endogenous RAN products exist at quantities sufficient to contribute to FXTAS pathogenesis. The abundance of the inclusion-associated ubiquitin- and SUMO-based modifiers supports a model for inclusion formation as the result of increased protein loads and elevated oxidative stress leading to maladaptive autophagy. These results highlight the need to further investigate FXTAS pathogenesis in the context of endogenous systems.
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Affiliation(s)
- Lisa Ma
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA
| | - Anthony W Herren
- Genome Center, University of California Davis, Davis, California, USA
| | - Glenda Espinal
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA
| | - Jamie Randol
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA
| | - Bridget McLaughlin
- Department of Pathology and Laboratory Medicine, University of California Davis, School of Medicine, Sacramento, California, USA
| | - Veronica Martinez-Cerdeño
- Department of Pathology and Laboratory Medicine, University of California Davis, School of Medicine, Sacramento, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital of Northern California, University of California Davis, School of Medicine, Sacramento, California, USA
- MIND Institute, University of California Davis Health, Sacramento, California, USA
| | - Isaac N Pessah
- MIND Institute, University of California Davis Health, Sacramento, California, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, California, USA
| | - Randi J Hagerman
- MIND Institute, University of California Davis Health, Sacramento, California, USA
- Department of Pediatrics, University of California Davis, School of Medicine, Sacramento, California, USA
| | - Paul J Hagerman
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, One Shields Ave, Davis, CA, USA.
- MIND Institute, University of California Davis Health, Sacramento, California, USA.
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4
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Ohkuni K, Pasupala N, Peek J, Holloway GL, Sclar GD, Levy-Myers R, Baker RE, Basrai MA, Kerscher O. SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin. Front Genet 2018; 9:379. [PMID: 30279700 PMCID: PMC6154015 DOI: 10.3389/fgene.2018.00379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/27/2018] [Indexed: 01/01/2023] Open
Abstract
Cell viability and gene expression profiles are altered in cellular models of neurodegenerative disorders such as Huntington’s Disease (HD). Using the yeast model system, we show that the SUMO-targeted ubiquitin ligase (STUbL) Slx5 reduces the toxicity and abnormal transcriptional activity associated with a mutant, aggregation-prone fragment of huntingtin (Htt), the causative agent of HD. We demonstrate that expression of an aggregation-prone Htt construct with 103 glutamine residues (103Q), but not the non-expanded form (25Q), results in severe growth defects in slx5Δ and slx8Δ cells. Since Slx5 is a nuclear protein and because Htt expression affects gene transcription, we assessed the effect of STUbLs on the transcriptional properties of aggregation-prone Htt. Expression of Htt 25Q and 55Q fused to the Gal4 activation domain (AD) resulted in reporter gene auto-activation. Remarkably, the auto-activation of Htt constructs was abolished by expression of Slx5 fused to the Gal4 DNA-binding domain (BD-Slx5). In support of these observations, RNF4, the human ortholog of Slx5, curbs the aberrant transcriptional activity of aggregation-prone Htt in yeast and a variety of cultured human cell lines. Functionally, we find that an extra copy of SLX5 specifically reduces Htt aggregates in the cytosol as well as chromatin-associated Htt aggregates in the nucleus. Finally, using RNA sequencing, we identified and confirmed specific targets of Htt’s transcriptional activity that are modulated by Slx5. In summary, this study of STUbLs uncovers a conserved pathway that counteracts the accumulation of aggregating, transcriptionally active Htt (and possibly other poly-glutamine expanded proteins) on chromatin in both yeast and in mammalian cells.
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Affiliation(s)
- Kentaro Ohkuni
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Nagesh Pasupala
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | - Jennifer Peek
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | | | - Gloria D Sclar
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | - Reuben Levy-Myers
- Biology Department, College of William & Mary, Williamsburg, VA, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Oliver Kerscher
- Biology Department, College of William & Mary, Williamsburg, VA, United States
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5
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Stankovic-Valentin N, Melchior F. Control of SUMO and Ubiquitin by ROS: Signaling and disease implications. Mol Aspects Med 2018; 63:3-17. [PMID: 30059710 DOI: 10.1016/j.mam.2018.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/23/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023]
Abstract
Reversible post-translational modifications (PTMs) ensure rapid signal transmission from sensors to effectors. Reversible modification of proteins by the small proteins Ubiquitin and SUMO are involved in virtually all cellular processes and can modify thousands of proteins. Ubiquitination or SUMOylation is the reversible attachment of these modifiers to lysine residues of a target via isopeptide bond formation. These modifications require ATP and an enzymatic cascade composed of three classes of proteins: E1 activating enzymes, E2 conjugating enzymes and E3 ligases. The reversibility of the modification is ensured by specific isopeptidases. E1 and E2 enzymes, some E3 ligases and most isopeptidases have catalytic cysteine residues, which make them potentially susceptible for oxidation. Indeed, an increasing number of examples reveal regulation of ubiquitination and SUMOylation by reactive oxygen species, both in the context of redox signaling and in severe oxidative stress. Importantly, ubiquitination and SUMOylation play essential roles in the regulation of ROS homeostasis, participating in the control of ROS production and clearance. In this review, we will discuss the interplay between ROS homeostasis, Ubiquitin and SUMO pathways and the implications for the oxidative stress response and cell signaling.
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Affiliation(s)
- Nicolas Stankovic-Valentin
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany.
| | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ - ZMBH Alliance, Heidelberg, Germany.
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6
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Abstract
The segregation of homologous chromosomes in meiosis depends on their ability to locate one another in the nucleus and establish a physical association through crossing over. A tightly regulated number of crossovers (COs) emerges following repair of induced DNA double-strand breaks by homologous recombination (HR), but the process of how HR intermediates transition into COs is still poorly understood. Two recent studies by Ahuja et al. and Rao et al. have revealed a role for chromosomally localized proteasomes in choreographing both homologous chromosome pairing and the evolution of HR intermediates into segregation-competent COs. Using chemical inhibition of the proteasome and mutant analysis, the collective data reveal conserved functions for both the proteasome and a family of E3 ligases that can direct or compete with its activity in ensuring CO formation. Here, we review these findings and the impact of the discovery that protein modification dynamics and proteasomal activity cooperate to regulate key meiotic processes.
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Affiliation(s)
- Aleksandar Vujin
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Monique Zetka
- Department of Biology, McGill University, Montreal, Quebec, Canada
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7
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Silva S, Altmannova V, Eckert-Boulet N, Kolesar P, Gallina I, Hang L, Chung I, Arneric M, Zhao X, Buron LD, Mortensen UH, Krejci L, Lisby M. SUMOylation of Rad52-Rad59 synergistically change the outcome of mitotic recombination. DNA Repair (Amst) 2016; 42:11-25. [PMID: 27130983 DOI: 10.1016/j.dnarep.2016.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/02/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022]
Abstract
Homologous recombination (HR) is essential for maintenance of genome stability through double-strand break (DSB) repair, but at the same time HR can lead to loss of heterozygosity and uncontrolled recombination can be genotoxic. The post-translational modification by SUMO (small ubiquitin-like modifier) has been shown to modulate recombination, but the exact mechanism of this regulation remains unclear. Here we show that SUMOylation stabilizes the interaction between the recombination mediator Rad52 and its paralogue Rad59 in Saccharomyces cerevisiae. Although Rad59 SUMOylation is not required for survival after genotoxic stress, it affects the outcome of recombination to promote conservative DNA repair. In some genetic assays, Rad52 and Rad59 SUMOylation act synergistically. Collectively, our data indicate that the described SUMO modifications affect the balance between conservative and non-conservative mechanisms of HR.
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Affiliation(s)
- Sonia Silva
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Veronika Altmannova
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic
| | - Nadine Eckert-Boulet
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter Kolesar
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic
| | - Irene Gallina
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Lisa Hang
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Inn Chung
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Milica Arneric
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Line Due Buron
- Department of Systems Biology, Technical University of Denmark, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Systems Biology, Technical University of Denmark, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Lumir Krejci
- Department of Biology, Masaryk University, Kamenice 5/A7, 62500 Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, Brno 625 00, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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8
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Isolation of ubiquitinated substrates by tandem affinity purification of E3 ligase-polyubiquitin-binding domain fusions (ligase traps). Nat Protoc 2016; 11:291-301. [PMID: 26766115 DOI: 10.1038/nprot.2016.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ubiquitination is an essential protein modification that influences eukaryotic processes ranging from substrate degradation to nonproteolytic pathway alterations, including DNA repair and endocytosis. Previous attempts to analyze substrates via physical association with their respective ubiquitin ligases have had some success. However, because of the transient nature of enzyme-substrate interactions and rapid protein degradation, detection of substrates remains a challenge. Ligase trapping is an affinity purification approach in which ubiquitin ligases are fused to a polyubiquitin-binding domain, which allows the isolation of ubiquitinated substrates. Immunoprecipitation is first used to enrich for proteins that are bound to the ligase trap. Subsequently, affinity purification is used under denaturing conditions to capture proteins conjugated with hexahistidine-tagged ubiquitin. By using this protocol, ubiquitinated substrates that are specific for a given ligase can be isolated for mass spectrometry or western blot analysis. After cells have been collected, the described protocol can be completed in 2-3 d.
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9
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Bursomanno S, McGouran JF, Kessler BM, Hickson ID, Liu Y. Regulation of SUMO2 target proteins by the proteasome in human cells exposed to replication stress. J Proteome Res 2015; 14:1687-99. [PMID: 25748227 DOI: 10.1021/pr500997p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In human cells, SUMO2 is predominantly conjugated to target proteins in response to cellular stress. Previous studies suggested that proteins conjugated to SUMO2, but not to SUMO1, could be regulated by the ubiquitin-mediated proteasome system. Hence, we set out to understand the role of the proteasome in determining the fate of proteins conjugated to SUMO2 when cells are treated with DNA replication stress conditions. We conducted a quantitative proteomic analysis in a U2OS cell line stably expressing SUMO2(Q87R) tagged with StrepHA in the presence or absence of epoxomicin (EPOX), a proteasome inhibitor. We identified subgroups of putative SUMO2 targets that were either degraded or stabilized by EPOX upon SUMO2 conjugation in response to replication stress. Interestingly, the subgroup of proteins degraded upon SUMO2 conjugation was enriched in proteins playing roles in DNA damage repair and replication, while the proteins stabilized upon SUMOylation were mainly involved in chromatin maintenance. In addition, we identified 43 SUMOylation sites in target proteins, of which 17 are located in the proximity of phosphorylated residues. Considering that DNA replication stress is a major source of genome instability, which is suggested to drive tumorigenesis and possibly aging, our data will facilitate future functional studies in the fields of DNA metabolism and cancer biology.
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Affiliation(s)
- Sara Bursomanno
- †Center for Chromosome Stability, and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Joanna F McGouran
- ‡Ubiquitin Proteolysis Group, TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, OX3 7FZ Oxford, UK
| | - Benedikt M Kessler
- ‡Ubiquitin Proteolysis Group, TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, OX3 7FZ Oxford, UK
| | - Ian D Hickson
- †Center for Chromosome Stability, and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| | - Ying Liu
- †Center for Chromosome Stability, and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
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10
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Sarangi P, Zhao X. SUMO-mediated regulation of DNA damage repair and responses. Trends Biochem Sci 2015; 40:233-42. [PMID: 25778614 DOI: 10.1016/j.tibs.2015.02.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/17/2015] [Accepted: 02/17/2015] [Indexed: 12/21/2022]
Abstract
Sumoylation has important roles during DNA damage repair and responses. Recent broad-scope and substrate-based studies have shed light on the regulation and significance of sumoylation during these processes. An emerging paradigm is that sumoylation of many DNA metabolism proteins is controlled by DNA engagement. Such 'on-site modification' can explain low substrate modification levels and has important implications in sumoylation mechanisms and effects. New studies also suggest that sumoylation can regulate a process through an ensemble effect or via major substrates. Additionally, we describe new trends in the functional effects of sumoylation, such as bi-directional changes in biomolecule binding and multilevel coordination with other modifications. These emerging themes and models will stimulate our thinking and research in sumoylation and genome maintenance.
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Affiliation(s)
- Prabha Sarangi
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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11
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Abstract
Posttranslational modification with small ubiquitin-related modifier (SUMO) proteins is now established as one of the key regulatory protein modifications in eukaryotic cells. Hundreds of proteins involved in processes such as chromatin organization, transcription, DNA repair, macromolecular assembly, protein homeostasis, trafficking, and signal transduction are subject to reversible sumoylation. Hence, it is not surprising that disease links are beginning to emerge and that interference with sumoylation is being considered for intervention. Here, we summarize basic mechanisms and highlight recent developments in the physiology of sumoylation.
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Affiliation(s)
- Annette Flotho
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH, Heidelberg D-69120, Germany.
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12
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van Wijk SJL, Fiškin E, Dikic I. Selective monitoring of ubiquitin signals with genetically encoded ubiquitin chain-specific sensors. Nat Protoc 2013; 8:1449-58. [PMID: 23807287 DOI: 10.1038/nprot.2013.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Despite intensive research, there is a distinct lack of methodology for visualizing endogenous ubiquitination in living cells. In this protocol, we describe how unique properties of ubiquitin (Ub)-binding domains (UBDs) can be used to selectively detect, visualize and inhibit Ub-dependent processes in mammalian cells. The procedure deals with designing and validating the binding selectivity of GFP-tagged K63- and linear-linked sensors (TAB2 NZF and NEMO UBAN, respectively) in vitro. We describe how these moieties can be used to inhibit tumor necrosis factor (TNF)-mediated NF-κB signaling and to detect ubiquitinated cytosolic Salmonella in living cells, emphasizing a more flexible use compared with chain-specific antibodies. These chain-specific sensors can be used to detect Ub-like or autophagy-related modifiers and, in combination with mass spectrometry, to identify new Ub targets. These Ub (-like) sensors can be designed, constructed and tested in ~2-3 weeks.
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Affiliation(s)
- Sjoerd J L van Wijk
- Institute of Biochemistry II, School of Medicine, Goethe University, Frankfurt am Main, Germany
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13
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Monribot-Villanueva J, Juárez-Uribe RA, Palomera-Sánchez Z, Gutiérrez-Aguiar L, Zurita M, Kennison JA, Vázquez M. TnaA, an SP-RING protein, interacts with Osa, a subunit of the chromatin remodeling complex BRAHMA and with the SUMOylation pathway in Drosophila melanogaster. PLoS One 2013; 8:e62251. [PMID: 23620817 PMCID: PMC3631182 DOI: 10.1371/journal.pone.0062251] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/19/2013] [Indexed: 12/15/2022] Open
Abstract
Tonalli A (TnaA) is a Drosophila melanogaster protein with an XSPRING domain. The XSPRING domain harbors an SP-RING zinc-finger, which is characteristic of proteins with SUMO E3 ligase activity. TnaA is required for homeotic gene expression and is presumably involved in the SUMOylation pathway. Here we analyzed some aspects of the TnaA location in embryo and larval stages and its genetic and biochemical interaction with SUMOylation pathway proteins. We describe that there are at least two TnaA proteins (TnaA130 and TnaA123) differentially expressed throughout development. We show that TnaA is chromatin-associated at discrete sites on polytene salivary gland chromosomes of third instar larvae and that tna mutant individuals do not survive to adulthood, with most dying as third instar larvae or pupae. The tna mutants that ultimately die as third instar larvae have an extended life span of at least 4 to 15 days as other SUMOylation pathway mutants. We show that TnaA physically interacts with the SUMO E2 conjugating enzyme Ubc9, and with the BRM complex subunit Osa. Furthermore, we show that tna and osa interact genetically with SUMOylation pathway components and individuals carrying mutations for these genes show a phenotype that can be the consequence of misexpression of developmental-related genes.
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Affiliation(s)
- Juan Monribot-Villanueva
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - R. Alejandro Juárez-Uribe
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Zoraya Palomera-Sánchez
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Lucía Gutiérrez-Aguiar
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - James A. Kennison
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martha Vázquez
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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14
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An acetylation switch regulates SUMO-dependent protein interaction networks. Mol Cell 2012; 46:759-70. [PMID: 22578841 DOI: 10.1016/j.molcel.2012.04.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/21/2012] [Accepted: 04/05/2012] [Indexed: 11/23/2022]
Abstract
The attachment of the SUMO modifier to proteins controls cellular signaling pathways through noncovalent binding to SUMO-interaction motifs (SIMs). Canonical SIMs contain a core of hydrophobic residues that bind to a hydrophobic pocket on SUMO. Negatively charged residues of SIMs frequently contribute to binding by interacting with a basic surface on SUMO. Here we define acetylation within this basic interface as a central mechanism for the control of SUMO-mediated interactions. The acetyl-mediated neutralization of basic charges on SUMO prevents binding to SIMs in PML, Daxx, and PIAS family members but does not affect the interaction between RanBP2 and SUMO. Acetylation is controlled by HDACs and attenuates SUMO- and PIAS-mediated gene silencing. Moreover, it affects the assembly of PML nuclear bodies and restrains the recruitment of the corepressor Daxx to these structures. This acetyl-dependent switch thus expands the regulatory repertoire of SUMO signaling and determines the selectivity and dynamics of SUMO-SIM interactions.
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